GeneMatcher

Installation

pip install git+https://github.com/DBRetina/geneMatcher

Usage

geneMatcher --help

Simple run examples

1. Create a TSV file

Create a TSV file with col1: ref1_URL, col2: ref2_url

filename: refs.tsv

http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/GRCh37_mapping/gencode.v28lift37.transcripts.fa.gz	http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/gencode.v38.transcripts.fa.gz
http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_20/gencode.v20.pc_transcripts.fa.gz	http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.pc_transcripts.fa.gz

2. Run geneMatcher

geneMatcher auto -k 25 --refs-tsv refs.tsv --min-jac 20 --min-cont 80 --cores 8