Features

• Install a Python module named pygenomes.py

• Install a Python command-line script named pygenomes

• Easily check available taxa and genomes in commend-line

• Simply download genomes via comman, scientific, or assembly name

• Using interactive mode, simply download specific assembly genome

• Easily download genome and chromosome in specific file format

• Pure Python module and without any third-party dependence

Examples

You can use pygenomes as a Python module e.g. like in the following interactive Python session (the function’s signature might still change a bit in the future):

>>> from pygenomes import genomes
>>>
# prints out available taxa in group of mammals
>>> genomes(group='mammals')
# download human reference genome (hg19) in .2bit format
>>> genomes(taxa='human')
# interactive mode, ask for inputing and downloading specific assembly
>>> genomes(taxa='cow', assembly='1')
# try to download chromosome data, per fa.gz file per chromosome
>>> genomes(taxa='cow', chrs='1')

In addition there is a script named pygenomes, which can be used more easily from the system command-line like this (you can see many more examples when typing pygenomes -h on the command-line):

$ pygenomes -g -1                 # prints out all available taxa

$ pygenomes -g mammal             # prints out all available taxa in group
                                    of mammal
$ pygenomes -t yeast              # download yeast reference genome in
                                    .2bit format
$ pygenomes -t yeast -a 1         # interactive mode, ask for inputing and
                                    downloading specific assembly
$ pygenomes -t cow -f fa.gz       # try to download cow reference genome
                                    in fa.gz format
$ pygenomes -t dog -a 1 -o /tmp   # interactive mode, ask for inputing,
                                    file will be stored in /tmp
$ pygenomes -t cat -c 1           # download cat chromosome data, per
                                    chromosome per fa.gz file