genomepy 0.0.1

Genomes in Python

Easily install and use genomes in Python and elsewhere!

Installation

Via pip, for now.

$ pip install genomepy

Usage

>>> import genomepy
>>> for row in genomepy.search("human"):
...     print "\t".join(row)
...
UCSC    hg38    Human Dec. 2013 (GRCh38/hg38) Genome at UCSC
UCSC    hg19    Human Feb. 2009 (GRCh37/hg19) Genome at UCSC
UCSC    hg18    Human Mar. 2006 (NCBI36/hg18) Genome at UCSC
UCSC    hg17    Human May 2004 (NCBI35/hg17) Genome at UCSC
UCSC    hg16    Human July 2003 (NCBI34/hg16) Genome at UCSC
Ensembl bacteria_102_collection_core_34_87_1    Brucella melitensis (GCA_000988815)
Ensembl bacteria_94_collection_core_34_87_1 Brucella suis (GCA_000875695)
Ensembl bacteria_131_collection_core_34_87_1    Candidatus Paraburkholderia schumannianae
Ensembl homo_sapiens_core_86_38 Human
Ensembl pediculus_humanus_core_34_87_2  Pediculus humanus
>>> genomepy.install_genome("hg38", "UCSC", "/data/genomes")
downloading...
done...
name: hg38
fasta: /data/genomes/hg38/hg38.fa
>>> g = genomepy.genome("hg38", "/data/genomes")
>>> g["chr6"][166502000:166503000]
tgtatggtccctagaggggccagagtcacagagatggaaagtggatggcgggtgccgggggctggggagctactgtgcagggggacagagctttagttctgcaagatgaaacagttctggagatggacggtggggatgggggcccagcaatgggaacgtgcttaatgccactgaactgggcacttaaacgtggtgaaaactgtaaaagtcatgtgtatttttctacaattaaaaaaaATCTGCCACAGAGTTAAAAAAATAACCACTATTTTCTGGAAATGGGAAGGAAAAGTTACAGCATGTAATTAAGATGACAATTTATAATGAACAAGGCAAATCTTTTCATCTTTGCCTTTTGGGCATATTCAATCTTTGCCCAGAATTAAGCACCTTTCAAGATTAATTCTCTAATAATTCTAGTTGAACAACACAACCTTTTCCTTCAAGCTTGCAATTAAATAAGGCTATTTTTAGCTGTAAGGATCACGCTGACCTTCAGGAGCAATGAGAACCGGCACTCCCGGCCTGAGTGGATGCACGGGGAGTGTGTCTAACACACAGGCGTCAACAGCCAGGGCCGCACGAGGAGGAGGAGTGGCAACGTCCACACAGACTCACAACACGGCACTCCGACTTGGAGGGTAATTAATACCAGGTTAACTTCTGGGATGACCTTGGCAACGACCCAAGGTGACAGGCCAGGCTCTGCAATCACCTCCCAATTAAGGAGAGGCGAAAGGGGACTCCCAGGGCTCAGAGCACCACGGGGTTCTAGGTCAGACCCACTTTGAAATGGAAATCTGGCCTTGTGCTGCTGCTCTTGTGGGGAGACAGCAGCTGCGGAGGCTGCTCTCTTCATGGGATTACTCTGGATAAAGTCTTTTTTGATTCTACgttgagcatcccttatctgaaatgcctgaaaccggaagtgtttaggatttggggattttgcaatatttacttatatataatgagatatcttggagatgggccacaa

The genomepy.genome() method returns a pyfaidx.Fasta object, see the documentation for more examples on how to use this.

Command line

$ genomepy

Usage: genomepy [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  genomes    list available genomes
  install    install genome
  providers  list available providers
  search     search for genomes

List available genomes.

$ genomepy genomes -p UCSC
UCSC    hg38    Human Dec. 2013 (GRCh38/hg38) Genome at UCSC
UCSC    hg19    Human Feb. 2009 (GRCh37/hg19) Genome at UCSC
UCSC    hg18    Human Mar. 2006 (NCBI36/hg18) Genome at UCSC
...
UCSC    danRer4 Zebrafish Mar. 2006 (Zv6/danRer4) Genome at UCSC
UCSC    danRer3 Zebrafish May 2005 (Zv5/danRer3) Genome at UCSC

Install a genome.

$ genomepy  install hg38 UCSC /data/genomes/
downloading...
done...
name: hg38
fasta: /data/genomes/hg38/hg38.fa

Todo

• Tests!

• Ensembl bacteria

• Automatic indexing (such as bwa)

• Caching of UCSC/Ensembl genome listings

• Configurable default genome installation directory

License

This module is licensed under the terms of the MIT license.