README.md

gene_annotate

CLI tool to annotate csv or tsv files containing a column of gene symbols. Outputs formal gene name and protein function/class to table.

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Installation:

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

Example Usage:

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