# HG changeset patch
# User davidvanzessen
# Date 1481896900 18000
# Node ID 54f6756bacb1b0bcb558e86f3b71668838cffe4e
# Parent  d001d0c05dbe8d918de49e3435d82aa3f50e3329
Uploaded

diff -r d001d0c05dbe -r 54f6756bacb1 complete.sh
--- a/complete.sh	Fri Dec 16 07:30:32 2016 -0500
+++ b/complete.sh	Fri Dec 16 09:01:40 2016 -0500
@@ -46,7 +46,7 @@
 		bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName "${fileName}"
 	else
 		echo "<tr><td>Sample $count of patient $id is not a zip file so assuming fasta/fastq, using igBLASTn</td></tr>" >> $html
-		bash ${dir}/igblast/igblast.sh $current $species $locus $parsedFileName
+		bash ${dir}/igblast/igblast.sh $current "$species" $locus $parsedFileName
 	fi
 	mergerInput+=($parsedFileName)
 	count=$((count+1))
diff -r d001d0c05dbe -r 54f6756bacb1 igblast/igblast.sh
--- a/igblast/igblast.sh	Fri Dec 16 07:30:32 2016 -0500
+++ b/igblast/igblast.sh	Fri Dec 16 09:01:40 2016 -0500
@@ -9,10 +9,16 @@
 
 declare -A speciesdict
 
-speciesdict=(["Bos taurus functional"]="BosTaurus" ["Bos taurus non-functional"]="BosTaurus" ["Camelus dromedarius functional"]="CamelusDromedarius" ["Camelus dromedarius non-functional"]="CamelusDromedarius" ["Canis lupus familiaris functional"]="CanisLupusFamiliaris" ["Canis lupus familiaris non-functional"]="CanisLupusFamiliaris" ["Danio rerio non-functional"]="DanioRerio" ["Danio rerio functional"]="DanioRerio" ["Homo sapiens functional"]="HomoSapiens" ["Homo sapiens non-functional"]="HomoSapiens" ["Macaca mulatta non-functional"]="MacacaMulatta" ["Macaca mulatta functional"]="MacacaMulatta" ["Mus musculus functional"]="MusMusculus" ["Mus musculus non-functional"]="MusMusculus" ["Mus spretus functional"]="MusSpretus" ["Mus spretus non-functional"]="MusSpretus" ["Oncorhynchus mykiss functional"]="OncorhynchusMykiss" ["Oncorhynchus mykiss non-functional"]="OncorhynchusMykiss" ["Oryctolagus cuniculus functional"]="OryctolagusCuniculus" ["Oryctolagus cuniculus non-functional"]="OryctolagusCuniculus" ["Rattus norvegicus functional"]="RattusNorvegicus" ["Rattus norvegicus non-functional"]="RattusNorvegicus" ["Sus scrofa functional"]="SusScrofa" ["Sus scrofa non-functional"]="SusScrofa" ["BosTaurus"]="BosTaurus" ["CamelusDromedarius"]="CamelusDromedarius" ["CanisLupusFamiliaris"]="CanisLupusFamiliaris" ["DanioRerio"]="DanioRerio" ["HomoSapiens"]="HomoSapiens" ["MacacaMulatta"]="MacacaMulatta" ["MusMusculus"]="MusMusculus" ["MusSpretus"]="MusSpretus" ["OncorhynchusMykiss"]="OncorhynchusMykiss" ["OryctolagusCuniculus"]="OryctolagusCuniculus" ["RattusNorvegicus"]="RattusNorvegicus" ["SusScrofa"]="SusScrofa")
+speciesdict=(["Rattus norvegicus functional"]="rat" ["Rattus norvegicus non-functional"]="rat" ["Oryctolagus cuniculus functional"]="rabbit" ["Oryctolagus cuniculus non-functional"]="rabbit" ["Mus musculus functional"]="mouse" ["Mus musculus non-functional"]="mouse" ["Homo sapiens functional"]="human" ["Homo sapiens non-functional"]="human" ["Macaca mulatta non-functional"]="rhesus_monkey" ["Macaca mulatta functional"]="rhesus_monkey")
+
+echo "Species: $species ${speciesdict[$species]}"
+
+species="${speciesdict[$species]}"
 
 echo "$input $species $locus $output"
 
 java -Xmx64G -jar $IGBLASTWRP/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1
+#java -Xmx64G -jar $dir/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1
+#java -Xmx64G -jar $dir/migmap-1.0.1.jar -p 4 -S "$species" -R $locus ${input} $PWD/blasted_output 2>&1
 
 Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1