diff bin/mapping_bowtie.sh @ 1:adc0f7765d85 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/mapping_bowtie.sh	Thu Sep 07 15:06:58 2017 -0400
@@ -0,0 +1,89 @@
+#!/bin/bash
+#SrcFolder='/data/zhang/wuj/scripts/SpliceTrap.0.8'
+InputFileName=$1
+faorfq=$2
+DatabasePrefix=$3
+Outputfolder=$4
+SrcFolder=$5
+Threads=$6
+DatabaseFolder=$SrcFolder'/../db/'$DatabasePrefix'/btw/TXdb'
+TmpFolderName=`basename $1`
+#fasta or fastq
+
+cd $Outputfolder;
+#prepare the folder
+if [ -d $TmpFolderName.result ];then
+        echo "MAPPING: !!!Error, there is already a folder named "$TmpFolderName".result !"
+        echo "MAPPING: !!!change the name of that folder first in case I erase them..."
+        exit
+fi
+echo "MAPPING: Start mapping $InputFileName...Creating cache folder $TmpFolderName.result"
+mkdir  $TmpFolderName".result"
+mkdir $TmpFolderName".result"/cache
+
+cd $TmpFolderName".result"
+cd cache
+echo "MAPPING: Split to pieces ..."
+split -l 1000000 $InputFileName
+for name in x*
+do
+
+	if [ $faorfq == "fasta" ];then
+		add="-f"
+	fi
+#	if [ $name != $InputFileName ];then
+		echo "bowtie -p $Threads -a -v 2 $DatabaseFolder $name $add >$name.btw; perl $SrcFolder/bowtie2eland.pl $name.btw $name $name.eland;rm $name.btw ;perl $SrcFolder/mark.mt.4eland.pl $name.eland >$name.nomt;rm $name.eland">>map.sh
+		echo $name >>checklist
+#	fi
+done
+
+echo "MAPPING: submit scripts..."
+perl $SrcFolder/batchqsub.pl map.sh
+
+tasknum=`wc -l map.sh |tr -d "\n"`
+#checking..
+
+echo "MAPPING: mapping $InputFileName to TXdb done...start to check.."
+while [ 1 ]
+do
+	if [ -f mapcheck.sh ];then
+		rm mapcheck.sh
+	fi
+	while read checklist
+	do
+
+		name=`echo $checklist |tr -d "\n"`
+		echo "MAPPING: checking $name...."
+		readnum=`wc -l $name | cut -f1 -d" "`
+		if [ $faorfq == "fasta" ];then 
+			readnum=`echo "$readnum/2"|bc`
+		else
+			readnum=`echo "$readnum/4"|bc`
+		fi
+		if [ -f $name.nomt ];then
+			bowtienum=`wc -l $name.nomt | cut -f1 -d" "`
+		else
+			bowtienum=0
+		fi
+		if [ $bowtienum != $readnum ];then
+			echo "bowtie -p $Threads -a -v 2 $DatabaseFolder $name $add >$name.btw; perl $SrcFolder/bowtie2eland.pl $name.btw $name $name.eland;rm $name.btw ;perl $SrcFolder/mark.mt.4eland.pl $name.eland >$name.nomt;rm $name.eland">>mapcheck.sh
+
+		fi
+	done <checklist
+	if [ -f mapcheck.sh ];then
+		checktasknum=`wc -l mapcheck.sh |tr -d "\n"`
+		if [ $checktasknum == $tasknum ];then
+			echo "MAPPING: warning! none of the mapping tasks properly finished!"
+		fi
+		echo "MAPPING: resubmit TASKS...."
+		perl $SrcFolder/batchqsub.pl mapcheck.sh
+	else
+		break
+	fi
+done
+echo "MAPPING: Done.....merging files..."
+cat *.nomt >$Outputfolder/$TmpFolderName.nomt
+cd ../../
+rm $TmpFolderName.result -rf
+#/data/zhang/wuj/tools/bowtie-0.12.3/bowtie -a $DatabaseFolderTXdb -f
+