Mercurial > repos > davidvanzessen > report_clonality_igg

comparison r_wrapper.sh @ 23:5f0597a3fd8b draft

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Uploaded
author davidvanzessen
date Fri, 16 Jan 2015 07:37:41 -0500
parents 2555b94dbdb2
children 5454af6fece1
comparison
equal deleted inserted replaced
22:2555b94dbdb2 23:5f0597a3fd8b
8 locus=$6 8 locus=$6
9 filterproductive=$7 9 filterproductive=$7
10 dir="$(cd "$(dirname "$0")" && pwd)" 10 dir="$(cd "$(dirname "$0")" && pwd)"
11 useD="false" 11 useD="false"
12 if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then 12 if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then
13 echo "species D region in reference db"
13 useD="true" 14 useD="true"
15 fi
16 echo "$species"
17 if [[ "$species" == *"custom"* ]] ; then
18 loci=(${locus//;/ })
19 useD="true"
20 echo "${loci[@]}"
21 if [[ "${#loci[@]}" -eq "2" ]] ; then
22 useD="false"
23 fi
14 fi 24 fi
15 mkdir $3 25 mkdir $3
16 cp $dir/genes.txt $outputDir 26 cp $dir/genes.txt $outputDir
17 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive 2>&1 27 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive 2>&1
18 cp $dir/tabber.js $outputDir 28 cp $dir/tabber.js $outputDir