| Previous changeset 13:cff0a5f324d4 (2017-04-01) Next changeset 15:491a5e3e4b78 (2017-04-03) |
|
Commit message:
Bug fix in output files headers |
|
added:
isoDE2.sh |
| b |
| diff -r cff0a5f324d4 -r 007e2dd3fe8b isoDE2.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/isoDE2.sh Mon Apr 03 17:55:22 2017 -0400 |
| [ |
| @@ -0,0 +1,218 @@ +#!/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 + + |