CLI tool to annotate csv or tsv files containing a column of gene symbols. Outputs formal gene name and protein function/class to table.
Prefered method of installation using pipx: https://pypa.github.io/pipx/
pip install pipx
pipx install git+https://github.com/MLKaufman/gene_annotate.git
can also be installed with vanilla pip:
pip install git+https://github.com/MLKaufman/gene_annotate.git
Once installed the package is available as a command line executable:
gene_annotate
usage: gene_annotate [-h] [-i] [-s SPECIES] [-a ANNOTATEMODE] [-c COLUMN]
optional arguments:
-h, --help show this help message and exit
-i, --interactivemode
activate interactive mode
-s SPECIES, --species SPECIES
species to use; defualt = human; currently
supported:human,mouse,gallus,danio
-a ANNOTATEMODE, --annotatemode ANNOTATEMODE
input file to annotate (csv or tsv)
-c COLUMN, --column COLUMN
column # to use for getting gene symbol for annotating