pyreference 0.6.3

Library for working with reference genomes and gene GTF/GFFs

PyReference

A Python library for working with reference gene annotations.

PyReference loads GTF annotations extremely rapidly, and makes it easy to write code which can be run against different genomes.

Example

import numpy as np
import pyreference

reference = pyreference.Reference()

my_gene_ids = ["MSN", "GATA2", "ZEB1"]
for gene in reference[my_gene_ids]:
	average_length = np.mean([t.length for t in gene.transcripts])
	print("%s average length = %.2f" % (gene, average_length))
	print(gene.iv)
	for transcript in gene.transcripts:
		if transcript.is_coding:
			threep_utr = transcript.get_3putr_sequence()
			print("%s end of 3putr: %s" % (transcript.get_id(), threep_utr[-20:]))

Outputs:

MSN (MSN) 1 transcripts average length = 3970.00
chrX:[64887510,64961793)/+
NM_002444 end of 3putr: TAAAATTTAGGAAGACTTCA

GATA2 (GATA2) 3 transcripts average length = 3367.67
chr3:[128198264,128212030)/-
NM_001145662 end of 3putr: AATACTTTTTGTGAATGCCC
NM_001145661 end of 3putr: AATACTTTTTGTGAATGCCC
NM_032638 end of 3putr: AATACTTTTTGTGAATGCCC

ZEB1 (ZEB1) 6 transcripts average length = 6037.83
chr10:[31608100,31818742)/+
NM_001174093 end of 3putr: CTTCTTTTTCTATTGCCTTA
NM_001174094 end of 3putr: CTTCTTTTTCTATTGCCTTA
NM_030751 end of 3putr: CTTCTTTTTCTATTGCCTTA
NM_001174096 end of 3putr: CTTCTTTTTCTATTGCCTTA
NM_001174095 end of 3putr: CTTCTTTTTCTATTGCCTTA
NM_001128128 end of 3putr: CTTCTTTTTCTATTGCCTTA

This takes less than 4 seconds to load via a network drive on my machine.

Installation

sudo pip install pyreference

Choose your annotation:

# Latest Ensembl GRCh37
wget ftp://ftp.ensembl.org/pub/grch37/release-87/gff3/homo_sapiens/Homo_sapiens.GRCh37.87.gff3.gz

# Latest Ensembl GRCh38
wget ftp://ftp.ensembl.org/pub/release-104/gff3/homo_sapiens/Homo_sapiens.GRCh38.104.gff3.gz

# Latest RefSeq GRCh37
wget http://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/annotation_releases/105.20201022/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz

# Latest RefSeq GRCh38
http://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/annotation_releases/109.20210514/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz

Pre-process your GFF3 or GTF files to create genes.gtf.json.gz (~1/20th the size of the input GTF file)

pyreference_gff_to_json.py --gff3 genes.gff.gz

Create a ~/pyreference.cfg file pointing to your references.

[global]
default_build=hg19

[hg19]
genes_json=/data/reference/hg19/genes.gtf.json.gz
mature_mir_sequence_fasta=/data/reference/hg19/mature.fa
genome_sequence_fasta=/data/reference/hg19/genome.fa

[mm10]
genes_json=/data/reference/mm10/genes.gtf.json.gz
mature_mir_sequence_fasta=/data/reference/mm10/mature.fa
genome_sequence_fasta=/data/reference/mm10/genome.fa

Command line arguments

Substitute ArgumentParser with pyreference.ReferenceArgumentParser to add a --build option to your command line arguments.

args.reference is now initialised to the correct build/annotation.

from pyreference import ReferenceArgumentParser

parser = ReferenceArgumentParser()
parser.add("mirna_name")

args = parser.parse_args()
reference = args.reference.get_mirna(args.mirna_name)
print(mir.get_8mer_target())