Mercurial > repos > davidvanzessen > report_clonality_igg
diff r_wrapper.sh @ 23:5f0597a3fd8b draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Fri, 16 Jan 2015 07:37:41 -0500 |
| parents | 2555b94dbdb2 |
| children | 5454af6fece1 |
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--- a/r_wrapper.sh Thu Jan 15 09:16:19 2015 -0500 +++ b/r_wrapper.sh Fri Jan 16 07:37:41 2015 -0500 @@ -10,8 +10,18 @@ dir="$(cd "$(dirname "$0")" && pwd)" useD="false" if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then + echo "species D region in reference db" useD="true" fi +echo "$species" +if [[ "$species" == *"custom"* ]] ; then + loci=(${locus//;/ }) + useD="true" + echo "${loci[@]}" + if [[ "${#loci[@]}" -eq "2" ]] ; then + useD="false" + fi +fi mkdir $3 cp $dir/genes.txt $outputDir Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive 2>&1