# HG changeset patch
# User saharlcc
# Date 1491256522 14400
# Node ID 007e2dd3fe8b6efb51c5bc7993672a67fbffde3e
# Parent  cff0a5f324d4faa449279ad0072dc5e57229fb8f
Bug fix in output files headers

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
+
+