genomepy 0.2.2

Genomes in Python

Easily install and use genomes in Python and elsewhere!

The goal is to have a simple and straightforward way to download and use genomic sequences. Currently, genomepy supports UCSC, Ensembl and NCBI.

Installation

Via pip, for now.

$ pip install genomepy

Configuration

By default genomes will be saved in ~/.local/share/genomes. This default can be changed by creating a configuration file called ~/.config/genomepy/genomepy.yaml. For instance, to set the default genome directory to /data/genomes, edit ~/.config/genomepy/genomepy.yaml and add the following line:

genome_dir: /data/genomes

The genome directory can also be explicitly specified in both the Python API as well as on the command-line.

Usage

From Python

>>> import genomepy
>>> for row in genomepy.search("GRCh38"):
...     print("\t".join(row))
...
UCSC    hg38    Human Dec. 2013 (GRCh38/hg38) Genome at UCSC
NCBI    GRCh38.p10  Homo sapiens; Genome Reference Consortium
NCBI    GRCh38  Homo sapiens; Genome Reference Consortium
NCBI    GRCh38.p1   Homo sapiens; Genome Reference Consortium
NCBI    GRCh38.p2   Homo sapiens; Genome Reference Consortium
NCBI    GRCh38.p3   Homo sapiens; Genome Reference Consortium
NCBI    GRCh38.p4   Homo sapiens; Genome Reference Consortium
NCBI    GRCh38.p5   Homo sapiens; Genome Reference Consortium
NCBI    GRCh38.p6   Homo sapiens; Genome Reference Consortium
NCBI    GRCh38.p7   Homo sapiens; Genome Reference Consortium
NCBI    GRCh38.p8   Homo sapiens; Genome Reference Consortium
NCBI    GRCh38.p9   Homo sapiens; Genome Reference Consortium
Ensembl GRCh38.p10  Human
>>> genomepy.install_genome("hg38", "UCSC", genome_dir="/data/genomes")
downloading...
done...
name: hg38
fasta: /data/genomes/hg38/hg38.fa
>>> g = genomepy.genome("hg38", genome_dir="/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 -g /data/genomes
downloading...
done...
name: hg38
fasta: /data/genomes/hg38/hg38.fa

Known issues

There might be issues with specific genome sequences. Sadly, not everything (naming, structure, filenames) is always consistent on the provider end. Let me know if you encounter issues with certain downloads.

Todo

• More tests!

• Caching of genome listings

• Automatic indexing (such as bwa)

• Ensembl bacteria

Contributing

Contributions welcome! Send me a pull request or get in touch.

License

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