Quick Start

pybio is tightly integrated with Ensembl and lets you search any genomic position for the annotated features that overlap it — genes, their transcripts, and each transcript's exons and 5'/3' UTRs.

First, download and prepare a genome (here, human):

pybio genome homo_sapiens

Then query a genomic position from Python with pybio.core.genomes.annotate(species, chr, strand, pos):

import pybio
result = pybio.core.genomes.annotate("homo_sapiens", "1", "+", 11012344)
genes, transcripts, exons, utr3, utr5 = result

This returns five lists of feature objects — genes, transcripts, exons, 3'-UTRs and 5'-UTRs — all overlapping the given position. (See pybio/core/genomes.py for the full Gene/Transcript/Exon/Utr5/Utr3 class definitions.)

Note

Positions are 0-based, left+right inclusive. See Genomic coordinates.

To list the genes that span the position:

for gene in genes:
    print(gene.gene_id, gene.gene_name, gene.start, gene.stop)

...and every transcript of each gene:

for gene in genes:
    print(gene.gene_id, gene.gene_name, gene.start, gene.stop)
    for transcript in gene.transcripts:
        print(transcript.transcript_id)

You can also start from transcripts directly, and walk back up to the gene each one belongs to:

for transcript in transcripts:
    print(transcript.gene.gene_id, transcript.transcript_id)

Feature relationships

Feature objects link to each other in both directions, so you can navigate the annotation graph from whichever level is most convenient:

gene <-> transcript_1 <-> exon_1
                          <-> exon_2
                          ...
                          <-> utr5
                          <-> utr3
         <-> transcript_2 <-> exon_1
                          <-> exon_2
                          ...
                          <-> utr5
                          <-> utr3

Object	Attribute	Points to
gene	.transcripts	list of all transcripts of the gene
transcript	.gene	the gene the transcript belongs to
transcript	.exons	list of all exons of the transcript
transcript	.utr5 / .utr3	the transcript's 5'-UTR / 3'-UTR object
exon	.transcript	the transcript the exon belongs to
utr5 / utr3	.transcript	the transcript the UTR belongs to

Next steps

• Genomes — downloading more species, custom genomes, and where the data is stored.
• Sequences & annotation — pulling raw sequence for a region, and more on annotate().
• Read mapping — aligning FASTQ reads to the genomes you've downloaded.