milchdealer/isoform-lister

Isoform Lister

Uses gene names saved as a list in .txt to lookup all isoform entry list IDs, specific to organism (common name, used in Entry ID column), and creates an isoform list, aligned with initial gene name row.

The .txt list is newline delimited.

Output Format

Output is the initial gene name, followed by the isoform entries for that gene. Thus a row can have N (>=2) columns, separated by space.

Requirements

• python3
• venv (if you want to run in venv)

Setup (venv)

python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

Setup (global)

pip install requests beautifulsoup4

Usage

usage: main.py [-h] [--searchlist SEARCHLIST] [--organism ORGANISM] [--output OUTPUT]

optional arguments:
  -h, --help            show this help message and exit
  --searchlist SEARCHLIST
                        Path to file which contains a list of gene names. Default: searchlist.txt
  --organism ORGANISM   Specify organism to search for by common name. Default: MOUSE
  --output OUTPUT       Path to file where to store the results. Default: results.txt

Contributors

Initial idea goes to Suzuka, who does this tedious work occasionally for her research.