Mercurial > repos > davidvanzessen > baseline_fasta_generator
view wrapper.sh @ 3:be17e1e7dc2b draft
Uploaded
author | davidvanzessen |
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date | Wed, 23 Jul 2014 07:51:10 -0400 |
parents | fac36e2248fd |
children | 048f8cdbb6d2 |
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#!/bin/bash dir="$(cd "$(dirname "$0")" && pwd)" input=$1 ref=$2 output=$3 f=$(file $input) zipType="Zip archive" if [[ "$f" == *"$zipType"* ]] then echo "Zip archive, assuming IMGT output file" echo "Trying: unzip $input -d $PWD/files/" unzip $input -d $PWD/files/ > $PWD/unziplog.log cat $PWD/files/*/2_* | cut -f2,4,7 > $PWD/gappednt.txt python $dir/script_imgt.py --input $PWD/gappednt.txt --ref $ref --output $output else python $dir/script_xlsx.py --input $input --ref $ref --output $output fi