pyranges.data
Module of example data.
See also
pyranges.randomgenerate random PyRanges
Examples
>>> pr.data.f1()
+--------------+-----------+-----------+------------+-----------+--------------+
| Chromosome | Start | End | Name | Score | Strand |
| (category) | (int64) | (int64) | (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.
Module Contents
Functions
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>>> # +--------------+------------+--------------+-----------+-----------+------------+--------------+------------+------------------------------------+-------+
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>>> # +--------------+-----------+-----------+----------------------------------------+-----------+--------------+
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>>> # +--------------+------------+--------------+-----------+-----------+------------+--------------+------------+-------------------+-------+
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>>> # +--------------+-----------+-----------+------------+------------+-----------------+--------------+---------------+-------------------+
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- pyranges.data.aorta()
>>> # +--------------+-----------+-----------+------------+-----------+--------------+ >>> # | Chromosome | Start | End | Name | Score | Strand | >>> # | (category) | (int64) | (int64) | (object) | (int64) | (category) | >>> # |--------------+-----------+-----------+------------+-----------+--------------| >>> # | chr1 | 9939 | 10138 | H3K27me3 | 7 | + | >>> # | chr1 | 9953 | 10152 | H3K27me3 | 5 | + | >>> # | chr1 | 10024 | 10223 | H3K27me3 | 1 | + | >>> # | chr1 | 10246 | 10445 | H3K27me3 | 4 | + | >>> # | ... | ... | ... | ... | ... | ... | >>> # | chr1 | 9978 | 10177 | H3K27me3 | 7 | - | >>> # | chr1 | 10001 | 10200 | H3K27me3 | 5 | - | >>> # | chr1 | 10127 | 10326 | H3K27me3 | 1 | - | >>> # | chr1 | 10241 | 10440 | H3K27me3 | 6 | - | >>> # +--------------+-----------+-----------+------------+-----------+--------------+ >>> # Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes. >>> # For printing, the PyRanges was sorted on Chromosome and Strand.
- pyranges.data.aorta2()
>>> # +--------------+-----------+-----------+------------+-----------+--------------+ >>> # | Chromosome | Start | End | Name | Score | Strand | >>> # | (category) | (int64) | (int64) | (object) | (int64) | (category) | >>> # |--------------+-----------+-----------+------------+-----------+--------------| >>> # | chr1 | 10073 | 10272 | Input | 1 | + | >>> # | chr1 | 10280 | 10479 | Input | 1 | + | >>> # | chr1 | 16056 | 16255 | Input | 1 | + | >>> # | chr1 | 16064 | 16263 | Input | 1 | + | >>> # | ... | ... | ... | ... | ... | ... | >>> # | chr1 | 10079 | 10278 | Input | 1 | - | >>> # | chr1 | 10082 | 10281 | Input | 1 | - | >>> # | chr1 | 10149 | 10348 | Input | 1 | - | >>> # | chr1 | 19958 | 20157 | Input | 1 | - | >>> # +--------------+-----------+-----------+------------+-----------+--------------+ >>> # Stranded PyRanges object has 10 rows and 6 columns from 1 chromosomes. >>> # For printing, the PyRanges was sorted on Chromosome and Strand.
- pyranges.data.chipseq()
>>> # +--------------+-----------+-----------+------------+-----------+--------------+ >>> # | Chromosome | Start | End | Name | Score | Strand | >>> # | (category) | (int64) | (int64) | (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.
- pyranges.data.chipseq_background()
>>> # +--------------+-----------+-----------+------------+-----------+--------------+ >>> # | Chromosome | Start | End | Name | Score | Strand | >>> # | (category) | (int64) | (int64) | (object) | (int64) | (category) | >>> # |--------------+-----------+-----------+------------+-----------+--------------| >>> # | chr1 | 39036822 | 39036847 | U0 | 0 | + | >>> # | chr1 | 224145989 | 224146014 | U0 | 0 | + | >>> # | chr1 | 167802964 | 167802989 | U0 | 0 | + | >>> # | chr1 | 69101066 | 69101091 | U0 | 0 | + | >>> # | ... | ... | ... | ... | ... | ... | >>> # | chrY | 11936866 | 11936891 | U0 | 0 | - | >>> # | chrY | 10629111 | 10629136 | U0 | 0 | - | >>> # | chrY | 10632456 | 10632481 | U0 | 0 | - | >>> # | chrY | 11918814 | 11918839 | U0 | 0 | - | >>> # +--------------+-----------+-----------+------------+-----------+--------------+ >>> # Stranded PyRanges object has 10,000 rows and 6 columns from 25 chromosomes. >>> # For printing, the PyRanges was sorted on Chromosome and Strand.
- pyranges.data.chromsizes()
>>> # +--------------+-----------+-----------+ >>> # | Chromosome | Start | End | >>> # | (category) | (int64) | (int64) | >>> # |--------------+-----------+-----------| >>> # | chr1 | 0 | 249250621 | >>> # | chr2 | 0 | 243199373 | >>> # | chr3 | 0 | 198022430 | >>> # | chr4 | 0 | 191154276 | >>> # | ... | ... | ... | >>> # | chrY | 0 | 59373566 | >>> # | chrX | 0 | 155270560 | >>> # | chrM | 0 | 16571 | >>> # | chr22 | 0 | 51304566 | >>> # +--------------+-----------+-----------+ >>> # Unstranded PyRanges object has 25 rows and 3 columns from 25 chromosomes. >>> # For printing, the PyRanges was sorted on Chromosome.
- pyranges.data.control_bam()
>>> # +--------------+-----------+-----------+--------------+------------+ >>> # | Chromosome | Start | End | Strand | Flag | >>> # | (category) | (int64) | (int64) | (category) | (uint16) | >>> # |--------------+-----------+-----------+--------------+------------| >>> # | chr1 | 887771 | 887796 | + | 16 | >>> # | chr1 | 994660 | 994685 | + | 16 | >>> # | chr1 | 1770383 | 1770408 | + | 16 | >>> # | chr1 | 1995141 | 1995166 | + | 16 | >>> # | ... | ... | ... | ... | ... | >>> # | chrY | 57402214 | 57402239 | + | 16 | >>> # | chrY | 10643526 | 10643551 | - | 0 | >>> # | chrY | 11776321 | 11776346 | - | 0 | >>> # | chrY | 20557165 | 20557190 | - | 0 | >>> # +--------------+-----------+-----------+--------------+------------+ >>> # Stranded PyRanges object has 10,000 rows and 5 columns from 25 chromosomes. >>> # For printing, the PyRanges was sorted on Chromosome and Strand.
- pyranges.data.cpg()
>>> # +--------------+-----------+-----------+-----------+ >>> # | Chromosome | Start | End | CpG | >>> # | (category) | (int64) | (int64) | (int64) | >>> # |--------------+-----------+-----------+-----------| >>> # | chrX | 64181 | 64793 | 62 | >>> # | chrX | 69133 | 70029 | 100 | >>> # | chrX | 148685 | 149461 | 85 | >>> # | chrX | 166504 | 167721 | 96 | >>> # | ... | ... | ... | ... | >>> # | chrY | 28555535 | 28555932 | 32 | >>> # | chrY | 28773315 | 28773544 | 25 | >>> # | chrY | 59213794 | 59214183 | 36 | >>> # | chrY | 59349266 | 59349574 | 29 | >>> # +--------------+-----------+-----------+-----------+ >>> # Unstranded PyRanges object has 1,077 rows and 4 columns from 2 chromosomes. >>> # For printing, the PyRanges was sorted on Chromosome.
- pyranges.data.ensembl_gtf()
>>> # +--------------+------------+--------------+-----------+-----------+------------+--------------+------------+------------------------------------+-------+ >>> # | Chromosome | Source | Feature | Start | End | Score | Strand | Frame | gene_biotype | +19 | >>> # | (category) | (object) | (category) | (int64) | (int64) | (object) | (category) | (object) | (object) | ... | >>> # |--------------+------------+--------------+-----------+-----------+------------+--------------+------------+------------------------------------+-------| >>> # | 1 | havana | gene | 11868 | 14409 | . | + | . | transcribed_unprocessed_pseudogene | ... | >>> # | 1 | havana | transcript | 11868 | 14409 | . | + | . | transcribed_unprocessed_pseudogene | ... | >>> # | 1 | havana | exon | 11868 | 12227 | . | + | . | transcribed_unprocessed_pseudogene | ... | >>> # | 1 | havana | exon | 12612 | 12721 | . | + | . | transcribed_unprocessed_pseudogene | ... | >>> # | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | >>> # | 1 | havana | gene | 1173055 | 1179555 | . | - | . | lncRNA | ... | >>> # | 1 | havana | transcript | 1173055 | 1179555 | . | - | . | lncRNA | ... | >>> # | 1 | havana | exon | 1179364 | 1179555 | . | - | . | lncRNA | ... | >>> # | 1 | havana | exon | 1173055 | 1176396 | . | - | . | lncRNA | ... | >>> # +--------------+------------+--------------+-----------+-----------+------------+--------------+------------+------------------------------------+-------+ >>> # Stranded PyRanges object has 2,446 rows and 28 columns from 1 chromosomes. >>> # For printing, the PyRanges was sorted on Chromosome and Strand. >>> # 19 hidden columns: gene_id, gene_name, gene_source, gene_version, tag, transcript_biotype, transcript_id, transcript_name, transcript_source, transcript_support_level, ... (+ 9 more.)
- pyranges.data.exons()
>>> # +--------------+-----------+-----------+----------------------------------------+-----------+--------------+ >>> # | Chromosome | Start | End | Name | Score | Strand | >>> # | (category) | (int64) | (int64) | (object) | (int64) | (category) | >>> # |--------------+-----------+-----------+----------------------------------------+-----------+--------------| >>> # | chrX | 135721701 | 135721963 | NR_038462_exon_0_0_chrX_135721702_f | 0 | + | >>> # | chrX | 135574120 | 135574598 | NM_001727_exon_2_0_chrX_135574121_f | 0 | + | >>> # | chrX | 47868945 | 47869126 | NM_205856_exon_4_0_chrX_47868946_f | 0 | + | >>> # | chrX | 77294333 | 77294480 | NM_000052_exon_17_0_chrX_77294334_f | 0 | + | >>> # | ... | ... | ... | ... | ... | ... | >>> # | chrY | 15409586 | 15409728 | NR_047633_exon_3_0_chrY_15409587_r | 0 | - | >>> # | chrY | 15478146 | 15478273 | NR_047634_exon_18_0_chrY_15478147_r | 0 | - | >>> # | chrY | 15360258 | 15361762 | NR_047601_exon_0_0_chrY_15360259_r | 0 | - | >>> # | chrY | 15467254 | 15467278 | NM_001258270_exon_13_0_chrY_15467255_r | 0 | - | >>> # +--------------+-----------+-----------+----------------------------------------+-----------+--------------+ >>> # Stranded PyRanges object has 1,000 rows and 6 columns from 2 chromosomes. >>> # For printing, the PyRanges was sorted on Chromosome and Strand.
- pyranges.data.f1()
>>> # +--------------+-----------+-----------+------------+-----------+--------------+ >>> # | Chromosome | Start | End | Name | Score | Strand | >>> # | (category) | (int64) | (int64) | (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.
- pyranges.data.f2()
>>> # +--------------+-----------+-----------+------------+-----------+--------------+ >>> # | Chromosome | Start | End | Name | Score | Strand | >>> # | (category) | (int64) | (int64) | (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.
- pyranges.data.gencode_gtf()
>>> # +--------------+------------+--------------+-----------+-----------+------------+--------------+------------+-------------------+-------+ >>> # | Chromosome | Source | Feature | Start | End | Score | Strand | Frame | gene_id | +15 | >>> # | (category) | (object) | (category) | (int64) | (int64) | (object) | (category) | (object) | (object) | ... | >>> # |--------------+------------+--------------+-----------+-----------+------------+--------------+------------+-------------------+-------| >>> # | chr1 | HAVANA | gene | 11868 | 14409 | . | + | . | ENSG00000223972.5 | ... | >>> # | chr1 | HAVANA | transcript | 11868 | 14409 | . | + | . | ENSG00000223972.5 | ... | >>> # | chr1 | HAVANA | exon | 11868 | 12227 | . | + | . | ENSG00000223972.5 | ... | >>> # | chr1 | HAVANA | exon | 12612 | 12721 | . | + | . | ENSG00000223972.5 | ... | >>> # | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | >>> # | chr1 | HAVANA | exon | 1430549 | 1430662 | . | - | . | ENSG00000225285.1 | ... | >>> # | chr1 | HAVANA | transcript | 1430663 | 1434520 | . | - | . | ENSG00000225285.1 | ... | >>> # | chr1 | HAVANA | exon | 1434177 | 1434520 | . | - | . | ENSG00000225285.1 | ... | >>> # | chr1 | HAVANA | exon | 1430663 | 1430954 | . | - | . | ENSG00000225285.1 | ... | >>> # +--------------+------------+--------------+-----------+-----------+------------+--------------+------------+-------------------+-------+ >>> # Stranded PyRanges object has 4,995 rows and 24 columns from 1 chromosomes. >>> # For printing, the PyRanges was sorted on Chromosome and Strand. >>> # 15 hidden columns: gene_type, gene_name, level, havana_gene, transcript_id, transcript_type, transcript_name, transcript_support_level, tag, ... (+ 6 more.)
- pyranges.data.ucsc_bed()
>>> # +--------------+-----------+-----------+------------+------------+-----------------+--------------+---------------+-------------------+ >>> # | Chromosome | Start | End | Feature | gene_id | transcript_id | Strand | exon_number | transcript_name | >>> # | (category) | (int64) | (int64) | (object) | (object) | (float64) | (category) | (float64) | (object) | >>> # |--------------+-----------+-----------+------------+------------+-----------------+--------------+---------------+-------------------| >>> # | chr1 | 12776117 | 12788726 | gene | AADACL3 | nan | + | nan | nan | >>> # | chr1 | 169075927 | 169101957 | gene | ATP1B1 | nan | + | nan | nan | >>> # | chr1 | 6845383 | 7829766 | gene | CAMTA1 | nan | + | nan | nan | >>> # | chr1 | 20915589 | 20945396 | gene | CDA | nan | + | nan | nan | >>> # | ... | ... | ... | ... | ... | ... | ... | ... | ... | >>> # | chrX | 152661096 | 152663330 | exon | PNMA6E | 260.0 | - | 0.0 | NM_001351293 | >>> # | chrX | 152661096 | 152666808 | transcript | PNMA6E | 260.0 | - | nan | NM_001351293 | >>> # | chrX | 152664164 | 152664378 | exon | PNMA6E | 260.0 | - | 1.0 | NM_001351293 | >>> # | chrX | 152666701 | 152666808 | exon | PNMA6E | 260.0 | - | 2.0 | NM_001351293 | >>> # +--------------+-----------+-----------+------------+------------+-----------------+--------------+---------------+-------------------+ >>> # Stranded PyRanges object has 5,519 rows and 9 columns from 30 chromosomes. >>> # For printing, the PyRanges was sorted on Chromosome and Strand.