pyranges.pyranges¶
Data structure for genomic intervals and their annotation.
Module Contents¶
Classes¶
Two-dimensional representation of genomic intervals and their annotations. |
- class pyranges.pyranges.PyRanges(df=None, chromosomes=None, starts=None, ends=None, strands=None, int64=False, copy_df=True)¶
Two-dimensional representation of genomic intervals and their annotations.
A PyRanges object must have the columns Chromosome, Start and End. These describe the genomic position and function as implicit row labels. A Strand column is optional and adds strand information to the intervals. Any other columns are allowed and are considered metadata.
Operations between PyRanges align intervals based on their position.
If a PyRanges is built using the arguments chromosomes, starts, ends and optionally strands, all non-scalars must be of the same length.
- Parameters
df (pandas.DataFrame or dict of pandas.DataFrame, default None) – The data to be stored in the PyRanges.
chromosomes (array-like or scalar value, default None) – The chromosome(s) in the PyRanges.
starts (array-like, default None) – The start postions in the PyRanges.
ends (array-like, default None) – The end postions in the PyRanges.
strands (array-like or scalar value, default None) – The strands in the PyRanges.
int64 (bool, default False) – Use np.int64 to represent starts and ends
copy_df (bool, default True) – Copy input pandas.DataFrame
See also
pyranges.read_bedread bed-file into PyRanges
pyranges.read_bamread bam-file into PyRanges
pyranges.read_gffread gff-file into PyRanges
pyranges.read_gtfread gtf-file into PyRanges
pyranges.from_dictcreate PyRanges from dict of columns
pyranges.from_stringcreate PyRanges from multiline string
Notes
A PyRanges object is represented internally as a dictionary efficiency. The keys are chromosomes or chromosome/strand tuples and the values are pandas DataFrames.
Examples
>>> pr.PyRanges() Empty PyRanges
>>> pr.PyRanges(chromosomes="chr1", starts=(1, 5), ends=[3, 149], ... strands=("+", "-"), int64=True) +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int64) | (int64) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 1 | 3 | + | | chr1 | 5 | 149 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> df = pd.DataFrame({"Chromosome": ["chr1", "chr2"], "Start": [100, 200], ... "End": [150, 201]}) >>> df Chromosome Start End 0 chr1 100 150 1 chr2 200 201 >>> pr.PyRanges(df) +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 100 | 150 | | chr2 | 200 | 201 | +--------------+-----------+-----------+ Unstranded PyRanges object has 2 rows and 3 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr = pr.from_dict({"Chromosome": [1, 1], "Strand": ["+", "-"], "Start": [1, 4], "End": [2, 27], ... "TP": [0, 1], "FP": [12, 11], "TN": [10, 9], "FN": [2, 3]}) >>> gr +--------------+--------------+-----------+-----------+-----------+-----------+-----------+-----------+ | Chromosome | Strand | Start | End | TP | FP | TN | FN | | (category) | (category) | (int32) | (int32) | (int64) | (int64) | (int64) | (int64) | |--------------+--------------+-----------+-----------+-----------+-----------+-----------+-----------| | 1 | + | 1 | 2 | 0 | 12 | 10 | 2 | | 1 | - | 4 | 27 | 1 | 11 | 9 | 3 | +--------------+--------------+-----------+-----------+-----------+-----------+-----------+-----------+ Stranded PyRanges object has 2 rows and 8 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- dfs¶
Dict mapping chromosomes or chromosome/strand pairs to pandas DataFrames.
- features¶
Namespace for genomic-features methods.
See also
pyranges.genomicfeaturesnamespace for feature-functionality
pyranges.genomicfeatures.GenomicFeaturesMethodsnamespace for feature-functionality
- stats¶
Namespace for statistcal methods.
See also
pyranges.statisticsnamespace for statistics
pyranges.stats.StatisticsMethodsnamespace for statistics
- __array_ufunc__(self, *args, **kwargs)¶
Apply unary numpy-function.
Apply function to all columns which are not index, i.e. Chromosome, Start, End nor Strand.
Notes
Function must produce a vector of equal length.
Examples
>>> gr = pr.from_dict({"Chromosome": [1, 2, 3], "Start": [1, 2, 3], ... "End": [2, 3, 4], "Score": [9, 16, 25], "Score2": [121, 144, 169], ... "Name": ["n1", "n2", "n3"]}) >>> gr +--------------+-----------+-----------+-----------+-----------+------------+ | Chromosome | Start | End | Score | Score2 | Name | | (category) | (int32) | (int32) | (int64) | (int64) | (object) | |--------------+-----------+-----------+-----------+-----------+------------| | 1 | 1 | 2 | 9 | 121 | n1 | | 2 | 2 | 3 | 16 | 144 | n2 | | 3 | 3 | 4 | 25 | 169 | n3 | +--------------+-----------+-----------+-----------+-----------+------------+ Unstranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> np.sqrt(gr) +--------------+-----------+-----------+-------------+-------------+------------+ | Chromosome | Start | End | Score | Score2 | Name | | (category) | (int32) | (int32) | (float64) | (float64) | (object) | |--------------+-----------+-----------+-------------+-------------+------------| | 1 | 1 | 2 | 3 | 11 | n1 | | 2 | 2 | 3 | 4 | 12 | n2 | | 3 | 3 | 4 | 5 | 13 | n3 | +--------------+-----------+-----------+-------------+-------------+------------+ Unstranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- __getattr__(self, name)¶
Return column.
- Parameters
name (str) – Column to return
- Returns
- Return type
pandas.Series
Example
>>> gr = pr.from_dict({"Chromosome": [1, 1, 1], "Start": [0, 100, 250], "End": [10, 125, 251]}) >>> gr.Start 0 0 1 100 2 250 Name: Start, dtype: int32
- __setattr__(self, column_name, column)¶
Insert or update column.
- Parameters
column_name (str) – Name of column to update or insert.
column (list, np.array or pd.Series) – Data to insert.
Example
>>> gr = pr.from_dict({"Chromosome": [1, 1, 1], "Start": [0, 100, 250], "End": [10, 125, 251]}) >>> gr.Start = np.array([1, 1, 2]) >>> gr +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int64) | (int32) | |--------------+-----------+-----------| | 1 | 1 | 10 | | 1 | 1 | 125 | | 1 | 2 | 251 | +--------------+-----------+-----------+ Unstranded PyRanges object has 3 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- __getitem__(self, val)¶
Fetch columns or subset on position.
If a list is provided, the column(s) in the list is returned. This subsets on columns.
If a numpy array is provided, it must be of type bool and the same length as the PyRanges.
Otherwise, a subset of the rows is returned with the location info provided.
- Parameters
val (bool array/Series, tuple, list, str or slice) – Data to fetch.
Examples
>>> gr = pr.data.ensembl_gtf() >>> gr.columns Index(['Chromosome', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'gene_biotype', 'gene_id', 'gene_name', 'gene_source', 'gene_version', 'tag', 'transcript_biotype', 'transcript_id', 'transcript_name', 'transcript_source', 'transcript_support_level', 'transcript_version', 'exon_id', 'exon_number', 'exon_version', '(assigned', 'previous', 'protein_id', 'protein_version', 'ccds_id'], dtype='object')
>>> gr = gr[["Source", "Feature", "gene_id"]] >>> gr +--------------+------------+--------------+-----------+-----------+--------------+-----------------+ | Chromosome | Source | Feature | Start | End | Strand | gene_id | | (category) | (object) | (category) | (int32) | (int32) | (category) | (object) | |--------------+------------+--------------+-----------+-----------+--------------+-----------------| | 1 | havana | gene | 11868 | 14409 | + | ENSG00000223972 | | 1 | havana | transcript | 11868 | 14409 | + | ENSG00000223972 | | 1 | havana | exon | 11868 | 12227 | + | ENSG00000223972 | | 1 | havana | exon | 12612 | 12721 | + | ENSG00000223972 | | ... | ... | ... | ... | ... | ... | ... | | 1 | havana | gene | 1173055 | 1179555 | - | ENSG00000205231 | | 1 | havana | transcript | 1173055 | 1179555 | - | ENSG00000205231 | | 1 | havana | exon | 1179364 | 1179555 | - | ENSG00000205231 | | 1 | havana | exon | 1173055 | 1176396 | - | ENSG00000205231 | +--------------+------------+--------------+-----------+-----------+--------------+-----------------+ Stranded PyRanges object has 2,446 rows and 7 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
Create boolean Series and use it to subset:
>>> s = (gr.Feature == "gene") | (gr.gene_id == "ENSG00000223972") >>> gr[s] +--------------+----------------+--------------+-----------+-----------+--------------+-----------------+ | Chromosome | Source | Feature | Start | End | Strand | gene_id | | (category) | (object) | (category) | (int32) | (int32) | (category) | (object) | |--------------+----------------+--------------+-----------+-----------+--------------+-----------------| | 1 | havana | gene | 11868 | 14409 | + | ENSG00000223972 | | 1 | havana | transcript | 11868 | 14409 | + | ENSG00000223972 | | 1 | havana | exon | 11868 | 12227 | + | ENSG00000223972 | | 1 | havana | exon | 12612 | 12721 | + | ENSG00000223972 | | ... | ... | ... | ... | ... | ... | ... | | 1 | havana | gene | 1062207 | 1063288 | - | ENSG00000273443 | | 1 | ensembl_havana | gene | 1070966 | 1074306 | - | ENSG00000237330 | | 1 | ensembl_havana | gene | 1081817 | 1116361 | - | ENSG00000131591 | | 1 | havana | gene | 1173055 | 1179555 | - | ENSG00000205231 | +--------------+----------------+--------------+-----------+-----------+--------------+-----------------+ Stranded PyRanges object has 95 rows and 7 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> cs = pr.data.chipseq() >>> cs[10000:100000] +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 33241 | 33266 | U0 | 0 | + | | chr2 | 13611 | 13636 | U0 | 0 | - | | chr2 | 32620 | 32645 | U0 | 0 | - | | chr3 | 87179 | 87204 | U0 | 0 | + | | chr4 | 45413 | 45438 | U0 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 5 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> cs["chr1", "-"] +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 100079649 | 100079674 | U0 | 0 | - | | chr1 | 223587418 | 223587443 | U0 | 0 | - | | chr1 | 202450161 | 202450186 | U0 | 0 | - | | chr1 | 156338310 | 156338335 | U0 | 0 | - | | ... | ... | ... | ... | ... | ... | | chr1 | 203557775 | 203557800 | U0 | 0 | - | | chr1 | 28114107 | 28114132 | U0 | 0 | - | | chr1 | 21622765 | 21622790 | U0 | 0 | - | | chr1 | 80668132 | 80668157 | U0 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 437 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> cs["chr5", "-", 90000:] +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr5 | 399682 | 399707 | U0 | 0 | - | | chr5 | 1847502 | 1847527 | U0 | 0 | - | | chr5 | 5247533 | 5247558 | U0 | 0 | - | | chr5 | 5300394 | 5300419 | U0 | 0 | - | | ... | ... | ... | ... | ... | ... | | chr5 | 178786234 | 178786259 | U0 | 0 | - | | chr5 | 179268931 | 179268956 | U0 | 0 | - | | chr5 | 179289594 | 179289619 | U0 | 0 | - | | chr5 | 180513795 | 180513820 | U0 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 285 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> cs["chrM"] Empty PyRanges
- __iter__(self)¶
Iterate over the keys and values.
See also
pyranges.iter()iterate over multiple PyRanges
Examples
>>> gr = pr.from_dict({"Chromosome": [1, 1, 1], "Start": [0, 100, 250], ... "End": [10, 125, 251], "Strand": ["+", "+", "-"]})
>>> for k, v in gr: ... print(k) ... print(v) ('1', '+') Chromosome Start End Strand 0 1 0 10 + 1 1 100 125 + ('1', '-') Chromosome Start End Strand 2 1 250 251 -
- __len__(self)¶
Return the number of intervals in the PyRanges.
- __str__(self)¶
Return string representation.
- __repr__(self)¶
Return REPL representation.
- _repr_html_(self)¶
Return REPL HTML representation for Jupyter Noteboooks.
- apply(self, f, strand=None, as_pyranges=True, nb_cpu=1, **kwargs)¶
Apply a function to the PyRanges.
- Parameters
f (function) – Function to apply on each DataFrame in a PyRanges
strand (bool, default None, i.e. auto) – Whether to do operations on chromosome/strand pairs or chromosomes. If None, will use chromosome/strand pairs if the PyRanges is stranded.
as_pyranges (bool, default True) – Whether to return as a PyRanges or dict. If f does not return a DataFrame valid for PyRanges, as_pyranges must be False.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
**kwargs – Additional keyword arguments to pass as keyword arguments to f
- Returns
Result of applying f to each DataFrame in the PyRanges
- Return type
PyRanges or dict
See also
pyranges.PyRanges.apply_pair()apply a function to a pair of PyRanges
pyranges.PyRanges.apply_chunks()apply a row-based function to a PyRanges in parallel
Note
This is the function used internally to carry out almost all unary PyRanges methods.
Examples
>>> gr = pr.from_dict({"Chromosome": [1, 1, 2, 2], "Strand": ["+", "+", "-", "+"], ... "Start": [1, 4, 2, 9], "End": [2, 27, 13, 10]}) >>> gr +--------------+--------------+-----------+-----------+ | Chromosome | Strand | Start | End | | (category) | (category) | (int32) | (int32) | |--------------+--------------+-----------+-----------| | 1 | + | 1 | 2 | | 1 | + | 4 | 27 | | 2 | + | 9 | 10 | | 2 | - | 2 | 13 | +--------------+--------------+-----------+-----------+ Stranded PyRanges object has 4 rows and 4 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.apply(lambda df: len(df), as_pyranges=False) {('1', '+'): 2, ('2', '+'): 1, ('2', '-'): 1}
>>> gr.apply(lambda df: len(df), as_pyranges=False, strand=False) {'1': 2, '2': 2}
>>> def add_to_ends(df, **kwargs): ... df.loc[:, "End"] = kwargs["slack"] + df.End ... return df >>> gr.apply(add_to_ends, slack=500) +--------------+--------------+-----------+-----------+ | Chromosome | Strand | Start | End | | (category) | (category) | (int32) | (int32) | |--------------+--------------+-----------+-----------| | 1 | + | 1 | 502 | | 1 | + | 4 | 527 | | 2 | + | 9 | 510 | | 2 | - | 2 | 513 | +--------------+--------------+-----------+-----------+ Stranded PyRanges object has 4 rows and 4 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- apply_chunks(self, f, as_pyranges=False, nb_cpu=1, **kwargs)¶
Apply a row-based function to arbitrary partitions of the PyRanges.
apply_chunks speeds up the application of functions where the result is not affected by applying the function to ordered, non-overlapping splits of the data.
- Parameters
f (function) – Row-based or associative function to apply on the partitions.
as_pyranges (bool, default False) – Whether to return as a PyRanges or dict.
nb_cpu (int, default 1) – How many cpus to use. The data is split into nb_cpu partitions.
**kwargs – Additional keyword arguments to pass as keyword arguments to f
- Returns
Result of applying f to each partition of the DataFrames in the PyRanges.
- Return type
dict of lists
See also
pyranges.PyRanges.apply_pair()apply a function to a pair of PyRanges
pyranges.PyRanges.apply_chunks()apply a row-based function to a PyRanges in parallel
Note
apply_chunks will only lead to speedups on large datasets or slow-running functions. Using it with nb_cpu=1 is pointless; use apply instead.
Examples
>>> gr = pr.from_dict({"Chromosome": [1, 1, 1], "Start": [2, 3, 5], "End": [9, 4, 6]}) >>> gr +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | 1 | 2 | 9 | | 1 | 3 | 4 | | 1 | 5 | 6 | +--------------+-----------+-----------+ Unstranded PyRanges object has 3 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.apply_chunks( ... lambda df, **kwargs: list(df.End + kwargs["add"]), nb_cpu=1, add=1000) {'1': [[1009, 1004, 1006]]}
- apply_pair(self, other, f, strandedness=None, as_pyranges=True, **kwargs)¶
Apply a function to a pair of PyRanges.
The function is applied to each chromosome or chromosome/strand pair found in at least one of the PyRanges.
- Parameters
f (function) – Row-based or associative function to apply on the DataFrames.
strandedness ({None, "same", "opposite", False}, default None, i.e. auto) – Whether to compare PyRanges on the same strand, the opposite or ignore strand information. The default, None, means use “same” if both PyRanges are strande, otherwise ignore the strand information.
as_pyranges (bool, default False) – Whether to return as a PyRanges or dict. If f does not return a DataFrame valid for PyRanges, as_pyranges must be False.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
**kwargs – Additional keyword arguments to pass as keyword arguments to f
- Returns
Result of applying f to each partition of the DataFrames in the PyRanges.
- Return type
dict of lists
See also
pyranges.PyRanges.apply_pair()apply a function to a pair of PyRanges
pyranges.PyRanges.apply_chunks()apply a row-based function to a PyRanges in parallel
pyranges.iter()iterate over two or more PyRanges
Note
This is the function used internally to carry out almost all comparison functions in PyRanges.
Examples
>>> gr = pr.data.chipseq() >>> gr2 = pr.data.chipseq_background()
>>> gr.apply_pair(gr2, pr.methods.intersection._intersection) # same as gr.intersect(gr2) +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 226987603 | 226987617 | U0 | 0 | + | | chr8 | 38747236 | 38747251 | U0 | 0 | - | | chr15 | 26105515 | 26105518 | U0 | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> f1 = pr.data.f1() >>> f1 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3 | 6 | interval1 | 0 | + | | chr1 | 8 | 9 | interval3 | 0 | + | | chr1 | 5 | 7 | interval2 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> f2 = pr.data.f2() >>> f2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 6 | 7 | b | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> f1.apply_pair(f2, lambda df, df2: (len(df), len(df2)), as_pyranges=False) {('chr1', '+'): (2, 2), ('chr1', '-'): (1, 2)}
- as_df(self)¶
Return PyRanges as DataFrame.
- Returns
A DataFrame natural sorted on Chromosome and Strand. The ordering of rows within chromosomes and strands is preserved.
- Return type
DataFrame
See also
PyRanges.df()Return PyRanges as DataFrame.
Examples
>>> gr = pr.from_dict({"Chromosome": [1, 1, 2, 2], "Start": [1, 2, 3, 9], ... "End": [3, 3, 10, 12], "Gene": ["A", "B", "C", "D"]}) >>> gr +--------------+-----------+-----------+------------+ | Chromosome | Start | End | Gene | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | 1 | 1 | 3 | A | | 1 | 2 | 3 | B | | 2 | 3 | 10 | C | | 2 | 9 | 12 | D | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 4 rows and 4 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.as_df() Chromosome Start End Gene 0 1 1 3 A 1 1 2 3 B 2 2 3 10 C 3 2 9 12 D
- assign(self, col, f, strand=None, nb_cpu=1, **kwargs)¶
Add or replace a column.
Does not change the original PyRanges.
- Parameters
col (str) – Name of column.
f (function) – Function to create new column.
strand (bool, default None, i.e. auto) – Whether to do operations on chromosome/strand pairs or chromosomes. If None, will use chromosome/strand pairs if the PyRanges is stranded.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
**kwargs – Additional keyword arguments to pass as keyword arguments to f
- Returns
A copy of the PyRanges with the column inserted.
- Return type
Examples
>>> gr = pr.from_dict({"Chromosome": [1, 1], "Start": [1, 2], "End": [3, 5], ... "Name": ["a", "b"]}) >>> gr +--------------+-----------+-----------+------------+ | Chromosome | Start | End | Name | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | 1 | 1 | 3 | a | | 1 | 2 | 5 | b | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.assign("Blabla", lambda df: df.Chromosome.astype(str) + "_yadayada") +--------------+-----------+-----------+------------+------------+ | Chromosome | Start | End | Name | Blabla | | (category) | (int32) | (int32) | (object) | (object) | |--------------+-----------+-----------+------------+------------| | 1 | 1 | 3 | a | 1_yadayada | | 1 | 2 | 5 | b | 1_yadayada | +--------------+-----------+-----------+------------+------------+ Unstranded PyRanges object has 2 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
Note that assigning to an existing name replaces the column:
>>> gr.assign("Name", ... lambda df, **kwargs: df.Start.astype(str) + kwargs["sep"] + ... df.Name.str.capitalize(), sep="_") +--------------+-----------+-----------+------------+ | Chromosome | Start | End | Name | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | 1 | 1 | 3 | 1_A | | 1 | 2 | 5 | 2_B | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- property chromosomes(self)¶
Return chromosomes in natsorted order.
- cluster(self, strand=None, by=None, slack=0, count=False, nb_cpu=1)¶
Give overlapping intervals a common id.
- Parameters
strand (bool, default None, i.e. auto) – Whether to ignore strand information if PyRanges is stranded.
by (str or list, default None) – Only intervals with an equal value in column(s) by are clustered.
slack (int, default 0) – Consider intervals separated by less than slack to be in the same cluster. If slack is negative, intervals overlapping less than slack are not considered to be in the same cluster.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
- Returns
PyRanges with an ID-column “Cluster” added.
- Return type
See also
PyRanges.merge()combine overlapping intervals into one
Examples
>>> gr = pr.from_dict({"Chromosome": [1, 1, 1, 1], "Start": [1, 2, 3, 9], ... "End": [3, 3, 10, 12], "Gene": [1, 2, 3, 3]}) >>> gr +--------------+-----------+-----------+-----------+ | Chromosome | Start | End | Gene | | (category) | (int32) | (int32) | (int64) | |--------------+-----------+-----------+-----------| | 1 | 1 | 3 | 1 | | 1 | 2 | 3 | 2 | | 1 | 3 | 10 | 3 | | 1 | 9 | 12 | 3 | +--------------+-----------+-----------+-----------+ Unstranded PyRanges object has 4 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.cluster() +--------------+-----------+-----------+-----------+-----------+ | Chromosome | Start | End | Gene | Cluster | | (category) | (int32) | (int32) | (int64) | (int32) | |--------------+-----------+-----------+-----------+-----------| | 1 | 1 | 3 | 1 | 1 | | 1 | 2 | 3 | 2 | 1 | | 1 | 3 | 10 | 3 | 1 | | 1 | 9 | 12 | 3 | 1 | +--------------+-----------+-----------+-----------+-----------+ Unstranded PyRanges object has 4 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.cluster(by="Gene", count=True) +--------------+-----------+-----------+-----------+-----------+-----------+ | Chromosome | Start | End | Gene | Cluster | Count | | (category) | (int32) | (int32) | (int64) | (int32) | (int64) | |--------------+-----------+-----------+-----------+-----------+-----------| | 1 | 1 | 3 | 1 | 1 | 1 | | 1 | 2 | 3 | 2 | 2 | 1 | | 1 | 3 | 10 | 3 | 3 | 2 | | 1 | 9 | 12 | 3 | 3 | 2 | +--------------+-----------+-----------+-----------+-----------+-----------+ Unstranded PyRanges object has 4 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
Avoid clustering bookended intervals with slack=-1:
>>> gr.cluster(slack=-1) +--------------+-----------+-----------+-----------+-----------+ | Chromosome | Start | End | Gene | Cluster | | (category) | (int32) | (int32) | (int64) | (int32) | |--------------+-----------+-----------+-----------+-----------| | 1 | 1 | 3 | 1 | 1 | | 1 | 2 | 3 | 2 | 1 | | 1 | 3 | 10 | 3 | 2 | | 1 | 9 | 12 | 3 | 2 | +--------------+-----------+-----------+-----------+-----------+ Unstranded PyRanges object has 4 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr2 = pr.data.ensembl_gtf()[["Feature", "Source"]] >>> gr2.cluster(by=["Feature", "Source"]) +--------------+--------------+---------------+-----------+-----------+--------------+-----------+ | Chromosome | Feature | Source | Start | End | Strand | Cluster | | (category) | (category) | (object) | (int32) | (int32) | (category) | (int32) | |--------------+--------------+---------------+-----------+-----------+--------------+-----------| | 1 | CDS | ensembl | 69090 | 70005 | + | 1 | | 1 | CDS | ensembl | 925941 | 926013 | + | 2 | | 1 | CDS | ensembl | 925941 | 926013 | + | 2 | | 1 | CDS | ensembl | 925941 | 926013 | + | 2 | | ... | ... | ... | ... | ... | ... | ... | | 1 | transcript | havana_tagene | 167128 | 169240 | - | 1142 | | 1 | transcript | mirbase | 17368 | 17436 | - | 1143 | | 1 | transcript | mirbase | 187890 | 187958 | - | 1144 | | 1 | transcript | mirbase | 632324 | 632413 | - | 1145 | +--------------+--------------+---------------+-----------+-----------+--------------+-----------+ Stranded PyRanges object has 2,446 rows and 7 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- copy(self)¶
Make a deep copy of the PyRanges.
Notes
See the pandas docs for deep-copying caveats.
- property columns(self)¶
Return the column labels of the PyRanges.
- Returns
- Return type
pandas.Index
See also
PyRanges.chromosomes()return the chromosomes in the PyRanges
Examples
>>> f2 = pr.data.f2() >>> f2 +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 6 | 7 | b | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> f2.columns Index(['Chromosome', 'Start', 'End', 'Name', 'Score', 'Strand'], dtype='object')
>>> f2.columns = f2.columns.str.replace("Sco|re", "NYAN") >>> f2 +--------------+-----------+-----------+------------+------------+--------------+ | Chromosome | Start | End | Name | NYANNYAN | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+------------+--------------| | chr1 | 1 | 2 | a | 0 | + | | chr1 | 6 | 7 | b | 0 | - | +--------------+-----------+-----------+------------+------------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- count_overlaps(self, other, strandedness=None, keep_nonoverlapping=True, overlap_col='NumberOverlaps')¶
Count number of overlaps per interval.
Count how many intervals in self overlap with those in other.
- Parameters
strandedness ({"same", "opposite", None, False}, default None, i.e. auto) – Whether to perform the operation on the same, opposite or no strand. Use False to ignore the strand. None means use “same” if both PyRanges are stranded, otherwise ignore.
keep_nonoverlapping (bool, default True) – Keep intervals without overlaps.
overlap_col (str, default "NumberOverlaps") – Name of column with overlap counts.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
- Returns
PyRanges with a column of overlaps added.
- Return type
See also
PyRanges.coverage()find coverage of PyRanges
pyranges.count_overlaps()count overlaps from multiple PyRanges
Examples
>>> f1 = pr.data.f1().drop() >>> f1 +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 3 | 6 | + | | chr1 | 8 | 9 | + | | chr1 | 5 | 7 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 3 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. >>> f2 = pr.data.f2().drop() >>> f2 +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 1 | 2 | + | | chr1 | 6 | 7 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> f1.count_overlaps(f2, overlap_col="Count") +--------------+-----------+-----------+--------------+-----------+ | Chromosome | Start | End | Strand | Count | | (category) | (int32) | (int32) | (category) | (int64) | |--------------+-----------+-----------+--------------+-----------| | chr1 | 3 | 6 | + | 0 | | chr1 | 8 | 9 | + | 0 | | chr1 | 5 | 7 | - | 1 | +--------------+-----------+-----------+--------------+-----------+ Stranded PyRanges object has 3 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- coverage(self, other, strandedness=None, keep_nonoverlapping=True, overlap_col='NumberOverlaps', fraction_col='FractionOverlaps', nb_cpu=1)¶
Count number of overlaps and their fraction per interval.
Count how many intervals in self overlap with those in other.
- Parameters
strandedness ({"same", "opposite", None, False}, default None, i.e. auto) – Whether to perform the operation on the same, opposite or no strand. Use False to ignore the strand. None means use “same” if both PyRanges are stranded, otherwise ignore.
keep_nonoverlapping (bool, default True) – Keep intervals without overlaps.
overlap_col (str, default "NumberOverlaps") – Name of column with overlap counts.
fraction_col (str, default "FractionOverlaps") – Name of column with fraction of counts.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
- Returns
PyRanges with a column of overlaps added.
- Return type
See also
pyranges.count_overlaps()count overlaps from multiple PyRanges
Examples
>>> f1 = pr.from_dict({"Chromosome": [1, 1, 1], "Start": [3, 8, 5], ... "End": [6, 9, 7]}) >>> f1 +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | 1 | 3 | 6 | | 1 | 8 | 9 | | 1 | 5 | 7 | +--------------+-----------+-----------+ Unstranded PyRanges object has 3 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome. >>> f2 = pr.from_dict({"Chromosome": [1, 1], "Start": [1, 6], ... "End": [2, 7]}) >>> f2 +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | 1 | 1 | 2 | | 1 | 6 | 7 | +--------------+-----------+-----------+ Unstranded PyRanges object has 2 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> f1.coverage(f2, overlap_col="C", fraction_col="F") +--------------+-----------+-----------+-----------+-------------+ | Chromosome | Start | End | C | F | | (category) | (int32) | (int32) | (int64) | (float64) | |--------------+-----------+-----------+-----------+-------------| | 1 | 3 | 6 | 0 | 0 | | 1 | 8 | 9 | 0 | 0 | | 1 | 5 | 7 | 1 | 0.5 | +--------------+-----------+-----------+-----------+-------------+ Unstranded PyRanges object has 3 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- property df(self)¶
Return PyRanges as DataFrame.
See also
PyRanges.as_df()return PyRanges as DataFrame.
- drop(self, drop=None, like=None)¶
Drop column(s).
If no arguments are given, all the columns except Chromosome, Start, End and Strand are dropped.
- Parameters
drop (str or list, default None) – Columns to drop.
like (str, default None) – Regex-string matching columns to drop. Matches with Chromosome, Start, End or Strand are ignored.
See also
PyRanges.unstrand()drop strand information
Examples
>>> gr = pr.from_dict({"Chromosome": [1, 1], "Start": [1, 4], "End": [5, 6], ... "Strand": ["+", "-"], "Count": [1, 2], ... "Type": ["exon", "exon"]}) >>> gr +--------------+-----------+-----------+--------------+-----------+------------+ | Chromosome | Start | End | Strand | Count | Type | | (category) | (int32) | (int32) | (category) | (int64) | (object) | |--------------+-----------+-----------+--------------+-----------+------------| | 1 | 1 | 5 | + | 1 | exon | | 1 | 4 | 6 | - | 2 | exon | +--------------+-----------+-----------+--------------+-----------+------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.drop() +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | 1 | 1 | 5 | + | | 1 | 4 | 6 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
Matches with position-columns are ignored:
>>> gr.drop(like="Chromosome|Strand") +--------------+-----------+-----------+--------------+-----------+------------+ | Chromosome | Start | End | Strand | Count | Type | | (category) | (int32) | (int32) | (category) | (int64) | (object) | |--------------+-----------+-----------+--------------+-----------+------------| | 1 | 1 | 5 | + | 1 | exon | | 1 | 4 | 6 | - | 2 | exon | +--------------+-----------+-----------+--------------+-----------+------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.drop(like="e$") +--------------+-----------+-----------+--------------+-----------+ | Chromosome | Start | End | Strand | Count | | (category) | (int32) | (int32) | (category) | (int64) | |--------------+-----------+-----------+--------------+-----------| | 1 | 1 | 5 | + | 1 | | 1 | 4 | 6 | - | 2 | +--------------+-----------+-----------+--------------+-----------+ Stranded PyRanges object has 2 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- drop_duplicate_positions(self, strand=None, keep='first')¶
Return PyRanges with duplicate postion rows removed.
- Parameters
strand (bool, default None, i.e. auto) – Whether to take strand-information into account when considering duplicates.
keep ({"first", "last", False}) – Whether to keep first, last or drop all duplicates.
Examples
>>> gr = pr.from_string('''Chromosome Start End Strand Name ... 1 1 2 + A ... 1 1 2 - B ... 1 1 2 + Z''') >>> gr +--------------+-----------+-----------+--------------+------------+ | Chromosome | Start | End | Strand | Name | | (category) | (int32) | (int32) | (category) | (object) | |--------------+-----------+-----------+--------------+------------| | 1 | 1 | 2 | + | A | | 1 | 1 | 2 | + | Z | | 1 | 1 | 2 | - | B | +--------------+-----------+-----------+--------------+------------+ Stranded PyRanges object has 3 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.drop_duplicate_positions() +--------------+-----------+-----------+--------------+------------+ | Chromosome | Start | End | Strand | Name | | (category) | (int32) | (int32) | (category) | (object) | |--------------+-----------+-----------+--------------+------------| | 1 | 1 | 2 | + | A | | 1 | 1 | 2 | - | B | +--------------+-----------+-----------+--------------+------------+ Stranded PyRanges object has 2 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.drop_duplicate_positions(keep="last") +--------------+-----------+-----------+--------------+------------+ | Chromosome | Start | End | Strand | Name | | (category) | (int32) | (int32) | (category) | (object) | |--------------+-----------+-----------+--------------+------------| | 1 | 1 | 2 | + | Z | | 1 | 1 | 2 | - | B | +--------------+-----------+-----------+--------------+------------+ Stranded PyRanges object has 2 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
Note that the reverse strand is considered to be behind the forward strand:
>>> gr.drop_duplicate_positions(keep="last", strand=False) +--------------+-----------+-----------+--------------+------------+ | Chromosome | Start | End | Strand | Name | | (category) | (int32) | (int32) | (category) | (object) | |--------------+-----------+-----------+--------------+------------| | 1 | 1 | 2 | - | B | +--------------+-----------+-----------+--------------+------------+ Stranded PyRanges object has 1 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.drop_duplicate_positions(keep=False, strand=False) Empty PyRanges
- property dtypes(self)¶
Return the dtypes of the PyRanges.
Examples
>>> gr = pr.data.chipseq() >>> gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 212609534 | 212609559 | U0 | 0 | + | | chr1 | 169887529 | 169887554 | U0 | 0 | + | | chr1 | 216711011 | 216711036 | U0 | 0 | + | | chr1 | 144227079 | 144227104 | U0 | 0 | + | | ... | ... | ... | ... | ... | ... | | chrY | 15224235 | 15224260 | U0 | 0 | - | | chrY | 13517892 | 13517917 | U0 | 0 | - | | chrY | 8010951 | 8010976 | U0 | 0 | - | | chrY | 7405376 | 7405401 | U0 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10,000 rows and 6 columns from 24 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.dtypes Chromosome category Start int32 End int32 Name object Score int64 Strand category dtype: object
- property empty(self)¶
Indicate whether PyRanges is empty.
- extend(self, ext)¶
Extend the intervals from the ends.
- Parameters
ext (int or dict of ints with "3" and/or "5" as keys.) – The number of nucleotides to extend the ends with. If an int is provided, the same extension is applied to both the start and end of intervals, while a dict input allows to control differently the two ends. Note also that 5’ and 3’ extensions take the strand into account, if the intervals are stranded.
See also
PyRanges.subsequence()obtain subsequences of intervals
PyRanges.spliced_subsequence()obtain subsequences of intervals, providing transcript-level coordinates
Examples
>>> d = {'Chromosome': ['chr1', 'chr1', 'chr1'], 'Start': [3, 8, 5], 'End': [6, 9, 7], ... 'Strand': ['+', '+', '-']} >>> gr = pr.from_dict(d) >>> gr +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 3 | 6 | + | | chr1 | 8 | 9 | + | | chr1 | 5 | 7 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 3 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.extend(4) +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 0 | 10 | + | | chr1 | 4 | 13 | + | | chr1 | 1 | 11 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 3 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.extend({"3": 1}) +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 3 | 7 | + | | chr1 | 8 | 10 | + | | chr1 | 4 | 7 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 3 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.extend({"3": 1, "5": 2}) +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 1 | 7 | + | | chr1 | 6 | 10 | + | | chr1 | 4 | 9 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 3 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.extend(-1) Traceback (most recent call last): ... AssertionError: Some intervals are negative or zero length after applying extend!
- five_end(self)¶
Return the five prime end of intervals.
The five prime end is the start of a forward strand or the end of a reverse strand.
- Returns
PyRanges with the five prime ends
- Return type
Notes
Requires the PyRanges to be stranded.
See also
PyRanges.three_end()return the 3’ end
Examples
>>> gr = pr.from_dict({'Chromosome': ['chr1', 'chr1'], 'Start': [3, 5], 'End': [9, 7], ... 'Strand': ["+", "-"]}) >>> gr +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 3 | 9 | + | | chr1 | 5 | 7 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.five_end() +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 3 | 4 | + | | chr1 | 7 | 8 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- head(self, n=8)¶
Return the n first rows.
- Parameters
n (int, default 8) – Return n rows.
- Returns
PyRanges with the n first rows.
- Return type
See also
PyRanges.tail()return the last rows
PyRanges.sample()return random rows
Examples
>>> gr = pr.data.chipseq() >>> gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 212609534 | 212609559 | U0 | 0 | + | | chr1 | 169887529 | 169887554 | U0 | 0 | + | | chr1 | 216711011 | 216711036 | U0 | 0 | + | | chr1 | 144227079 | 144227104 | U0 | 0 | + | | ... | ... | ... | ... | ... | ... | | chrY | 15224235 | 15224260 | U0 | 0 | - | | chrY | 13517892 | 13517917 | U0 | 0 | - | | chrY | 8010951 | 8010976 | U0 | 0 | - | | chrY | 7405376 | 7405401 | U0 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10,000 rows and 6 columns from 24 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.head(3) +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 212609534 | 212609559 | U0 | 0 | + | | chr1 | 169887529 | 169887554 | U0 | 0 | + | | chr1 | 216711011 | 216711036 | U0 | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- insert(self, other, loc=None)¶
Add one or more columns to the PyRanges.
- Parameters
other (Series, DataFrame or dict) – Data to insert into the PyRanges. other must have the same number of rows as the PyRanges.
loc (int, default None, i.e. after last column of PyRanges.) – Insertion index.
- Returns
A copy of the PyRanges with the column(s) inserted starting at loc.
- Return type
Note
If a Series, or a dict of Series is used, the Series must have a name.
Examples
>>> gr = pr.from_dict({"Chromosome": ["L", "E", "E", "T"], "Start": [1, 1, 2, 3], "End": [5, 8, 13, 21]}) >>> gr +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | E | 1 | 8 | | E | 2 | 13 | | L | 1 | 5 | | T | 3 | 21 | +--------------+-----------+-----------+ Unstranded PyRanges object has 4 rows and 3 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> s = pd.Series(data = [1, 3, 3, 7], name="Column") >>> gr.insert(s) +--------------+-----------+-----------+-----------+ | Chromosome | Start | End | Column | | (category) | (int32) | (int32) | (int64) | |--------------+-----------+-----------+-----------| | E | 1 | 8 | 1 | | E | 2 | 13 | 3 | | L | 1 | 5 | 3 | | T | 3 | 21 | 7 | +--------------+-----------+-----------+-----------+ Unstranded PyRanges object has 4 rows and 4 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> df = pd.DataFrame({"NY": s, "AN": s}) >>> df NY AN 0 1 1 1 3 3 2 3 3 3 7 7
Note that the original PyRanges was not affected by previously inserting Column:
>>> gr.insert(df, 1) +--------------+-----------+-----------+-----------+-----------+ | Chromosome | NY | AN | Start | End | | (category) | (int64) | (int64) | (int32) | (int32) | |--------------+-----------+-----------+-----------+-----------| | E | 1 | 1 | 1 | 8 | | E | 3 | 3 | 2 | 13 | | L | 3 | 3 | 1 | 5 | | T | 7 | 7 | 3 | 21 | +--------------+-----------+-----------+-----------+-----------+ Unstranded PyRanges object has 4 rows and 5 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> arbitrary_result = gr.apply( ... lambda df: pd.Series(df.Start + df.End, name="Hi!"), as_pyranges=False) >>> arbitrary_result {'E': 1 9 2 15 Name: Hi!, dtype: int32, 'L': 0 6 Name: Hi!, dtype: int32, 'T': 3 24 Name: Hi!, dtype: int32}
>>> gr.insert(arbitrary_result) +--------------+-----------+-----------+-----------+ | Chromosome | Start | End | Hi! | | (category) | (int32) | (int32) | (int32) | |--------------+-----------+-----------+-----------| | E | 1 | 8 | 9 | | E | 2 | 13 | 15 | | L | 1 | 5 | 6 | | T | 3 | 21 | 24 | +--------------+-----------+-----------+-----------+ Unstranded PyRanges object has 4 rows and 4 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- intersect(self, other, strandedness=None, how=None, invert=False, nb_cpu=1)¶
Return overlapping subintervals.
Returns the segments of the intervals in self which overlap with those in other.
- Parameters
other (PyRanges) – PyRanges to intersect.
strandedness ({None, "same", "opposite", False}, default None, i.e. auto) – Whether to compare PyRanges on the same strand, the opposite or ignore strand information. The default, None, means use “same” if both PyRanges are strande, otherwise ignore the strand information.
how ({None, "first", "last", "containment"}, default None, i.e. all) – What intervals to report. By default reports all overlapping intervals. “containment” reports intervals where the overlapping is contained within it.
invert (bool, default False) – Whether to return the intervals without overlaps.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
- Returns
A PyRanges with overlapping subintervals.
- Return type
See also
PyRanges.set_intersect()set-intersect PyRanges
PyRanges.overlap()report overlapping intervals
Examples
>>> gr = pr.from_dict({"Chromosome": ["chr1"] * 3, "Start": [1, 4, 10], ... "End": [3, 9, 11], "ID": ["a", "b", "c"]}) >>> gr +--------------+-----------+-----------+------------+ | Chromosome | Start | End | ID | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 1 | 3 | a | | chr1 | 4 | 9 | b | | chr1 | 10 | 11 | c | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 3 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr2 = pr.from_dict({"Chromosome": ["chr1"] * 3, "Start": [2, 2, 9], "End": [3, 9, 10]}) >>> gr2 +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 2 | 3 | | chr1 | 2 | 9 | | chr1 | 9 | 10 | +--------------+-----------+-----------+ Unstranded PyRanges object has 3 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.intersect(gr2) +--------------+-----------+-----------+------------+ | Chromosome | Start | End | ID | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 2 | 3 | a | | chr1 | 2 | 3 | a | | chr1 | 4 | 9 | b | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 3 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.intersect(gr2, how="first") +--------------+-----------+-----------+------------+ | Chromosome | Start | End | ID | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 2 | 3 | a | | chr1 | 4 | 9 | b | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.intersect(gr2, how="containment") +--------------+-----------+-----------+------------+ | Chromosome | Start | End | ID | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 4 | 9 | b | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 1 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- items(self)¶
Return the pairs of keys and DataFrames.
- Returns
The dict mapping keys to DataFrames in the PyRanges.
- Return type
dict
See also
PyRanges.chromosomes()return the chromosomes
PyRanges.keys()return the keys
PyRanges.values()return the DataFrames in the PyRanges
Examples
>>> gr = pr.data.f1() >>> gr.items() [(('chr1', '+'), Chromosome Start End Name Score Strand 0 chr1 3 6 interval1 0 + 2 chr1 8 9 interval3 0 +), (('chr1', '-'), Chromosome Start End Name Score Strand 1 chr1 5 7 interval2 0 -)]
- join(self, other, strandedness=None, how=None, report_overlap=False, slack=0, suffix='_b', nb_cpu=1, apply_strand_suffix=None)¶
Join PyRanges on genomic location.
- Parameters
other (PyRanges) – PyRanges to join.
strandedness ({None, "same", "opposite", False}, default None, i.e. auto) – Whether to compare PyRanges on the same strand, the opposite or ignore strand information. The default, None, means use “same” if both PyRanges are strande, otherwise ignore the strand information.
how ({None, "left", "right"}, default None, i.e. "inner") – How to handle intervals without overlap. None means only keep overlapping intervals. “left” keeps all intervals in self, “right” keeps all intervals in other.
report_overlap (bool, default False) – Report amount of overlap in base pairs.
slack (int, default 0) – Lengthen intervals in self before joining.
suffix (str or tuple, default "_b") – Suffix to give overlapping columns in other.
apply_strand_suffix (bool, default None) – If first pyranges is unstranded, but the second is not, the first will be given a strand column. apply_strand_suffix makes the added strand column a regular data column instead by adding a suffix.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
- Returns
A PyRanges appended with columns of another.
- Return type
Notes
The chromosome from other will never be reported as it is always the same as in self.
As pandas did not have NaN for non-float datatypes until recently, “left” and “right” join give non-overlapping rows the value -1 to avoid promoting columns to object. This will change to NaN in a future version as general NaN becomes stable in pandas.
See also
PyRanges.new_position()give joined PyRanges new coordinates
Examples
>>> f1 = pr.from_dict({'Chromosome': ['chr1', 'chr1', 'chr1'], 'Start': [3, 8, 5], ... 'End': [6, 9, 7], 'Name': ['interval1', 'interval3', 'interval2']}) >>> f1 +--------------+-----------+-----------+------------+ | Chromosome | Start | End | Name | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 3 | 6 | interval1 | | chr1 | 8 | 9 | interval3 | | chr1 | 5 | 7 | interval2 | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 3 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> f2 = pr.from_dict({'Chromosome': ['chr1', 'chr1'], 'Start': [1, 6], ... 'End': [2, 7], 'Name': ['a', 'b']}) >>> f2 +--------------+-----------+-----------+------------+ | Chromosome | Start | End | Name | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 1 | 2 | a | | chr1 | 6 | 7 | b | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> f1.join(f2) +--------------+-----------+-----------+------------+-----------+-----------+------------+ | Chromosome | Start | End | Name | Start_b | End_b | Name_b | | (category) | (int32) | (int32) | (object) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------+-----------+-----------+------------| | chr1 | 5 | 7 | interval2 | 6 | 7 | b | +--------------+-----------+-----------+------------+-----------+-----------+------------+ Unstranded PyRanges object has 1 rows and 7 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> f1.join(f2, how="right") +--------------+-----------+-----------+------------+-----------+-----------+------------+ | Chromosome | Start | End | Name | Start_b | End_b | Name_b | | (category) | (int32) | (int32) | (object) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------+-----------+-----------+------------| | chr1 | 5 | 7 | interval2 | 6 | 7 | b | | chr1 | -1 | -1 | -1 | 1 | 2 | a | +--------------+-----------+-----------+------------+-----------+-----------+------------+ Unstranded PyRanges object has 2 rows and 7 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
With slack 1, bookended features are joined (see row 1):
>>> f1.join(f2, slack=1) +--------------+-----------+-----------+------------+-----------+-----------+------------+ | Chromosome | Start | End | Name | Start_b | End_b | Name_b | | (category) | (int32) | (int32) | (object) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------+-----------+-----------+------------| | chr1 | 3 | 6 | interval1 | 6 | 7 | b | | chr1 | 5 | 7 | interval2 | 6 | 7 | b | +--------------+-----------+-----------+------------+-----------+-----------+------------+ Unstranded PyRanges object has 2 rows and 7 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- keys(self)¶
Return the keys.
- Returns
Returns the keys (chromosomes or chromosome/strand pairs) as strings or tuples of strings
in natsorted order.
See also
PyRanges.chromosomes()return the chromosomes
Examples
>>> gr = pr.data.chipseq() >>> gr.keys() [('chr1', '+'), ('chr1', '-'), ('chr2', '+'), ('chr2', '-'), ('chr3', '+'), ('chr3', '-'), ('chr4', '+'), ('chr4', '-'), ('chr5', '+'), ('chr5', '-'), ('chr6', '+'), ('chr6', '-'), ('chr7', '+'), ('chr7', '-'), ('chr8', '+'), ('chr8', '-'), ('chr9', '+'), ('chr9', '-'), ('chr10', '+'), ('chr10', '-'), ('chr11', '+'), ('chr11', '-'), ('chr12', '+'), ('chr12', '-'), ('chr13', '+'), ('chr13', '-'), ('chr14', '+'), ('chr14', '-'), ('chr15', '+'), ('chr15', '-'), ('chr16', '+'), ('chr16', '-'), ('chr17', '+'), ('chr17', '-'), ('chr18', '+'), ('chr18', '-'), ('chr19', '+'), ('chr19', '-'), ('chr20', '+'), ('chr20', '-'), ('chr21', '+'), ('chr21', '-'), ('chr22', '+'), ('chr22', '-'), ('chrX', '+'), ('chrX', '-'), ('chrY', '+'), ('chrY', '-')] >>> gr.unstrand().keys() ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY']
- k_nearest(self, other, k=1, ties=None, strandedness=None, overlap=True, how=None, suffix='_b', nb_cpu=1, apply_strand_suffix=None)¶
Find k nearest intervals.
- Parameters
other (PyRanges) – PyRanges to find nearest interval in.
k (int or list/array/Series of int) – Number of closest to return. If iterable, must be same length as PyRanges.
ties ({None, "first", "last", "different"}, default None) – How to resolve ties, i.e. closest intervals with equal distance. None means that the k nearest intervals are kept. “first” means that the first tie is kept, “last” meanst that the last is kept. “different” means that all nearest intervals with the k unique nearest distances are kept.
strandedness ({None, "same", "opposite", False}, default None, i.e. auto) – Whether to compare PyRanges on the same strand, the opposite or ignore strand information. The default, None, means use “same” if both PyRanges are stranded, otherwise ignore the strand information.
overlap (bool, default True) – Whether to include overlaps.
how ({None, "upstream", "downstream"}, default None, i.e. both directions) – Whether to only look for nearest in one direction. Always with respect to the PyRanges it is called on.
suffix (str, default "_b") – Suffix to give columns with shared name in other.
apply_strand_suffix (bool, default None) – If first pyranges is unstranded, but the second is not, the first will be given a strand column. apply_strand_suffix makes the added strand column a regular data column instead by adding a suffix.
nb_cpu: int, default 1
How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
- Returns
A PyRanges with columns of nearest interval horizontally appended.
- Return type
Notes
nearest also exists, and is more performant.
See also
PyRanges.new_position()give joined PyRanges new coordinates
PyRanges.nearest()find nearest intervals
Examples
>>> f1 = pr.from_dict({'Chromosome': ['chr1', 'chr1', 'chr1'], 'Start': [3, 8, 5], ... 'End': [6, 9, 7], 'Strand': ['+', '+', '-']}) >>> f1 +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 3 | 6 | + | | chr1 | 8 | 9 | + | | chr1 | 5 | 7 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 3 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> f2 = pr.from_dict({'Chromosome': ['chr1', 'chr1'], 'Start': [1, 6], ... 'End': [2, 7], 'Strand': ['+', '-']}) >>> f2 +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 1 | 2 | + | | chr1 | 6 | 7 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> f1.k_nearest(f2, k=2) +--------------+-----------+-----------+--------------+-----------+-----------+--------------+------------+ | Chromosome | Start | End | Strand | Start_b | End_b | Strand_b | Distance | | (category) | (int32) | (int32) | (category) | (int32) | (int32) | (category) | (int32) | |--------------+-----------+-----------+--------------+-----------+-----------+--------------+------------| | chr1 | 3 | 6 | + | 6 | 7 | - | 1 | | chr1 | 3 | 6 | + | 1 | 2 | + | -2 | | chr1 | 8 | 9 | + | 6 | 7 | - | -2 | | chr1 | 8 | 9 | + | 1 | 2 | + | -7 | | chr1 | 5 | 7 | - | 6 | 7 | - | 0 | | chr1 | 5 | 7 | - | 1 | 2 | + | 4 | +--------------+-----------+-----------+--------------+-----------+-----------+--------------+------------+ Stranded PyRanges object has 6 rows and 8 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> f1.k_nearest(f2, how="upstream", k=2) +--------------+-----------+-----------+--------------+-----------+-----------+--------------+------------+ | Chromosome | Start | End | Strand | Start_b | End_b | Strand_b | Distance | | (category) | (int32) | (int32) | (category) | (int32) | (int32) | (category) | (int32) | |--------------+-----------+-----------+--------------+-----------+-----------+--------------+------------| | chr1 | 3 | 6 | + | 1 | 2 | + | -2 | | chr1 | 8 | 9 | + | 6 | 7 | - | -2 | | chr1 | 8 | 9 | + | 1 | 2 | + | -7 | | chr1 | 5 | 7 | - | 6 | 7 | - | 0 | +--------------+-----------+-----------+--------------+-----------+-----------+--------------+------------+ Stranded PyRanges object has 4 rows and 8 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> f1.k_nearest(f2, k=[1, 2, 1]) +--------------+-----------+-----------+--------------+-----------+-----------+--------------+------------+ | Chromosome | Start | End | Strand | Start_b | End_b | Strand_b | Distance | | (category) | (int32) | (int32) | (category) | (int32) | (int32) | (category) | (int32) | |--------------+-----------+-----------+--------------+-----------+-----------+--------------+------------| | chr1 | 3 | 6 | + | 6 | 7 | - | 1 | | chr1 | 8 | 9 | + | 6 | 7 | - | -2 | | chr1 | 8 | 9 | + | 1 | 2 | + | -7 | | chr1 | 5 | 7 | - | 6 | 7 | - | 0 | +--------------+-----------+-----------+--------------+-----------+-----------+--------------+------------+ Stranded PyRanges object has 4 rows and 8 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> d1 = {"Chromosome": [1], "Start": [5], "End": [6]} >>> d2 = {"Chromosome": 1, "Start": [1] * 2 + [5] * 2 + [9] * 2, ... "End": [3] * 2 + [7] * 2 + [11] * 2, "ID": range(6)} >>> gr, gr2 = pr.from_dict(d1), pr.from_dict(d2)
>>> gr +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | 1 | 5 | 6 | +--------------+-----------+-----------+ Unstranded PyRanges object has 1 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr2 +--------------+-----------+-----------+-----------+ | Chromosome | Start | End | ID | | (category) | (int32) | (int32) | (int64) | |--------------+-----------+-----------+-----------| | 1 | 1 | 3 | 0 | | 1 | 1 | 3 | 1 | | 1 | 5 | 7 | 2 | | 1 | 5 | 7 | 3 | | 1 | 9 | 11 | 4 | | 1 | 9 | 11 | 5 | +--------------+-----------+-----------+-----------+ Unstranded PyRanges object has 6 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.k_nearest(gr2, k=2) +--------------+-----------+-----------+-----------+-----------+-----------+------------+ | Chromosome | Start | End | Start_b | End_b | ID | Distance | | (category) | (int32) | (int32) | (int32) | (int32) | (int64) | (int64) | |--------------+-----------+-----------+-----------+-----------+-----------+------------| | 1 | 5 | 6 | 5 | 7 | 2 | 0 | | 1 | 5 | 6 | 5 | 7 | 3 | 0 | +--------------+-----------+-----------+-----------+-----------+-----------+------------+ Unstranded PyRanges object has 2 rows and 7 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.k_nearest(gr2, k=2, ties="different") +--------------+-----------+-----------+-----------+-----------+-----------+------------+ | Chromosome | Start | End | Start_b | End_b | ID | Distance | | (category) | (int32) | (int32) | (int32) | (int32) | (int64) | (int64) | |--------------+-----------+-----------+-----------+-----------+-----------+------------| | 1 | 5 | 6 | 5 | 7 | 2 | 0 | | 1 | 5 | 6 | 5 | 7 | 3 | 0 | | 1 | 5 | 6 | 1 | 3 | 1 | -3 | | 1 | 5 | 6 | 1 | 3 | 0 | -3 | +--------------+-----------+-----------+-----------+-----------+-----------+------------+ Unstranded PyRanges object has 4 rows and 7 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.k_nearest(gr2, k=3, ties="first") +--------------+-----------+-----------+-----------+-----------+-----------+------------+ | Chromosome | Start | End | Start_b | End_b | ID | Distance | | (category) | (int32) | (int32) | (int32) | (int32) | (int64) | (int64) | |--------------+-----------+-----------+-----------+-----------+-----------+------------| | 1 | 5 | 6 | 5 | 7 | 2 | 0 | | 1 | 5 | 6 | 1 | 3 | 1 | -3 | | 1 | 5 | 6 | 9 | 11 | 4 | 4 | +--------------+-----------+-----------+-----------+-----------+-----------+------------+ Unstranded PyRanges object has 3 rows and 7 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.k_nearest(gr2, k=1, overlap=False) +--------------+-----------+-----------+-----------+-----------+-----------+------------+ | Chromosome | Start | End | Start_b | End_b | ID | Distance | | (category) | (int32) | (int32) | (int32) | (int32) | (int64) | (int32) | |--------------+-----------+-----------+-----------+-----------+-----------+------------| | 1 | 5 | 6 | 1 | 3 | 1 | -3 | | 1 | 5 | 6 | 1 | 3 | 0 | -3 | +--------------+-----------+-----------+-----------+-----------+-----------+------------+ Unstranded PyRanges object has 2 rows and 7 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- property length(self)¶
Return the total length of the intervals.
See also
PyRanges.lengths()return the intervals lengths
Examples
>>> gr = pr.data.f1() >>> gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3 | 6 | interval1 | 0 | + | | chr1 | 8 | 9 | interval3 | 0 | + | | chr1 | 5 | 7 | interval2 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.length 6
To find the length of the genome covered by the intervals, use merge first:
>>> gr.merge(strand=False).length 5
- lengths(self, as_dict=False)¶
Return the length of each interval.
- Parameters
as_dict (bool, default False) – Whether to return lengths as Series or dict of Series per key.
- Returns
- Return type
Series or dict of Series with the lengths of each interval.
See also
PyRanges.lengths()return the intervals lengths
Examples
>>> gr = pr.data.f1() >>> gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3 | 6 | interval1 | 0 | + | | chr1 | 8 | 9 | interval3 | 0 | + | | chr1 | 5 | 7 | interval2 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.lengths() 0 3 1 1 2 2 dtype: int32
To find the length of the genome covered by the intervals, use merge first:
>>> gr.Length = gr.lengths() >>> gr +--------------+-----------+-----------+------------+-----------+--------------+-----------+ | Chromosome | Start | End | Name | Score | Strand | Length | | (category) | (int32) | (int32) | (object) | (int64) | (category) | (int32) | |--------------+-----------+-----------+------------+-----------+--------------+-----------| | chr1 | 3 | 6 | interval1 | 0 | + | 3 | | chr1 | 8 | 9 | interval3 | 0 | + | 1 | | chr1 | 5 | 7 | interval2 | 0 | - | 2 | +--------------+-----------+-----------+------------+-----------+--------------+-----------+ Stranded PyRanges object has 3 rows and 7 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- max_disjoint(self, strand=None, slack=0, **kwargs)¶
Find the maximal disjoint set of intervals.
- Parameters
strand (bool, default None, i.e. auto) – Find the max disjoint set separately for each strand.
slack (int, default 0) – Consider intervals within a distance of slack to be overlapping.
- Returns
PyRanges with maximal disjoint set of intervals.
- Return type
Examples
>>> gr = pr.data.f1() +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3 | 6 | interval1 | 0 | + | | chr1 | 8 | 9 | interval3 | 0 | + | | chr1 | 5 | 7 | interval2 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.max_disjoint(strand=False) +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3 | 6 | interval1 | 0 | + | | chr1 | 8 | 9 | interval3 | 0 | + | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- merge(self, strand=None, count=False, count_col='Count', by=None, slack=0)¶
Merge overlapping intervals into one.
- Parameters
strand (bool, default None, i.e. auto) – Only merge intervals on same strand.
count (bool, default False) – Count intervals in each superinterval.
count_col (str, default "Count") – Name of column with counts.
by (str or list of str, default None) – Only merge intervals with equal values in these columns.
slack (int, default 0) – Allow this many nucleotides between each interval to merge.
- Returns
PyRanges with superintervals.
- Return type
Notes
To avoid losing metadata, use cluster instead. If you want to perform a reduction function on the metadata, use pandas groupby.
See also
PyRanges.cluster()annotate overlapping intervals with common ID
Examples
>>> gr = pr.data.ensembl_gtf()[["Feature", "gene_name"]] >>> gr +--------------+--------------+-----------+-----------+--------------+-------------+ | Chromosome | Feature | Start | End | Strand | gene_name | | (category) | (category) | (int32) | (int32) | (category) | (object) | |--------------+--------------+-----------+-----------+--------------+-------------| | 1 | gene | 11868 | 14409 | + | DDX11L1 | | 1 | transcript | 11868 | 14409 | + | DDX11L1 | | 1 | exon | 11868 | 12227 | + | DDX11L1 | | 1 | exon | 12612 | 12721 | + | DDX11L1 | | ... | ... | ... | ... | ... | ... | | 1 | gene | 1173055 | 1179555 | - | TTLL10-AS1 | | 1 | transcript | 1173055 | 1179555 | - | TTLL10-AS1 | | 1 | exon | 1179364 | 1179555 | - | TTLL10-AS1 | | 1 | exon | 1173055 | 1176396 | - | TTLL10-AS1 | +--------------+--------------+-----------+-----------+--------------+-------------+ Stranded PyRanges object has 2,446 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.merge(count=True, count_col="Count") +--------------+-----------+-----------+--------------+-----------+ | Chromosome | Start | End | Strand | Count | | (category) | (int32) | (int32) | (category) | (int32) | |--------------+-----------+-----------+--------------+-----------| | 1 | 11868 | 14409 | + | 12 | | 1 | 29553 | 31109 | + | 11 | | 1 | 52472 | 53312 | + | 3 | | 1 | 57597 | 64116 | + | 7 | | ... | ... | ... | ... | ... | | 1 | 1062207 | 1063288 | - | 4 | | 1 | 1070966 | 1074306 | - | 10 | | 1 | 1081817 | 1116361 | - | 319 | | 1 | 1173055 | 1179555 | - | 4 | +--------------+-----------+-----------+--------------+-----------+ Stranded PyRanges object has 62 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.merge(by="Feature", count=True) +--------------+-----------+-----------+--------------+--------------+-----------+ | Chromosome | Start | End | Strand | Feature | Count | | (category) | (int32) | (int32) | (category) | (category) | (int32) | |--------------+-----------+-----------+--------------+--------------+-----------| | 1 | 65564 | 65573 | + | CDS | 1 | | 1 | 69036 | 70005 | + | CDS | 2 | | 1 | 924431 | 924948 | + | CDS | 1 | | 1 | 925921 | 926013 | + | CDS | 11 | | ... | ... | ... | ... | ... | ... | | 1 | 1062207 | 1063288 | - | transcript | 1 | | 1 | 1070966 | 1074306 | - | transcript | 1 | | 1 | 1081817 | 1116361 | - | transcript | 19 | | 1 | 1173055 | 1179555 | - | transcript | 1 | +--------------+-----------+-----------+--------------+--------------+-----------+ Stranded PyRanges object has 748 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.merge(by=["Feature", "gene_name"], count=True) +--------------+-----------+-----------+--------------+--------------+-------------+-----------+ | Chromosome | Start | End | Strand | Feature | gene_name | Count | | (category) | (int32) | (int32) | (category) | (category) | (object) | (int32) | |--------------+-----------+-----------+--------------+--------------+-------------+-----------| | 1 | 1020172 | 1020373 | + | CDS | AGRN | 1 | | 1 | 1022200 | 1022462 | + | CDS | AGRN | 2 | | 1 | 1034555 | 1034703 | + | CDS | AGRN | 2 | | 1 | 1035276 | 1035324 | + | CDS | AGRN | 4 | | ... | ... | ... | ... | ... | ... | ... | | 1 | 347981 | 348366 | - | transcript | RPL23AP24 | 1 | | 1 | 1173055 | 1179555 | - | transcript | TTLL10-AS1 | 1 | | 1 | 14403 | 29570 | - | transcript | WASH7P | 1 | | 1 | 185216 | 195411 | - | transcript | WASH9P | 1 | +--------------+-----------+-----------+--------------+--------------+-------------+-----------+ Stranded PyRanges object has 807 rows and 7 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- mp(self, n=8, formatting=None)¶
Merge location and print.
See also
PyRanges.print()print PyRanges.
- mpc(self, n=8, formatting=None)¶
Merge location, print and return self.
See also
PyRanges.print()print PyRanges.
- msp(self, n=30, formatting=None)¶
Sort on location, merge location info and print.
See also
PyRanges.print()print PyRanges.
- mspc(self, n=30, formatting=None)¶
Sort on location, merge location, print and return self.
See also
PyRanges.print()print PyRanges.
- nearest(self, other, strandedness=None, overlap=True, how=None, suffix='_b', nb_cpu=1, apply_strand_suffix=None)¶
Find closest interval.
- Parameters
other (PyRanges) – PyRanges to find nearest interval in.
strandedness ({None, "same", "opposite", False}, default None, i.e. auto) – Whether to compare PyRanges on the same strand, the opposite or ignore strand information. The default, None, means use “same” if both PyRanges are strande, otherwise ignore the strand information.
overlap (bool, default True) – Whether to include overlaps.
how ({None, "upstream", "downstream"}, default None, i.e. both directions) – Whether to only look for nearest in one direction. Always with respect to the PyRanges it is called on.
suffix (str, default "_b") – Suffix to give columns with shared name in other.
apply_strand_suffix (bool, default None) – If first pyranges is unstranded, but the second is not, the first will be given the strand column of the second. apply_strand_suffix makes the added strand column a regular data column instead by adding a suffix.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
- Returns
A PyRanges with columns representing nearest interval horizontally appended.
- Return type
Notes
A k_nearest also exists, but is less performant.
See also
PyRanges.new_position()give joined PyRanges new coordinates
PyRanges.k_nearest()find k nearest intervals
Examples
>>> f1 = pr.from_dict({'Chromosome': ['chr1', 'chr1', 'chr1'], 'Start': [3, 8, 5], ... 'End': [6, 9, 7], 'Strand': ['+', '+', '-']}) >>> f1 +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 3 | 6 | + | | chr1 | 8 | 9 | + | | chr1 | 5 | 7 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 3 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> f2 = pr.from_dict({'Chromosome': ['chr1', 'chr1'], 'Start': [1, 6], ... 'End': [2, 7], 'Strand': ['+', '-']}) >>> f2 +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 1 | 2 | + | | chr1 | 6 | 7 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> f1.nearest(f2) +--------------+-----------+-----------+--------------+-----------+-----------+--------------+------------+ | Chromosome | Start | End | Strand | Start_b | End_b | Strand_b | Distance | | (category) | (int32) | (int32) | (category) | (int32) | (int32) | (category) | (int64) | |--------------+-----------+-----------+--------------+-----------+-----------+--------------+------------| | chr1 | 3 | 6 | + | 6 | 7 | - | 1 | | chr1 | 8 | 9 | + | 6 | 7 | - | 2 | | chr1 | 5 | 7 | - | 6 | 7 | - | 0 | +--------------+-----------+-----------+--------------+-----------+-----------+--------------+------------+ Stranded PyRanges object has 3 rows and 8 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> f1.nearest(f2, how="upstream") +--------------+-----------+-----------+--------------+-----------+-----------+--------------+------------+ | Chromosome | Start | End | Strand | Start_b | End_b | Strand_b | Distance | | (category) | (int32) | (int32) | (category) | (int32) | (int32) | (category) | (int64) | |--------------+-----------+-----------+--------------+-----------+-----------+--------------+------------| | chr1 | 3 | 6 | + | 1 | 2 | + | 2 | | chr1 | 8 | 9 | + | 6 | 7 | - | 2 | | chr1 | 5 | 7 | - | 6 | 7 | - | 0 | +--------------+-----------+-----------+--------------+-----------+-----------+--------------+------------+ Stranded PyRanges object has 3 rows and 8 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- new_position(self, new_pos, columns=None)¶
Give new position.
The operation join produces a PyRanges with two pairs of start coordinates and two pairs of end coordinates. This operation uses these to give the PyRanges a new position.
- Parameters
new_pos ({"union", "intersection", "swap"}) – Change of coordinates.
columns (tuple of str, default None, i.e. auto) – The name of the coordinate columns. By default uses the two first columns containing “Start” and the two first columns containing “End”.
See also
PyRanges.join()combine two PyRanges horizontally with SQL-style joins.
- Returns
PyRanges with new coordinates.
- Return type
Examples
>>> gr = pr.from_dict({'Chromosome': ['chr1', 'chr1', 'chr1'], ... 'Start': [3, 8, 5], 'End': [6, 9, 7]}) >>> gr +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 3 | 6 | | chr1 | 8 | 9 | | chr1 | 5 | 7 | +--------------+-----------+-----------+ Unstranded PyRanges object has 3 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr2 = pr.from_dict({'Chromosome': ['chr1', 'chr1'], 'Start': [1, 6], ... 'End': [4, 7]}) >>> gr2 +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 1 | 4 | | chr1 | 6 | 7 | +--------------+-----------+-----------+ Unstranded PyRanges object has 2 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> j = gr.join(gr2) >>> j +--------------+-----------+-----------+-----------+-----------+ | Chromosome | Start | End | Start_b | End_b | | (category) | (int32) | (int32) | (int32) | (int32) | |--------------+-----------+-----------+-----------+-----------| | chr1 | 3 | 6 | 1 | 4 | | chr1 | 5 | 7 | 6 | 7 | +--------------+-----------+-----------+-----------+-----------+ Unstranded PyRanges object has 2 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> j.new_position("swap") +--------------+-----------+-----------+-----------+-----------+ | Chromosome | Start | End | Start_b | End_b | | (category) | (int32) | (int32) | (int32) | (int32) | |--------------+-----------+-----------+-----------+-----------| | chr1 | 1 | 4 | 3 | 6 | | chr1 | 6 | 7 | 5 | 7 | +--------------+-----------+-----------+-----------+-----------+ Unstranded PyRanges object has 2 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> j.new_position("union").mp() +--------------------+-----------+-----------+ | - Position - | Start_b | End_b | | (Multiple types) | (int32) | (int32) | |--------------------+-----------+-----------| | chr1 1-6 | 1 | 4 | | chr1 5-7 | 6 | 7 | +--------------------+-----------+-----------+ Unstranded PyRanges object has 2 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> j.new_position("intersection").mp() +--------------------+-----------+-----------+ | - Position - | Start_b | End_b | | (Multiple types) | (int32) | (int32) | |--------------------+-----------+-----------| | chr1 1-4 | 1 | 4 | | chr1 6-7 | 6 | 7 | +--------------------+-----------+-----------+ Unstranded PyRanges object has 2 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> j2 = pr.from_dict({"Chromosome": [1], "Start": [3], ... "End": [4], "A": [1], "B": [3], "C": [2], "D": [5]}) >>> j2 +--------------+-----------+-----------+-----------+-----------+-----------+-----------+ | Chromosome | Start | End | A | B | C | D | | (category) | (int32) | (int32) | (int64) | (int64) | (int64) | (int64) | |--------------+-----------+-----------+-----------+-----------+-----------+-----------| | 1 | 3 | 4 | 1 | 3 | 2 | 5 | +--------------+-----------+-----------+-----------+-----------+-----------+-----------+ Unstranded PyRanges object has 1 rows and 7 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> j2.new_position("intersection", ("A", "B", "C", "D")) +--------------+-----------+-----------+-----------+-----------+-----------+-----------+ | Chromosome | Start | End | A | B | C | D | | (category) | (int32) | (int32) | (int64) | (int64) | (int64) | (int64) | |--------------+-----------+-----------+-----------+-----------+-----------+-----------| | 1 | 2 | 3 | 1 | 3 | 2 | 5 | +--------------+-----------+-----------+-----------+-----------+-----------+-----------+ Unstranded PyRanges object has 1 rows and 7 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- overlap(self, other, strandedness=None, how='first', invert=False, nb_cpu=1)¶
Return overlapping intervals.
Returns the intervals in self which overlap with those in other.
- Parameters
other (PyRanges) – PyRanges to find overlaps with.
strandedness ({None, "same", "opposite", False}, default None, i.e. auto) – Whether to compare PyRanges on the same strand, the opposite or ignore strand information. The default, None, means use “same” if both PyRanges are strande, otherwise ignore the strand information.
how ({"first", "containment", False, None}, default "first") – What intervals to report. By default reports every interval in self with overlap once. “containment” reports all intervals where the overlapping is contained within it.
invert (bool, default False) – Whether to return the intervals without overlaps.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
- Returns
A PyRanges with overlapping intervals.
- Return type
See also
PyRanges.intersect()report overlapping subintervals
PyRanges.set_intersect()set-intersect PyRanges
Examples
>>> gr = pr.from_dict({"Chromosome": ["chr1"] * 3, "Start": [1, 4, 10], ... "End": [3, 9, 11], "ID": ["a", "b", "c"]}) >>> gr +--------------+-----------+-----------+------------+ | Chromosome | Start | End | ID | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 1 | 3 | a | | chr1 | 4 | 9 | b | | chr1 | 10 | 11 | c | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 3 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr2 = pr.from_dict({"Chromosome": ["chr1"] * 3, "Start": [2, 2, 9], "End": [3, 9, 10]}) >>> gr2 +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 2 | 3 | | chr1 | 2 | 9 | | chr1 | 9 | 10 | +--------------+-----------+-----------+ Unstranded PyRanges object has 3 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.overlap(gr2) +--------------+-----------+-----------+------------+ | Chromosome | Start | End | ID | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 1 | 3 | a | | chr1 | 4 | 9 | b | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.overlap(gr2, how=None) +--------------+-----------+-----------+------------+ | Chromosome | Start | End | ID | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 1 | 3 | a | | chr1 | 1 | 3 | a | | chr1 | 4 | 9 | b | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 3 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.overlap(gr2, how="containment") +--------------+-----------+-----------+------------+ | Chromosome | Start | End | ID | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 4 | 9 | b | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 1 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.overlap(gr2, invert=True) +--------------+-----------+-----------+------------+ | Chromosome | Start | End | ID | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 10 | 11 | c | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 1 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- pc(self, n=8, formatting=None)¶
Print and return self.
See also
PyRanges.print()print PyRanges.
- print(self, n=8, merge_position=False, sort=False, formatting=None, chain=False)¶
Print the PyRanges.
- Parameters
n (int, default 8) – The number of rows to print.
merge_postion (bool, default False) – Print location in same column to save screen space.
sort (bool or str, default False) – Sort the PyRanges before printing. Will print chromosomsomes or strands interleaved on sort columns.
formatting (dict, default None) – Formatting options per column.
chain (False) – Return the PyRanges. Useful to print intermediate results in call chains.
See also
PyRanges.pc()print chain
PyRanges.sp()sort print
PyRanges.mp()merge print
PyRanges.spc()sort print chain
PyRanges.mpc()merge print chain
PyRanges.msp()merge sort print
PyRanges.mspc()merge sort print chain
PyRanges.rp()raw print dictionary of DataFrames
Examples
>>> d = {'Chromosome': ['chr1', 'chr1', 'chr1'], 'Start': [3, 8, 5000], ... 'End': [6, 9, 7000], 'Name': ['i1', 'i3', 'i2'], ... 'Score': [1.1, 2.3987, 5.9999995], 'Strand': ['+', '+', '-']} >>> gr = pr.from_dict(d) >>> gr +--------------+-----------+-----------+------------+-------------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (float64) | (category) | |--------------+-----------+-----------+------------+-------------+--------------| | chr1 | 3 | 6 | i1 | 1.1 | + | | chr1 | 8 | 9 | i3 | 2.3987 | + | | chr1 | 5000 | 7000 | i2 | 6 | - | +--------------+-----------+-----------+------------+-------------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.print(formatting={"Start": "{:,}", "Score": "{:.2f}"}) +--------------+-----------+-----------+------------+-------------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (float64) | (category) | |--------------+-----------+-----------+------------+-------------+--------------| | chr1 | 3 | 6 | i1 | 1.1 | + | | chr1 | 8 | 9 | i3 | 2.4 | + | | chr1 | 5,000 | 7000 | i2 | 6 | - | +--------------+-----------+-----------+------------+-------------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.print(merge_position=True) # gr.mp() +--------------------+------------+-------------+ | - Position - | Name | Score | | (Multiple types) | (object) | (float64) | |--------------------+------------+-------------| | chr1 3-6 + | i1 | 1.1 | | chr1 8-9 + | i3 | 2.3987 | | chr1 5000-7000 - | i2 | 6 | +--------------------+------------+-------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> chipseq = pr.data.chipseq() >>> chipseq +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 212609534 | 212609559 | U0 | 0 | + | | chr1 | 169887529 | 169887554 | U0 | 0 | + | | chr1 | 216711011 | 216711036 | U0 | 0 | + | | chr1 | 144227079 | 144227104 | U0 | 0 | + | | ... | ... | ... | ... | ... | ... | | chrY | 15224235 | 15224260 | U0 | 0 | - | | chrY | 13517892 | 13517917 | U0 | 0 | - | | chrY | 8010951 | 8010976 | U0 | 0 | - | | chrY | 7405376 | 7405401 | U0 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10,000 rows and 6 columns from 24 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
To interleave strands in output, use print with sort=True:
>>> chipseq.print(sort=True, n=20) # chipseq.sp() +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 1325303 | 1325328 | U0 | 0 | - | | chr1 | 1541598 | 1541623 | U0 | 0 | + | | chr1 | 1599121 | 1599146 | U0 | 0 | + | | chr1 | 1820285 | 1820310 | U0 | 0 | - | | chr1 | 2448322 | 2448347 | U0 | 0 | - | | chr1 | 3046141 | 3046166 | U0 | 0 | - | | chr1 | 3437168 | 3437193 | U0 | 0 | - | | chr1 | 3504032 | 3504057 | U0 | 0 | + | | chr1 | 3637087 | 3637112 | U0 | 0 | - | | chr1 | 3681903 | 3681928 | U0 | 0 | - | | ... | ... | ... | ... | ... | ... | | chrY | 15224235 | 15224260 | U0 | 0 | - | | chrY | 15548022 | 15548047 | U0 | 0 | + | | chrY | 16045242 | 16045267 | U0 | 0 | - | | chrY | 16495497 | 16495522 | U0 | 0 | - | | chrY | 21559181 | 21559206 | U0 | 0 | + | | chrY | 21707662 | 21707687 | U0 | 0 | - | | chrY | 21751211 | 21751236 | U0 | 0 | - | | chrY | 21910706 | 21910731 | U0 | 0 | - | | chrY | 22054002 | 22054027 | U0 | 0 | - | | chrY | 22210637 | 22210662 | U0 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10,000 rows and 6 columns from 24 chromosomes. For printing, the PyRanges was sorted on Chromosome, Start, End and Strand.
>>> pr.data.chromsizes().print() +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 0 | 249250621 | | chr2 | 0 | 243199373 | | chr3 | 0 | 198022430 | | chr4 | 0 | 191154276 | | ... | ... | ... | | chr22 | 0 | 51304566 | | chrM | 0 | 16571 | | chrX | 0 | 155270560 | | chrY | 0 | 59373566 | +--------------+-----------+-----------+ Unstranded PyRanges object has 25 rows and 3 columns from 25 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- rp(self)¶
Print dict of DataFrames.
See also
PyRanges.print()print PyRanges.
- rpc(self)¶
Print dict of DataFrames and return self.
See also
PyRanges.print()print PyRanges.
- sample(self, n=8, replace=False)¶
Subsample arbitrary rows of PyRanges.
If n is larger than length of PyRanges, replace must be True.
- Parameters
n (int, default 8) – Number of rows to return
replace (bool, False) – Reuse rows.
Examples
>>> gr = pr.data.chipseq() >>> np.random.seed(0) >>> gr.sample(n=3) +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr2 | 76564764 | 76564789 | U0 | 0 | + | | chr3 | 185739979 | 185740004 | U0 | 0 | - | | chr20 | 40373657 | 40373682 | U0 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.sample(10001) Traceback (most recent call last): ... ValueError: Cannot take a larger sample than population when 'replace=False'
- set_intersect(self, other, strandedness=None, how=None, new_pos=False, nb_cpu=1)¶
Return set-theoretical intersection.
Like intersect, but both PyRanges are merged first.
- Parameters
other (PyRanges) – PyRanges to set-intersect.
strandedness ({None, "same", "opposite", False}, default None, i.e. auto) – Whether to compare PyRanges on the same strand, the opposite or ignore strand information. The default, None, means use “same” if both PyRanges are strande, otherwise ignore the strand information.
how ({None, "first", "last", "containment"}, default None, i.e. all) – What intervals to report. By default reports all overlapping intervals. “containment” reports intervals where the overlapping is contained within it.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
- Returns
A PyRanges with overlapping subintervals.
- Return type
See also
PyRanges.intersect()find overlapping subintervals
PyRanges.overlap()report overlapping intervals
Examples
>>> gr = pr.from_dict({"Chromosome": ["chr1"] * 3, "Start": [1, 4, 10], ... "End": [3, 9, 11], "ID": ["a", "b", "c"]}) >>> gr +--------------+-----------+-----------+------------+ | Chromosome | Start | End | ID | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 1 | 3 | a | | chr1 | 4 | 9 | b | | chr1 | 10 | 11 | c | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 3 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr2 = pr.from_dict({"Chromosome": ["chr1"] * 3, "Start": [2, 2, 9], "End": [3, 9, 10]}) >>> gr2 +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 2 | 3 | | chr1 | 2 | 9 | | chr1 | 9 | 10 | +--------------+-----------+-----------+ Unstranded PyRanges object has 3 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.set_intersect(gr2) +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 2 | 3 | | chr1 | 4 | 9 | +--------------+-----------+-----------+ Unstranded PyRanges object has 2 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
In this simple unstranded case, this is the same as the below:
>>> gr.merge().intersect(gr2.merge()) +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 2 | 3 | | chr1 | 4 | 9 | +--------------+-----------+-----------+ Unstranded PyRanges object has 2 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.set_intersect(gr2, how="containment") +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 4 | 9 | +--------------+-----------+-----------+ Unstranded PyRanges object has 1 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- set_union(self, other, strandedness=None, nb_cpu=1)¶
Return set-theoretical union.
- Parameters
other (PyRanges) – PyRanges to do union with.
strandedness ({None, "same", "opposite", False}, default None, i.e. auto) – Whether to compare PyRanges on the same strand, the opposite or ignore strand information. The default, None, means use “same” if both PyRanges are strande, otherwise ignore the strand information.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
- Returns
A PyRanges with the union of intervals.
- Return type
See also
PyRanges.set_intersect()set-theoretical intersection
PyRanges.overlap()report overlapping intervals
Examples
>>> gr = pr.from_dict({"Chromosome": ["chr1"] * 3, "Start": [1, 4, 10], ... "End": [3, 9, 11], "ID": ["a", "b", "c"]}) >>> gr +--------------+-----------+-----------+------------+ | Chromosome | Start | End | ID | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 1 | 3 | a | | chr1 | 4 | 9 | b | | chr1 | 10 | 11 | c | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 3 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr2 = pr.from_dict({"Chromosome": ["chr1"] * 3, "Start": [2, 2, 9], "End": [3, 9, 10]}) >>> gr2 +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 2 | 3 | | chr1 | 2 | 9 | | chr1 | 9 | 10 | +--------------+-----------+-----------+ Unstranded PyRanges object has 3 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.set_union(gr2) +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 1 | 11 | +--------------+-----------+-----------+ Unstranded PyRanges object has 1 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- sort(self, by=None, nb_cpu=1)¶
Sort by position or columns.
- Parameters
by (str or list of str, default None) – Columns to sort by. Default is Start and End.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
Note
Since a PyRanges contains multiple DataFrames, the sorting only happens within dataframes.
- Returns
Sorted PyRanges
- Return type
See also
pyranges.multioverlap()find overlaps with multiple PyRanges
Examples
>>> gr = pr.data.f1() >>> gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3 | 6 | interval1 | 0 | + | | chr1 | 8 | 9 | interval3 | 0 | + | | chr1 | 5 | 7 | interval2 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.split(between=True) +--------------+-----------+-----------+------------+ | Chromosome | Start | End | Strand | | (object) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 3 | 6 | + | | chr1 | 6 | 8 | + | | chr1 | 8 | 9 | + | | chr1 | 5 | 7 | - | +--------------+-----------+-----------+------------+ Stranded PyRanges object has 4 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.split(strand=False) +--------------+-----------+-----------+ | Chromosome | Start | End | | (object) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 3 | 5 | | chr1 | 5 | 6 | | chr1 | 6 | 7 | | chr1 | 8 | 9 | +--------------+-----------+-----------+ Unstranded PyRanges object has 4 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.split(strand=False, between=True) +--------------+-----------+-----------+ | Chromosome | Start | End | | (object) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 3 | 5 | | chr1 | 5 | 6 | | chr1 | 6 | 7 | | chr1 | 7 | 8 | | chr1 | 8 | 9 | +--------------+-----------+-----------+ Unstranded PyRanges object has 5 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- sp(self, n=30, formatting=None)¶
Sort on location and print.
See also
PyRanges.print()print PyRanges.
- spc(self, n=30, formatting=None)¶
Sort on location, print and return self.
See also
PyRanges.print()print PyRanges.
- slack(self, slack)¶
Deprecated: this function has been moved to Pyranges.extend
- spliced_subsequence(self, start=0, end=None, by=None, strand=None, **kwargs)¶
Get subsequences of the intervals, using coordinates mapping to spliced transcripts (without introns)
The returned intervals are subregions of self, cut according to specifications. Start and end are relative to the 5’ end: 0 means the leftmost nucleotide for + strand intervals, while it means the rightmost one for - strand. This method also allows to manipulate groups of intervals (e.g. exons belonging to same transcripts) through the ‘by’ argument. When using it, start and end refer to the spliced transcript coordinates, meaning that introns are in the count.
- Parameters
start (int) – Start of subregion, 0-based and included, counting from the 5’ end. Use a negative int to count from the 3’ (e.g. -1 is the last nucleotide)
end (int, default None) – End of subregion, 0-based and excluded, counting from the 5’ end. Use a negative int to count from the 3’ (e.g. -1 is the last nucleotide) If None, the existing 3’ end is returned.
by (list of str, default None) – intervals are grouped by this/these ID column(s) beforehand, e.g. exons belonging to same transcripts
strand (bool, default None, i.e. auto) – Whether to do operations on chromosome/strand pairs or chromosomes. If None, will use chromosome/strand pairs if the PyRanges is stranded.
- Returns
Subregion of self, subsequenced as specified by arguments
- Return type
Note
If the request goes out of bounds (e.g. requesting 100 nts for a 90nt region), only the existing portion is returned
See also
subsequence()analogous to this method, but input coordinates refer to the unspliced transcript
Examples
>>> p = pr.from_dict({"Chromosome": [1, 1, 2, 2, 3], ... "Strand": ["+", "+", "-", "-", "+"], ... "Start": [1, 40, 10, 70, 140], ... "End": [11, 60, 25, 80, 152], ... "transcript_id":["t1", "t1", "t2", "t2", "t3"] }) +--------------+--------------+-----------+-----------+-----------------+ | Chromosome | Strand | Start | End | transcript_id | | (category) | (category) | (int32) | (int32) | (object) | |--------------+--------------+-----------+-----------+-----------------| | 1 | + | 1 | 11 | t1 | | 1 | + | 40 | 60 | t1 | | 2 | - | 10 | 25 | t2 | | 2 | - | 70 | 80 | t2 | | 3 | + | 140 | 152 | t3 | +--------------+--------------+-----------+-----------+-----------------+ Stranded PyRanges object has 5 rows and 5 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
# Get the first 15 nucleotides of each spliced transcript, grouping exons by transcript_id: >>> p.spliced_subsequence(0, 15, by=’transcript_id’) +————–+————–+———–+———–+—————–+ | Chromosome | Strand | Start | End | transcript_id | | (category) | (category) | (int64) | (int32) | (object) | |--------------+--------------+-----------+-----------+-----------------| | 1 | + | 1 | 11 | t1 | | 1 | + | 40 | 45 | t1 | | 2 | - | 20 | 25 | t2 | | 2 | - | 70 | 80 | t2 | | 3 | + | 140 | 152 | t3 | +————–+————–+———–+———–+—————–+ Stranded PyRanges object has 5 rows and 5 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
# Get the last 20 nucleotides of each spliced transcript: >>> p.spliced_subsequence(-20, by=’transcript_id’) +————–+————–+———–+———–+—————–+ | Chromosome | Strand | Start | End | transcript_id | | (category) | (category) | (int64) | (int32) | (object) | |--------------+--------------+-----------+-----------+-----------------| | 1 | + | 40 | 60 | t1 | | 2 | - | 10 | 25 | t2 | | 2 | - | 70 | 75 | t2 | | 3 | + | 140 | 155 | t3 | +————–+————–+———–+———–+—————–+ Stranded PyRanges object has 4 rows and 5 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
# Get region from 25 to 60 of each spliced transcript, or their existing subportion: >>> p.spliced_subsequence(25, 60, by=’transcript_id’) +————–+————–+———–+———–+—————–+ | Chromosome | Strand | Start | End | transcript_id | | (category) | (category) | (int32) | (int32) | (object) | |--------------+--------------+-----------+-----------+-----------------| | 1 | + | 55 | 60 | t1 | +————–+————–+———–+———–+—————–+ Stranded PyRanges object has 1 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
# Get region of each spliced transcript which excludes their first and last 3 nucleotides: >>> p.spliced_subsequence(3, -3, by=’transcript_id’) +————–+————–+———–+———–+—————–+ | Chromosome | Strand | Start | End | transcript_id | | (category) | (category) | (int32) | (int32) | (object) | |--------------+--------------+-----------+-----------+-----------------| | 1 | + | 1 | 11 | t1 | | 1 | + | 40 | 60 | t1 | | 2 | - | 10 | 25 | t2 | | 2 | - | 70 | 80 | t2 | | 3 | + | 140 | 155 | t3 | +————–+————–+———–+———–+—————–+ Stranded PyRanges object has 5 rows and 5 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- spliced_subsequence(self, start=0, end=None, by=None, strand=None, **kwargs)¶
Get subsequences of the intervals, using coordinates mapping to spliced transcripts (without introns)
The returned intervals are subregions of self, cut according to specifications. Start and end are relative to the 5’ end: 0 means the leftmost nucleotide for + strand intervals, while it means the rightmost one for - strand. This method also allows to manipulate groups of intervals (e.g. exons belonging to same transcripts) through the ‘by’ argument. When using it, start and end refer to the spliced transcript coordinates, meaning that introns are in the count.
- Parameters
start (int) – Start of subregion, 0-based and included, counting from the 5’ end. Use a negative int to count from the 3’ (e.g. -1 is the last nucleotide)
end (int, default None) – End of subregion, 0-based and excluded, counting from the 5’ end. If None, the existing 3’ end is returned.
by (list of str, default None) – intervals are grouped by this/these ID column(s) beforehand, e.g. exons belonging to same transcripts
strand (bool, default None, i.e. auto) – Whether to do operations on chromosome/strand pairs or chromosomes. If None, will use chromosome/strand pairs if the PyRanges is stranded.
- Returns
Subregion of self, subsequenced as specified by arguments
- Return type
Note
If the request goes out of bounds (e.g. requesting 100 nts for a 90nt region), only the existing portion is returned
See also
subsequence()analogous to this method, but input coordinates refer to the unspliced transcript
- split(self, strand=None, between=False, nb_cpu=1)¶
Split into non-overlapping intervals.
- Parameters
strand (bool, default None, i.e. auto) – Whether to ignore strand information if PyRanges is stranded.
between (bool, default False) – Include lengths between intervals.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
- Returns
PyRanges with intervals split at overlap points.
- Return type
See also
pyranges.multioverlap()find overlaps with multiple PyRanges
Examples
>>> d = {'Chromosome': ['chr1', 'chr1', 'chr1', 'chr1'], 'Start': [3, 5, 5, 11], ... 'End': [6, 9, 7, 12], 'Strand': ['+', '+', '-', '-']} >>> gr = pr.from_dict(d) >>> gr +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 3 | 6 | + | | chr1 | 5 | 9 | + | | chr1 | 5 | 7 | - | | chr1 | 11 | 12 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 4 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.split() +--------------+-----------+-----------+------------+ | Chromosome | Start | End | Strand | | (object) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 3 | 5 | + | | chr1 | 5 | 6 | + | | chr1 | 6 | 9 | + | | chr1 | 5 | 7 | - | | chr1 | 11 | 12 | - | +--------------+-----------+-----------+------------+ Stranded PyRanges object has 5 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.split(between=True) +--------------+-----------+-----------+------------+ | Chromosome | Start | End | Strand | | (object) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 3 | 5 | + | | chr1 | 5 | 6 | + | | chr1 | 6 | 9 | + | | chr1 | 5 | 7 | - | | chr1 | 7 | 11 | - | | chr1 | 11 | 12 | - | +--------------+-----------+-----------+------------+ Stranded PyRanges object has 6 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.split(strand=False) +--------------+-----------+-----------+ | Chromosome | Start | End | | (object) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 3 | 5 | | chr1 | 5 | 6 | | chr1 | 6 | 7 | | chr1 | 7 | 9 | | chr1 | 11 | 12 | +--------------+-----------+-----------+ Unstranded PyRanges object has 5 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.split(strand=False, between=True) +--------------+-----------+-----------+ | Chromosome | Start | End | | (object) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 3 | 5 | | chr1 | 5 | 6 | | chr1 | 6 | 7 | | chr1 | 7 | 9 | | chr1 | 9 | 11 | | chr1 | 11 | 12 | +--------------+-----------+-----------+ Unstranded PyRanges object has 6 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- property stranded(self)¶
Whether PyRanges has (valid) strand info.
Note
A PyRanges can have invalid values in the Strand-column. It is not considered stranded.
See also
PyRanges.strands()return the strands
Examples
>>> d = {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 6], ... 'End': [5, 8], 'Strand': ['+', '.']} >>> gr = pr.from_dict(d) >>> gr +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 1 | 5 | + | | chr1 | 6 | 8 | . | +--------------+-----------+-----------+--------------+ Unstranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome. Considered unstranded due to these Strand values: '.'
>>> gr.stranded False
>>> "Strand" in gr.columns True
- property strands(self)¶
Return strands.
Notes
If the strand-column contains an invalid value, [] is returned.
See also
PyRanges.stranded()whether has valid strand info
Examples
>>> d = {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 6], ... 'End': [5, 8], 'Strand': ['+', '.']} >>> gr = pr.from_dict(d) >>> gr +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 1 | 5 | + | | chr1 | 6 | 8 | . | +--------------+-----------+-----------+--------------+ Unstranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome. Considered unstranded due to these Strand values: '.'
>>> gr.strands []
>>> gr.Strand.drop_duplicates().to_list() ['+', '.']
>>> gr.Strand = ["+", "-"] >>> gr.strands ['+', '-']
- subset(self, f, strand=None, **kwargs)¶
Return a subset of the rows.
- Parameters
f (function) – Function which returns boolean Series equal to length of df.
strand (bool, default None, i.e. auto) – Whether to do operations on chromosome/strand pairs or chromosomes. If None, will use chromosome/strand pairs if the PyRanges is stranded.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
**kwargs – Additional keyword arguments to pass as keyword arguments to f
Notes
PyRanges can also be subsetted directly with a boolean Series. This function is slightly faster, but more cumbersome.
- Returns
PyRanges subset on rows.
- Return type
Examples
>>> gr = pr.data.f1() >>> gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 3 | 6 | interval1 | 0 | + | | chr1 | 8 | 9 | interval3 | 0 | + | | chr1 | 5 | 7 | interval2 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.subset(lambda df: df.Start > 4) +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8 | 9 | interval3 | 0 | + | | chr1 | 5 | 7 | interval2 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
Also possible:
>>> gr[gr.Start > 4] +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 8 | 9 | interval3 | 0 | + | | chr1 | 5 | 7 | interval2 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 2 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- subsequence(self, start=0, end=None, by=None, strand=None, **kwargs)¶
Get subsequences of the intervals.
The returned intervals are subregions of self, cut according to specifications. Start and end are relative to the 5’ end: 0 means the leftmost nucleotide for + strand intervals, while it means the rightmost one for - strand. This method also allows to manipulate groups of intervals (e.g. exons belonging to same transcripts) through the ‘by’ argument. When using it, start and end refer to the unspliced transcript coordinates, meaning that introns are included in the count.
- Parameters
start (int) – Start of subregion, 0-based and included, counting from the 5’ end. Use a negative int to count from the 3’ (e.g. -1 is the last nucleotide)
end (int, default None) –
End of subregion, 0-based and excluded, counting from the 5’ end. Use a negative int to count from the 3’ (e.g. -1 is the last nucleotide)
If None, the existing 3’ end is returned.
by (list of str, default None) – intervals are grouped by this/these ID column(s) beforehand, e.g. exons belonging to same transcripts
strand (bool, default None, i.e. auto) – Whether to do operations on chromosome/strand pairs or chromosomes. If None, will use chromosome/strand pairs if the PyRanges is stranded.
- Returns
Subregion of self, subsequenced as specified by arguments
- Return type
Note
If the request goes out of bounds (e.g. requesting 100 nts for a 90nt region), only the existing portion is returned
See also
spliced_subsequence()analogous to this method, but intronic regions are not counted, so that input coordinates refer to the spliced transcript
Examples
>>> p = pr.from_dict({"Chromosome": [1, 1, 2, 2, 3], ... "Strand": ["+", "+", "-", "-", "+"], ... "Start": [1, 40, 2, 30, 140], ... "End": [20, 60, 13, 45, 155], ... "transcript_id":["t1", "t1", "t2", "t2", "t3"] }) >>> p +--------------+--------------+-----------+-----------+-----------------+ | Chromosome | Strand | Start | End | transcript_id | | (category) | (category) | (int32) | (int32) | (object) | |--------------+--------------+-----------+-----------+-----------------| | 1 | + | 1 | 20 | t1 | | 1 | + | 40 | 60 | t1 | | 2 | - | 2 | 13 | t2 | | 2 | - | 30 | 45 | t2 | | 3 | + | 140 | 155 | t3 | +--------------+--------------+-----------+-----------+-----------------+ Stranded PyRanges object has 5 rows and 5 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. # Get the first 10 nucleotides (at the 5') of *each interval* (each line of the dataframe): >>> p.subsequence(0, 10) +--------------+--------------+-----------+-----------+-----------------+ | Chromosome | Strand | Start | End | transcript_id | | (category) | (category) | (int32) | (int32) | (object) | |--------------+--------------+-----------+-----------+-----------------| | 1 | + | 1 | 20 | t1 | | 1 | + | 40 | 60 | t1 | | 2 | - | 2 | 13 | t2 | | 2 | - | 30 | 45 | t2 | | 3 | + | 140 | 155 | t3 | +--------------+--------------+-----------+-----------+-----------------+ Stranded PyRanges object has 5 rows and 5 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. # Get the first 10 nucleotides of *each transcript*, grouping exons by transcript_id: >>> p.subsequence(0, 10, by='transcript_id') +--------------+--------------+-----------+-----------+-----------------+ | Chromosome | Strand | Start | End | transcript_id | | (category) | (category) | (int32) | (int32) | (object) | |--------------+--------------+-----------+-----------+-----------------| | 1 | + | 1 | 11 | t1 | | 2 | - | 35 | 45 | t2 | | 3 | + | 140 | 150 | t3 | +--------------+--------------+-----------+-----------+-----------------+ Stranded PyRanges object has 3 rows and 5 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. # Get the last 20 nucleotides of each transcript: >>> p.subsequence(-20, by='transcript_id') +--------------+--------------+-----------+-----------+-----------------+ | Chromosome | Strand | Start | End | transcript_id | | (category) | (category) | (int32) | (int32) | (object) | |--------------+--------------+-----------+-----------+-----------------| | 1 | + | 40 | 60 | t1 | | 2 | - | 30 | 39 | t2 | | 2 | - | 2 | 13 | t2 | | 3 | + | 140 | 150 | t3 | +--------------+--------------+-----------+-----------+-----------------+ Stranded PyRanges object has 4 rows and 5 columns from 3 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand. # Get region from 30 to 330 of each transcript, or their existing subportion: >>> p.subsequence(30, 300, by='transcript_id') +--------------+--------------+-----------+-----------+-----------------+ | Chromosome | Strand | Start | End | transcript_id | | (category) | (category) | (int32) | (int32) | (object) | |--------------+--------------+-----------+-----------+-----------------| | 1 | + | 51 | 60 | t1 | +--------------+--------------+-----------+-----------+-----------------+ Stranded PyRanges object has 1 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- subtract(self, other, strandedness=None, nb_cpu=1)¶
Subtract intervals.
- Parameters
strandedness ({None, "same", "opposite", False}, default None, i.e. auto) – Whether to compare PyRanges on the same strand, the opposite or ignore strand information. The default, None, means use “same” if both PyRanges are strande, otherwise ignore the strand information.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
See also
pyranges.PyRanges.overlap()use with invert=True to return all intervals without overlap
Examples
>>> gr = pr.from_dict({"Chromosome": ["chr1"] * 3, "Start": [1, 4, 10], ... "End": [3, 9, 11], "ID": ["a", "b", "c"]}) >>> gr2 = pr.from_dict({"Chromosome": ["chr1"] * 3, "Start": [2, 2, 9], "End": [3, 9, 10]}) >>> gr +--------------+-----------+-----------+------------+ | Chromosome | Start | End | ID | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 1 | 3 | a | | chr1 | 4 | 9 | b | | chr1 | 10 | 11 | c | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 3 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr2 +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 2 | 3 | | chr1 | 2 | 9 | | chr1 | 9 | 10 | +--------------+-----------+-----------+ Unstranded PyRanges object has 3 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.subtract(gr2) +--------------+-----------+-----------+------------+ | Chromosome | Start | End | ID | | (category) | (int32) | (int32) | (object) | |--------------+-----------+-----------+------------| | chr1 | 1 | 2 | a | | chr1 | 10 | 11 | c | +--------------+-----------+-----------+------------+ Unstranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- summary(self, to_stdout=True, return_df=False)¶
Return info.
Count refers to the number of intervals, the rest to the lengths.
The column “pyrange” describes the data as is. “coverage_forward” and “coverage_reverse” describe the data after strand-specific merging of overlapping intervals. “coverage_unstranded” describes the data after merging, without considering the strands.
The row “count” is the number of intervals and “sum” is their total length. The rest describe the lengths of the intervals.
- Parameters
to_stdout (bool, default True) – Print summary.
return_df (bool, default False) – Return df with summary.
- Returns
- Return type
None or DataFrame with summary.
Examples
>>> gr = pr.data.ensembl_gtf()[["Feature", "gene_id"]] >>> gr +--------------+--------------+-----------+-----------+--------------+-----------------+ | Chromosome | Feature | Start | End | Strand | gene_id | | (category) | (category) | (int32) | (int32) | (category) | (object) | |--------------+--------------+-----------+-----------+--------------+-----------------| | 1 | gene | 11868 | 14409 | + | ENSG00000223972 | | 1 | transcript | 11868 | 14409 | + | ENSG00000223972 | | 1 | exon | 11868 | 12227 | + | ENSG00000223972 | | 1 | exon | 12612 | 12721 | + | ENSG00000223972 | | ... | ... | ... | ... | ... | ... | | 1 | gene | 1173055 | 1179555 | - | ENSG00000205231 | | 1 | transcript | 1173055 | 1179555 | - | ENSG00000205231 | | 1 | exon | 1179364 | 1179555 | - | ENSG00000205231 | | 1 | exon | 1173055 | 1176396 | - | ENSG00000205231 | +--------------+--------------+-----------+-----------+--------------+-----------------+ Stranded PyRanges object has 2,446 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.summary() +-------+------------------+--------------------+--------------------+-----------------------+ | | pyrange | coverage_forward | coverage_reverse | coverage_unstranded | |-------+------------------+--------------------+--------------------+-----------------------| | count | 2446 | 39 | 23 | 32 | | mean | 2291.92 | 7058.1 | 30078.6 | 27704.2 | | std | 11906.9 | 10322.3 | 59467.7 | 67026.9 | | min | 1 | 83 | 154 | 83 | | 25% | 90 | 1051 | 1204 | 1155 | | 50% | 138 | 2541 | 6500 | 6343 | | 75% | 382.25 | 7168 | 23778 | 20650.8 | | max | 241726 | 43065 | 241726 | 291164 | | sum | 5.60603e+06 | 275266 | 691807 | 886534 | +-------+------------------+--------------------+--------------------+-----------------------+
>>> gr.summary(return_df=True, to_stdout=False) pyrange coverage_forward coverage_reverse coverage_unstranded count 2.446000e+03 39.000000 23.000000 32.000000 mean 2.291918e+03 7058.102564 30078.565217 27704.187500 std 1.190685e+04 10322.309347 59467.695265 67026.868647 min 1.000000e+00 83.000000 154.000000 83.000000 25% 9.000000e+01 1051.000000 1204.000000 1155.000000 50% 1.380000e+02 2541.000000 6500.000000 6343.000000 75% 3.822500e+02 7168.000000 23778.000000 20650.750000 max 2.417260e+05 43065.000000 241726.000000 291164.000000 sum 5.606031e+06 275266.000000 691807.000000 886534.000000
- tail(self, n=8)¶
Return the n last rows.
- Parameters
n (int, default 8) – Return n rows.
- Returns
PyRanges with the n last rows.
- Return type
See also
PyRanges.head()return the first rows
PyRanges.sample()return random rows
Examples
>>> gr = pr.data.chipseq() >>> gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 212609534 | 212609559 | U0 | 0 | + | | chr1 | 169887529 | 169887554 | U0 | 0 | + | | chr1 | 216711011 | 216711036 | U0 | 0 | + | | chr1 | 144227079 | 144227104 | U0 | 0 | + | | ... | ... | ... | ... | ... | ... | | chrY | 15224235 | 15224260 | U0 | 0 | - | | chrY | 13517892 | 13517917 | U0 | 0 | - | | chrY | 8010951 | 8010976 | U0 | 0 | - | | chrY | 7405376 | 7405401 | U0 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10,000 rows and 6 columns from 24 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.tail(3) +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chrY | 13517892 | 13517917 | U0 | 0 | - | | chrY | 8010951 | 8010976 | U0 | 0 | - | | chrY | 7405376 | 7405401 | U0 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 3 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- tile(self, tile_size, overlap=False, strand=None, nb_cpu=1)¶
Return overlapping genomic tiles.
The genome is divided into bookended tiles of length tile_size and one is returned per overlapping interval.
- Parameters
tile_size (int) – Length of the tiles.
overlap (bool, default False) – Add column of nucleotide overlap to each tile.
strand (bool, default None, i.e. auto) – Whether to do operations on chromosome/strand pairs or chromosomes. If None, will use chromosome/strand pairs if the PyRanges is stranded.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
**kwargs – Additional keyword arguments to pass as keyword arguments to f
- Returns
Tiled PyRanges.
- Return type
See also
pyranges.PyRanges.window()divide intervals into windows
Examples
>>> gr = pr.data.ensembl_gtf()[["Feature", "gene_name"]] >>> gr +--------------+--------------+-----------+-----------+--------------+-------------+ | Chromosome | Feature | Start | End | Strand | gene_name | | (category) | (category) | (int32) | (int32) | (category) | (object) | |--------------+--------------+-----------+-----------+--------------+-------------| | 1 | gene | 11868 | 14409 | + | DDX11L1 | | 1 | transcript | 11868 | 14409 | + | DDX11L1 | | 1 | exon | 11868 | 12227 | + | DDX11L1 | | 1 | exon | 12612 | 12721 | + | DDX11L1 | | ... | ... | ... | ... | ... | ... | | 1 | gene | 1173055 | 1179555 | - | TTLL10-AS1 | | 1 | transcript | 1173055 | 1179555 | - | TTLL10-AS1 | | 1 | exon | 1179364 | 1179555 | - | TTLL10-AS1 | | 1 | exon | 1173055 | 1176396 | - | TTLL10-AS1 | +--------------+--------------+-----------+-----------+--------------+-------------+ Stranded PyRanges object has 2,446 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.tile(200) +--------------+--------------+-----------+-----------+--------------+-------------+ | Chromosome | Feature | Start | End | Strand | gene_name | | (category) | (category) | (int32) | (int32) | (category) | (object) | |--------------+--------------+-----------+-----------+--------------+-------------| | 1 | gene | 11800 | 12000 | + | DDX11L1 | | 1 | gene | 12000 | 12200 | + | DDX11L1 | | 1 | gene | 12200 | 12400 | + | DDX11L1 | | 1 | gene | 12400 | 12600 | + | DDX11L1 | | ... | ... | ... | ... | ... | ... | | 1 | exon | 1175600 | 1175800 | - | TTLL10-AS1 | | 1 | exon | 1175800 | 1176000 | - | TTLL10-AS1 | | 1 | exon | 1176000 | 1176200 | - | TTLL10-AS1 | | 1 | exon | 1176200 | 1176400 | - | TTLL10-AS1 | +--------------+--------------+-----------+-----------+--------------+-------------+ Stranded PyRanges object has 30,538 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.tile(100, overlap=True) +--------------+--------------+-----------+-----------+--------------+-------------+---------------+ | Chromosome | Feature | Start | End | Strand | gene_name | TileOverlap | | (category) | (category) | (int32) | (int32) | (category) | (object) | (int32) | |--------------+--------------+-----------+-----------+--------------+-------------+---------------| | 1 | gene | 11800 | 11900 | + | DDX11L1 | 32 | | 1 | gene | 11900 | 12000 | + | DDX11L1 | 100 | | 1 | gene | 12000 | 12100 | + | DDX11L1 | 100 | | 1 | gene | 12100 | 12200 | + | DDX11L1 | 100 | | ... | ... | ... | ... | ... | ... | ... | | 1 | exon | 1176000 | 1176100 | - | TTLL10-AS1 | 100 | | 1 | exon | 1176100 | 1176200 | - | TTLL10-AS1 | 100 | | 1 | exon | 1176200 | 1176300 | - | TTLL10-AS1 | 100 | | 1 | exon | 1176300 | 1176400 | - | TTLL10-AS1 | 96 | +--------------+--------------+-----------+-----------+--------------+-------------+---------------+ Stranded PyRanges object has 58,516 rows and 7 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- to_example(self, n=10)¶
Return as dict.
Used for easily creating examples for copy and pasting.
- Parameters
n (int, default 10) – Number of rows. Half is taken from the start, the other half from the end.
See also
PyRanges.from_dict()create PyRanges from dict
Examples
>>> gr = pr.data.chipseq() >>> gr +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 212609534 | 212609559 | U0 | 0 | + | | chr1 | 169887529 | 169887554 | U0 | 0 | + | | chr1 | 216711011 | 216711036 | U0 | 0 | + | | chr1 | 144227079 | 144227104 | U0 | 0 | + | | ... | ... | ... | ... | ... | ... | | chrY | 15224235 | 15224260 | U0 | 0 | - | | chrY | 13517892 | 13517917 | U0 | 0 | - | | chrY | 8010951 | 8010976 | U0 | 0 | - | | chrY | 7405376 | 7405401 | U0 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 10,000 rows and 6 columns from 24 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> d = gr.to_example(n=4) >>> d {'Chromosome': ['chr1', 'chr1', 'chrY', 'chrY'], 'Start': [212609534, 169887529, 8010951, 7405376], 'End': [212609559, 169887554, 8010976, 7405401], 'Name': ['U0', 'U0', 'U0', 'U0'], 'Score': [0, 0, 0, 0], 'Strand': ['+', '+', '-', '-']} >>> pr.from_dict(d) +--------------+-----------+-----------+------------+-----------+--------------+ | Chromosome | Start | End | Name | Score | Strand | | (category) | (int32) | (int32) | (object) | (int64) | (category) | |--------------+-----------+-----------+------------+-----------+--------------| | chr1 | 212609534 | 212609559 | U0 | 0 | + | | chr1 | 169887529 | 169887554 | U0 | 0 | + | | chrY | 8010951 | 8010976 | U0 | 0 | - | | chrY | 7405376 | 7405401 | U0 | 0 | - | +--------------+-----------+-----------+------------+-----------+--------------+ Stranded PyRanges object has 4 rows and 6 columns from 2 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- three_end(self)¶
Return the 3’-end.
The 3’-end is the start of intervals on the reverse strand and the end of intervals on the forward strand.
- Returns
PyRanges with the 3’.
- Return type
See also
PyRanges.five_end()return the five prime end
Examples
>>> d = {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 6], ... 'End': [5, 8], 'Strand': ['+', '-']} >>> gr = pr.from_dict(d) >>> gr +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 1 | 5 | + | | chr1 | 6 | 8 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.three_end() +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 5 | 6 | + | | chr1 | 6 | 7 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- to_bed(self, path=None, keep=True, compression='infer', chain=False)¶
Write to bed.
- Parameters
path (str, default None) – Where to write. If None, returns string representation.
keep (bool, default True) – Whether to keep all columns, not just Chromosome, Start, End, Name, Score, Strand when writing.
compression (str, compression type to use, by default infer based on extension.) – See pandas.DataFree.to_csv for more info.
chain (bool, default False) – Whether to return the PyRanges after writing.
Examples
>>> d = {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 6], ... 'End': [5, 8], 'Strand': ['+', '-'], "Gene": [1, 2]} >>> gr = pr.from_dict(d) >>> gr +--------------+-----------+-----------+--------------+-----------+ | Chromosome | Start | End | Strand | Gene | | (category) | (int32) | (int32) | (category) | (int64) | |--------------+-----------+-----------+--------------+-----------| | chr1 | 1 | 5 | + | 1 | | chr1 | 6 | 8 | - | 2 | +--------------+-----------+-----------+--------------+-----------+ Stranded PyRanges object has 2 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> print(gr.to_bed()) chr1 1 5 . . + 1 chr1 6 8 . . - 2
Does not include noncanonical bed-column Gene:
>>> print(gr.to_bed(keep=False)) chr1 1 5 . . + chr1 6 8 . . -
>>> gr.to_bed("test.bed", chain=True) +--------------+-----------+-----------+--------------+-----------+ | Chromosome | Start | End | Strand | Gene | | (category) | (int32) | (int32) | (category) | (int64) | |--------------+-----------+-----------+--------------+-----------| | chr1 | 1 | 5 | + | 1 | | chr1 | 6 | 8 | - | 2 | +--------------+-----------+-----------+--------------+-----------+ Stranded PyRanges object has 2 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> open("test.bed").readlines() ['chr1\t1\t5\t.\t.\t+\t1\n', 'chr1\t6\t8\t.\t.\t-\t2\n']
- to_bigwig(self, path=None, chromosome_sizes=None, rpm=True, divide=None, value_col=None, dryrun=False, chain=False)¶
Write regular or value coverage to bigwig.
Note
To create one bigwig per strand, subset the PyRanges first.
- Parameters
path (str) – Where to write bigwig.
chromosome_sizes (PyRanges or dict) – If dict: map of chromosome names to chromosome length.
rpm (True) – Whether to normalize data by dividing by total number of intervals and multiplying by 1e6.
divide (bool, default False) – (Only useful with value_col) Divide value coverage by regular coverage and take log2.
value_col (str, default None) – Name of column to compute coverage of.
dryrun (bool, default False) – Return data that would be written without writing bigwigs.
chain (bool, default False) – Whether to return the PyRanges after writing.
Note
Requires pybigwig to be installed.
If you require more control over the normalization process, use pyranges.to_bigwig()
See also
pyranges.to_bigwig()write pandas DataFrame to bigwig.
Examples
>>> d = {'Chromosome': ['chr1', 'chr1', 'chr1'], 'Start': [1, 4, 6], ... 'End': [7, 8, 10], 'Strand': ['+', '-', '-'], ... 'Value': [10, 20, 30]} >>> gr = pr.from_dict(d) >>> gr +--------------+-----------+-----------+--------------+-----------+ | Chromosome | Start | End | Strand | Value | | (category) | (int32) | (int32) | (category) | (int64) | |--------------+-----------+-----------+--------------+-----------| | chr1 | 1 | 7 | + | 10 | | chr1 | 4 | 8 | - | 20 | | chr1 | 6 | 10 | - | 30 | +--------------+-----------+-----------+--------------+-----------+ Stranded PyRanges object has 3 rows and 5 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.to_bigwig(dryrun=True, rpm=False) +--------------+-----------+-----------+-------------+ | Chromosome | Start | End | Score | | (category) | (int32) | (int32) | (float64) | |--------------+-----------+-----------+-------------| | chr1 | 1 | 4 | 1 | | chr1 | 4 | 6 | 2 | | chr1 | 6 | 7 | 3 | | chr1 | 7 | 8 | 2 | | chr1 | 8 | 10 | 1 | +--------------+-----------+-----------+-------------+ Unstranded PyRanges object has 5 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.to_bigwig(dryrun=True, rpm=False, value_col="Value") +--------------+-----------+-----------+-------------+ | Chromosome | Start | End | Score | | (category) | (int32) | (int32) | (float64) | |--------------+-----------+-----------+-------------| | chr1 | 1 | 4 | 10 | | chr1 | 4 | 6 | 30 | | chr1 | 6 | 7 | 60 | | chr1 | 7 | 8 | 50 | | chr1 | 8 | 10 | 30 | +--------------+-----------+-----------+-------------+ Unstranded PyRanges object has 5 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.to_bigwig(dryrun=True, rpm=False, value_col="Value", divide=True) +--------------+-----------+-----------+-------------+ | Chromosome | Start | End | Score | | (category) | (int32) | (int32) | (float64) | |--------------+-----------+-----------+-------------| | chr1 | 0 | 1 | nan | | chr1 | 1 | 4 | 3.32193 | | chr1 | 4 | 6 | 3.90689 | | chr1 | 6 | 7 | 4.32193 | | chr1 | 7 | 8 | 4.64386 | | chr1 | 8 | 10 | 4.90689 | +--------------+-----------+-----------+-------------+ Unstranded PyRanges object has 6 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- to_csv(self, path=None, sep=',', header=True, compression='infer', chain=False)¶
Write to comma- or other value-separated file.
- Parameters
path (str, default None, i.e. return string representation.) – Where to write file.
sep (str, default ",") – String of length 1. Field delimiter for the output file.
header (bool, default True) – Write out the column names.
compression ({‘infer’, ‘gzip’, ‘bz2’, ‘zip’, ‘xz’, None}, default "infer") – Which compression to use. Uses file extension to infer by default.
chain (bool, default False) – Whether to return the PyRanges after writing.
Examples
>>> d = {"Chromosome": [1] * 3, "Start": [1, 3, 5], "End": [4, 6, 9], "Feature": ["gene", "exon", "exon"]} >>> gr = pr.from_dict(d) >>> print(gr.to_csv(sep="\t")) Chromosome Start End Feature 1 1 4 gene 1 3 6 exon 1 5 9 exon
- to_gff3(self, path=None, compression='infer', chain=False)¶
Write to General Feature Format.
- Parameters
path (str, default None, i.e. return string representation.) – Where to write file.
compression ({‘infer’, ‘gzip’, ‘bz2’, ‘zip’, ‘xz’, None}, default "infer") – Which compression to use. Uses file extension to infer by default.
chain (bool, default False) – Whether to return the PyRanges after writing.
Notes
GTF uses a different naming-convention for columns than PyRanges. This is the mapping between column names:
{"seqname": "Chromosome", "source": "Source", "type": "Feature", "start": "Start", "end": "End", "score": "Score", "strand": "Strand", "phase": "Frame", "attributes": "Attribute"}All other columns are appended as a field in the attribute string.
Nonexisting columns will be added with a ‘.’ to represent the missing values.
See also
pyranges.read_gff3()read GFF3 files
pyranges.to_gtf()write to GTF format
Examples
>>> d = {"Chromosome": [1] * 3, "Start": [1, 3, 5], "End": [4, 6, 9], "Feature": ["gene", "exon", "exon"]} >>> gr = pr.from_dict(d) >>> print(gr.to_gff3()) 1 . gene 2 4 . . . 1 . exon 4 6 . . . 1 . exon 6 9 . . .
>>> gr.Gene = [1, 2, 3] >>> gr.function = ["a b", "c", "def"] >>> print(gr.to_gff3()) 1 . gene 2 4 . . . Gene=1;function=a b 1 . exon 4 6 . . . Gene=2;function=c 1 . exon 6 9 . . . Gene=3;function=def
- to_gtf(self, path=None, compression='infer', chain=False)¶
Write to Gene Transfer Format.
- Parameters
path (str, default None, i.e. return string representation.) – Where to write file.
compression ({‘infer’, ‘gzip’, ‘bz2’, ‘zip’, ‘xz’, None}, default "infer") – Which compression to use. Uses file extension to infer by default.
chain (bool, default False) – Whether to return the PyRanges after writing.
Notes
GTF uses a different naming-convention for columns than PyRanges. This is the mapping between column names:
{"seqname": "Chromosome", "source": "Source", "feature": "Feature", "start": "Start", "end": "End", "score": "Score", "strand": "Strand", "frame": "Frame", "attribute": "Attribute"}All other columns are appended as a field in the attribute string.
Nonexisting columns will be added with a ‘.’ to represent the missing values.
See also
pyranges.read_gtf()read GTF files
pyranges.to_gff3()write to GFF3 format
Examples
>>> d = {"Chromosome": [1] * 3, "Start": [1, 3, 5], "End": [4, 6, 9], "Feature": ["gene", "exon", "exon"]} >>> gr = pr.from_dict(d) >>> print(gr.to_gtf()) 1 . gene 2 4 . . . 1 . exon 4 6 . . . 1 . exon 6 9 . . .
>>> gr.name = ["Tim", "Eric", "Endre"] >>> gr.prices = ["Cheap", "Premium", "Fine European"] >>> print(gr.to_gtf()) 1 . gene 2 4 . . . name "Tim"; prices "Cheap"; 1 . exon 4 6 . . . name "Eric"; prices "Premium"; 1 . exon 6 9 . . . name "Endre"; prices "Fine European";
- to_rle(self, value_col=None, strand=None, rpm=False, nb_cpu=1)¶
Return as RleDict.
Create collection of Rles representing the coverage or other numerical value.
- Parameters
value_col (str, default None) – Numerical column to create RleDict from.
strand (bool, default None, i.e. auto) – Whether to treat strands serparately.
rpm (bool, default False) – Normalize by multiplying with 1e6/(number_intervals).
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
- Returns
Rle with coverage or other info from the PyRanges.
- Return type
pyrle.RleDict
Examples
>>> d = {'Chromosome': ['chr1', 'chr1', 'chr1'], 'Start': [3, 8, 5], ... 'End': [6, 9, 7], 'Score': [0.1, 5, 3.14], 'Strand': ['+', '+', '-']} >>> gr = pr.from_dict(d) >>> gr.to_rle() chr1 + -- +--------+-----+-----+-----+-----+ | Runs | 3 | 3 | 2 | 1 | |--------+-----+-----+-----+-----| | Values | 0.0 | 1.0 | 0.0 | 1.0 | +--------+-----+-----+-----+-----+ Rle of length 9 containing 4 elements (avg. length 2.25) chr1 - -- +--------+-----+-----+ | Runs | 5 | 2 | |--------+-----+-----| | Values | 0.0 | 1.0 | +--------+-----+-----+ Rle of length 7 containing 2 elements (avg. length 3.5) RleDict object with 2 chromosomes/strand pairs.
>>> gr.to_rle(value_col="Score") chr1 + -- +--------+-----+-----+-----+-----+ | Runs | 3 | 3 | 2 | 1 | |--------+-----+-----+-----+-----| | Values | 0.0 | 0.1 | 0.0 | 5.0 | +--------+-----+-----+-----+-----+ Rle of length 9 containing 4 elements (avg. length 2.25) chr1 - -- +--------+-----+------+ | Runs | 5 | 2 | |--------+-----+------| | Values | 0.0 | 3.14 | +--------+-----+------+ Rle of length 7 containing 2 elements (avg. length 3.5) RleDict object with 2 chromosomes/strand pairs.
>>> gr.to_rle(value_col="Score", strand=False) chr1 +--------+-----+-----+------+------+-----+-----+ | Runs | 3 | 2 | 1 | 1 | 1 | 1 | |--------+-----+-----+------+------+-----+-----| | Values | 0.0 | 0.1 | 3.24 | 3.14 | 0.0 | 5.0 | +--------+-----+-----+------+------+-----+-----+ Rle of length 9 containing 6 elements (avg. length 1.5) Unstranded RleDict object with 1 chromosome.
>>> gr.to_rle(rpm=True) chr1 + -- +--------+-----+-------------------+-----+-------------------+ | Runs | 3 | 3 | 2 | 1 | |--------+-----+-------------------+-----+-------------------| | Values | 0.0 | 333333.3333333333 | 0.0 | 333333.3333333333 | +--------+-----+-------------------+-----+-------------------+ Rle of length 9 containing 4 elements (avg. length 2.25) chr1 - -- +--------+-----+-------------------+ | Runs | 5 | 2 | |--------+-----+-------------------| | Values | 0.0 | 333333.3333333333 | +--------+-----+-------------------+ Rle of length 7 containing 2 elements (avg. length 3.5) RleDict object with 2 chromosomes/strand pairs.
- unstrand(self)¶
Remove strand.
Note
Removes Strand column even if PyRanges is not stranded.
See also
PyRanges.stranded()whether PyRanges contains valid strand info.
Examples
>>> d = {'Chromosome': ['chr1', 'chr1'], 'Start': [1, 6], ... 'End': [5, 8], 'Strand': ['+', '-']} >>> gr = pr.from_dict(d) >>> gr +--------------+-----------+-----------+--------------+ | Chromosome | Start | End | Strand | | (category) | (int32) | (int32) | (category) | |--------------+-----------+-----------+--------------| | chr1 | 1 | 5 | + | | chr1 | 6 | 8 | - | +--------------+-----------+-----------+--------------+ Stranded PyRanges object has 2 rows and 4 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.unstrand() +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | chr1 | 1 | 5 | | chr1 | 6 | 8 | +--------------+-----------+-----------+ Unstranded PyRanges object has 2 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
- values(self)¶
Return the underlying DataFrames.
- window(self, window_size, strand=None)¶
Return overlapping genomic windows.
Windows of length window_size are returned.
- Parameters
window_size (int) – Length of the windows.
strand (bool, default None, i.e. auto) – Whether to do operations on chromosome/strand pairs or chromosomes. If None, will use chromosome/strand pairs if the PyRanges is stranded.
nb_cpu (int, default 1) – How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple. Will only lead to speedups on large datasets.
**kwargs – Additional keyword arguments to pass as keyword arguments to f
- Returns
Tiled PyRanges.
- Return type
See also
pyranges.PyRanges.tile()divide intervals into adjacent tiles.
Examples
>>> gr = pr.from_dict({"Chromosome": [1], "Start": [895], "End": [1259]}) >>> gr +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | 1 | 895 | 1259 | +--------------+-----------+-----------+ Unstranded PyRanges object has 1 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr.window(200) +--------------+-----------+-----------+ | Chromosome | Start | End | | (category) | (int32) | (int32) | |--------------+-----------+-----------| | 1 | 895 | 1095 | | 1 | 1095 | 1259 | +--------------+-----------+-----------+ Unstranded PyRanges object has 2 rows and 3 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome.
>>> gr = pr.data.ensembl_gtf()[["Feature", "gene_name"]] >>> gr +--------------+--------------+-----------+-----------+--------------+-------------+ | Chromosome | Feature | Start | End | Strand | gene_name | | (category) | (category) | (int32) | (int32) | (category) | (object) | |--------------+--------------+-----------+-----------+--------------+-------------| | 1 | gene | 11868 | 14409 | + | DDX11L1 | | 1 | transcript | 11868 | 14409 | + | DDX11L1 | | 1 | exon | 11868 | 12227 | + | DDX11L1 | | 1 | exon | 12612 | 12721 | + | DDX11L1 | | ... | ... | ... | ... | ... | ... | | 1 | gene | 1173055 | 1179555 | - | TTLL10-AS1 | | 1 | transcript | 1173055 | 1179555 | - | TTLL10-AS1 | | 1 | exon | 1179364 | 1179555 | - | TTLL10-AS1 | | 1 | exon | 1173055 | 1176396 | - | TTLL10-AS1 | +--------------+--------------+-----------+-----------+--------------+-------------+ Stranded PyRanges object has 2,446 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
>>> gr.window(1000) +--------------+--------------+-----------+-----------+--------------+-------------+ | Chromosome | Feature | Start | End | Strand | gene_name | | (category) | (category) | (int32) | (int32) | (category) | (object) | |--------------+--------------+-----------+-----------+--------------+-------------| | 1 | gene | 11868 | 12868 | + | DDX11L1 | | 1 | gene | 12868 | 13868 | + | DDX11L1 | | 1 | gene | 13868 | 14409 | + | DDX11L1 | | 1 | transcript | 11868 | 12868 | + | DDX11L1 | | ... | ... | ... | ... | ... | ... | | 1 | exon | 1173055 | 1174055 | - | TTLL10-AS1 | | 1 | exon | 1174055 | 1175055 | - | TTLL10-AS1 | | 1 | exon | 1175055 | 1176055 | - | TTLL10-AS1 | | 1 | exon | 1176055 | 1176396 | - | TTLL10-AS1 | +--------------+--------------+-----------+-----------+--------------+-------------+ Stranded PyRanges object has 7,516 rows and 6 columns from 1 chromosomes. For printing, the PyRanges was sorted on Chromosome and Strand.
- __getstate__(self)¶
- __setstate__(self, d)¶