Mercurial > repos > saharlcc > isoem2_isode2
view isoDE2.sh @ 2:7044191a603b draft
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author | saharlcc |
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date | Mon, 19 Sep 2016 22:00:03 -0400 |
parents | 581e4c6b483f |
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#!/bin/bash isoEMDir=/home/projects/isoem2/isoem-workingversion toolpath=${isoEMDir}/bin isoDEPath=${isoEMDir}/bin supportCalcPath=${isoEMDir}/src/calc fpkmGeneCommand="" fpkmIsoformCommand="" tpmGeneCommand="" tpmIsoformCommand="" arg=($*) 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 support=`java -cp ${supportCalcPath} support 200 200 $pval` fpkmGeneCommand="$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 FPKM\tc2 FPKM";} else {if ($6 == 0 && $7 == 0) {two="NDE";} 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 FPKM\tc2 FPKM";} else {if ($6 == 0 && $7 == 0) {two="NDE";} 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 TPM\tc2 TPM";} else {if ($6 == 0 && $7 == 0) {two="NDE";} 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 TPM\tc2 TPM";} else {if ($6 == 0 && $7 == 0) {two="NDE";} 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