diff bin/mapping_rmap.sh @ 1:adc0f7765d85 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/mapping_rmap.sh	Thu Sep 07 15:06:58 2017 -0400
@@ -0,0 +1,80 @@
+#/data/zhang/wuj/tools/bowtie-0.12.3/bowtie -a --best /data/zhang/wuj/database/hg18/AS/TXdb.2/btw/TXdb -f -t s_1_sequence.txtparta >s_1.map &
+#SrcFolder='/data/zhang/wuj/scripts/SpliceTrap.0.8'
+InputFileName=$1
+faorfq=$2
+DatabasePrefix=$3
+Outputfolder=$4
+SrcFolder=$5
+DatabaseFolder=$SrcFolder'/../db/'$DatabasePrefix'/TXdb.fasta'
+TmpFolderName=`basename $1`
+
+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 to map $InputFileName....Creating cache folder $TmpFolderName.result"
+mkdir  $TmpFolderName".result"
+cd $TmpFolderName".result"
+mkdir cache stat
+cd cache
+echo "MAPPING: Split file..."
+split -l 1000000 $InputFileName
+echo "MAPPING: generating shell scirpts...."
+for name in x*
+do
+
+	echo "rmap -M 100 -m 2 -c $DatabaseFolder -o $name.rmap $name; perl $SrcFolder/rmap2eland.pl $name.rmap $name $name.eland;rm $name.rmap ;perl $SrcFolder/mark.mt.4eland.pl $name.eland >$name.nomt;rm $name.eland">>map.sh
+	echo $name >>checklist	
+done
+tasknum=`wc -l map.sh |tr -d "\n"`
+perl $SrcFolder/batchqsub.pl map.sh
+
+echo "MAPPING: map $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
+                        rmapnum=`wc -l $name.nomt | cut -f1 -d" "`
+                else
+                        rmapnum=0
+                fi
+                if [ $rmapnum != $readnum ];then
+			echo "rmap -M 100 -m 2 -c $DatabaseFolder -o $name.rmap $name; perl $SrcFolder/rmap2eland.pl $name.rmap $name $name.eland;rm $name.rmap ;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: resubmiting TASKS...."
+                perl $SrcFolder/batchqsub.pl mapcheck.sh
+        else
+                break
+        fi
+done
+echo "MAPPING: Mapping is really done....merging files..."
+
+
+cat *.nomt >$Outputfolder/$TmpFolderName.nomt
+cd ../../
+
+rm $TmpFolderName.result -rf
+