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complete.sh igblast/igblast.sh |
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| 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 |
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| @@ -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)) |
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| 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 |
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| @@ -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 |