| Previous changeset 14:007e2dd3fe8b (2017-04-03) Next changeset 16:72e55a2c0bbf (2017-04-03) |
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Commit message:
Deleted selected files |
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removed:
isoDE2.sh |
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| diff -r 007e2dd3fe8b -r 491a5e3e4b78 isoDE2.sh --- a/isoDE2.sh Mon Apr 03 17:55:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,218 +0,0 @@ -#!/bin/bash - -isoEMDir=/galaxy/galaxy/tools-dependencies/bin/isoem2/ -toolpath=${isoEMDir}/bin -isoDEPath=${isoEMDir}/bin -supportCalcPath=${isoEMDir}/src/calc -fpkmGeneCommand="" -fpkmIsoformCommand="" -tpmGeneCommand="" -tpmIsoformCommand="" - -numberOfBootstrapIterationsPerSample=199 - -arg=($*) -i=0 -while [ $i -lt $# ] -do - a=${arg[i]} - if [ "$a" == "-c1" ]; then - fpkmGeneCommand="$fpkmGeneCommand -c1" - fpkmIsoformCommand="$fpkmIsoformCommand -c1" - tpmGeneCommand="$tpmGeneCommand -c1" - tpmIsoformCommand="$tpmIsoformCommand -c1" - - ((i++)) - a=${arg[i]} - rep=1 - while [[ `expr index "$a" "/"` -ne 0 && $i -lt $# ]] - do - condition1File=$a - ${toolpath}/convertToisoDEFormatWithIsoforms $condition1File c1_rep${rep} - - fpkmGeneCommand="$fpkmGeneCommand c1_rep${rep}_fpkm_G" - fpkmIsoformCommand="$fpkmIsoformCommand c1_rep${rep}_fpkm_I" - tpmGeneCommand="$tpmGeneCommand c1_rep${rep}_tpm_G" - tpmIsoformCommand="$tpmIsoformCommand c1_rep${rep}_tpm_I" - ((rep++)) - - ((i++)) - a=${arg[i]} - done - elif [ "$a" == "-c2" ]; then - fpkmGeneCommand="$fpkmGeneCommand -c2" - fpkmIsoformCommand="$fpkmIsoformCommand -c2" - tpmGeneCommand="$tpmGeneCommand -c2" - tpmIsoformCommand="$tpmIsoformCommand -c2" - - ((i++)) - a=${arg[i]} - rep=1 - while [[ `expr index "$a" "/"` -ne 0 && $i -lt $# ]] - do - condition1File=$a - #echo $condition1File - ${toolpath}/convertToisoDEFormatWithIsoforms $condition1File c2_rep${rep} - - fpkmGeneCommand="$fpkmGeneCommand c2_rep${rep}_fpkm_G" - fpkmIsoformCommand="$fpkmIsoformCommand c2_rep${rep}_fpkm_I" - tpmGeneCommand="$tpmGeneCommand c2_rep${rep}_tpm_G" - tpmIsoformCommand="$tpmIsoformCommand c2_rep${rep}_tpm_I" - ((rep++)) - - ((i++)) - a=${arg[i]} - done - elif [ "$a" == "-pval" ]; then - ((i++)) - pval=${arg[i]} - ((i++)) - - - elif [ "$a" == "-geneFPKMout" ]; then - ((i++)) - geneFPKMout_file=${arg[i]} - ((i++)) - - - elif [ "$a" == "-geneTPMout" ]; then - ((i++)) - geneTPMout_file=${arg[i]} - ((i++)) - - elif [ "$a" == "-isoFPKMout" ]; then - ((i++)) - isoFPKMout_file=${arg[i]} - ((i++)) - - elif [ "$a" == "-isoTPMout" ]; then - ((i++)) - isoTPMout_file=${arg[i]} - ((i++)) - else - - ((i++)) - fi - -done -((rep--)) -bootstrap=$(($rep*$numberOfBootstrapIterationsPerSample)) -echo boostrap iterations $bootstrap -#support=`java -cp ${supportCalcPath} support 200 200 $pval` -#support=`java -cp ${supportCalcPath} support $bootstrap $bootstrap $pval` -#Calculator assumes IsoDE does all pairs when calculation the number of ratios. It multiplies the number of bootstrap samples per condition -# changed the second parameter to make the number of ratios equal to the number of bootstrap samples (match, not all pairs) -echo calculate support based on p-value and number or replicates -support=`java -cp ${supportCalcPath} support $bootstrap 1 $pval` -fpkmGeneCommand="$fpkmGeneCommand -b $support" -fpkmIsoformCommand="$fpkmIsoformCommand -b $support" -tpmGeneCommand="$tpmGeneCommand -b $support" -tpmIsoformCommand="$tpmIsoformCommand -b $support" - -fpkmGeneCommand="$fpkmGeneCommand -dfc 2" -fpkmIsoformCommand="$fpkmIsoformCommand -dfc 2" -tpmGeneCommand="$tpmGeneCommand -dfc 2" -tpmIsoformCommand="$tpmIsoformCommand -dfc 2" - - -#if [ "${out_prefix}" == "$(basename ${out_prefix} )" ]; then -# pth=`pwd` -# out_prefix=${pth}/${out_prefix} -#fi - - -echo GENE FPKM -echo moving start -date - -mkdir fpkm_G -cd fpkm_G -mv ../c*_fpkm_G . - - -echo isoDE start -date - - -${isoDEPath}/isodecalls $fpkmGeneCommand -out "output.txt" -#awk '{for (f=1; f<=NF; f++) {if (f == NF) printf "%s",$f; else printf "%s\t", $f }; print ""}' Bootstrap_Merge1_DIR/output.txt | sed 1,1d > ${geneFPKMout_file} - -echo awk command -date - - -awk '{if (NR == 1) {print "Gene ID\tConfident log2 FC\t Single run log2 FC\t c1 average FPKM\tc2 average FPKM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t" $5 "\t" $6 "\t" $7}}' Bootstrap_Merge1_DIR/output.txt > ${geneFPKMout_file} - -cd .. - - -echo ISOFORM FPKM - -echo moving start -date - -mkdir fpkm_I -cd fpkm_I -mv ../c*_fpkm_I . - - -echo isoDE start -date - -${isoDEPath}/isodecalls $fpkmIsoformCommand -out "output.txt" - -echo awk command -date -pwd -awk '{if (NR == 1) {print "Isoform ID\tConfident log2 FC\t Single run log2 FC\t c1 average FPKM\tc2 average FPKM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t" $5 "\t" $6 "\t" $7}}' Bootstrap_Merge1_DIR/output.txt > ${isoFPKMout_file} -cd .. - - -echo ISOFORM TPM -echo moving start -date - -mkdir tpm_G -cd tpm_G -mv ../c*_tpm_G . - -echo isoDE start -date - -${isoDEPath}/isodecalls $tpmGeneCommand -out "output.txt" - -echo awk command -date -pwd -awk '{if (NR == 1) {print "Gene ID\tConfident log2 FC\t Single run log2 FC\t c1 average TPM\tc2 average TPM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t" $5 "\t" $6 "\t" $7}}' Bootstrap_Merge1_DIR/output.txt > ${geneTPMout_file} -cd .. - - -echo ISOFORM TPM -echo moving start -date - -mkdir tpm_I -cd tpm_I -mv ../c*_tpm_I . - -echo isoDE start -date - -${isoDEPath}/isodecalls $tpmIsoformCommand -out "output.txt" - -echo awk command -date - -awk '{if (NR == 1) {print "Isoform ID\tConfident log2 FC\t Single run log2 FC\t c1 average TPM\tc2 average TPM";} else {if ($6 == 0 && $7 == 0) {two="0";} else {two=$2;} print $1 "\t" two "\t" $5 "\t" $6 "\t" $7}}' Bootstrap_Merge1_DIR/output.txt > ${isoTPMout_file} - -cd .. - - -echo final cleanup -date -rm -fr fpkm_G fpkm_I tpm_G cd tpm_I -echo done -date - - |