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comparison wrapper.sh @ 3:38c038c17d0c draft

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Uploaded
author davidvanzessen
date Wed, 13 Aug 2014 09:07:54 -0400
parents 94fada165724
children d8de51314d3f
comparison
equal deleted inserted replaced
2:94fada165724 3:38c038c17d0c
12 inputs=($inputs) 12 inputs=($inputs)
13 IDs=$9 13 IDs=$9
14 IDs=($IDs) 14 IDs=($IDs)
15 ref=${10} 15 ref=${10}
16 output=${11} 16 output=${11}
17 selection=${12}
17 outID="result" 18 outID="result"
18 19
19 echo "testID = $testID" 20 echo "testID = $testID"
20 echo "species = $species" 21 echo "species = $species"
21 echo "substitutionModel = $substitutionModel" 22 echo "substitutionModel = $substitutionModel"
40 if [[ "$f" == *"$zipType"* ]] 41 if [[ "$f" == *"$zipType"* ]]
41 then 42 then
42 id=${IDs[$count]} 43 id=${IDs[$count]}
43 echo "id=$id" 44 echo "id=$id"
44 unzip $current -d $PWD/$id/ >> $PWD/unziplog.log 45 unzip $current -d $PWD/$id/ >> $PWD/unziplog.log
45 filename="$PWD/gappednt_${id}.txt" 46 summaryfile="$PWD/summary_${id}.txt"
46 cat $PWD/$id/*/2_* | cut -f2,4,7 > $filename 47 gappedfile="$PWD/gappednt_${id}.txt"
47 python $dir/script_imgt.py --input $filename --ref $ref --output $fasta --id $id 48 filtered="$PWD/filtered_${id}.txt"
49 cat $PWD/$id/*/1_* > $summaryfile
50 cat $PWD/$id/*/2_* > $gappedfile
51 Rscript $dir/filter.r $summaryfile $gappedfile "$selection" $filtered
52
53 final="$PWD/final_${id}.txt"
54 cat $filtered | cut -f2,4,7 > $final
55 python $dir/script_imgt.py --input $final --ref $ref --output $fasta --id $id
48 else 56 else
49 python $dir/script_xlsx.py --input $current --ref $ref --output $fasta 57 python $dir/script_xlsx.py --input $current --ref $ref --output $fasta
50 fi 58 fi
51 count=$((count+1)) 59 count=$((count+1))
52 done 60 done