Mercurial > repos > davidvanzessen > baseline_fasta_generator
comparison wrapper.sh @ 2:fac36e2248fd draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 23 Jul 2014 06:00:58 -0400 |
| parents | |
| children | 048f8cdbb6d2 |
comparison
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| 1:85f18c2f74dd | 2:fac36e2248fd |
|---|---|
| 1 #!/bin/bash | |
| 2 dir="$(cd "$(dirname "$0")" && pwd)" | |
| 3 | |
| 4 input=$1 | |
| 5 ref=$2 | |
| 6 output=$3 | |
| 7 f=$(file $input) | |
| 8 zipType="Zip archive" | |
| 9 if [[ "$f" == *"$zipType"* ]] | |
| 10 then | |
| 11 echo "Zip archive, assuming IMGT output file" | |
| 12 echo "Trying: unzip $input -d $PWD/files/" | |
| 13 unzip $input -d $PWD/files/ > $PWD/unziplog.log | |
| 14 cat $PWD/files/*/2_* | cut -f2,4,7 > $PWD/gappednt.txt | |
| 15 python $dir/script_imgt.py --input $PWD/gappednt.txt --ref $ref --output $output | |
| 16 else | |
| 17 python $dir/script_xlsx.py --input $input --ref $ref --output $output | |
| 18 fi |