Mercurial > repos > davidvanzessen > baseline_fasta_generator
view wrapper.sh @ 5:048f8cdbb6d2 draft default tip
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author | davidvanzessen |
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date | Thu, 07 Aug 2014 10:19:53 -0400 |
parents | fac36e2248fd |
children |
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#!/bin/bash dir="$(cd "$(dirname "$0")" && pwd)" input=$1 ids=$2 ref=$3 output=$4 input=($input) ids=($ids) first="${input[0]}" count=0 for current in ${input[@]} do f=$(file $current) zipType="Zip archive" if [[ "$f" == *"$zipType"* ]] then id=${ids[$count]} unzip $current -d $PWD/$id/ >> $PWD/unziplog.log filename="$PWD/gappednt_${id}.txt" cat $PWD/$id/*/2_* | cut -f2,4,7 > $filename python $dir/script_imgt.py --input $filename --ref $ref --output $output --id $id else python $dir/script_xlsx.py --input $current --ref $ref --output $output fi count=$((count+1)) done