diff scripts/TEMP_Absence.sh @ 0:28d1a6f8143f draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/TEMP_Absence.sh	Mon Apr 25 13:08:56 2016 -0400
@@ -0,0 +1,138 @@
+#!/bin/bash -x
+# TEMP (Transposable Element Movement present in a Population)
+# 2013-06-14
+# Jiali Zhuang([e-mail])
+# Zhiping Weng Lab
+# Programs in Bioinformatics and Integrative Biology
+# University of Massachusetts Medical School
+
+#usage function
+usage() {
+echo -en "\e[1;36m"
+cat <<EOF
+
+usage: $0 -i input_file.sorted.bam -s scripts_directory -o output_directory -r transposon_rpmk.bed -t reference.2bit -f fragment_size -c CPUs -h 
+
+TEMP is a software package for detecting transposable elements (TEs) 
+insertions and excisions from pooled high-throughput sequencing data. 
+Please send questions, suggestions and bug reports to:
[e-mail]
+
+Options:
+        -i     Input file in bam format with full path. Please sort and index the file before calling this program. 
+               Sorting and indexing can be done by 'samtools sort' and 'samtools index'
+        -s     Directory where all the scripts are
+        -o     Path to output directory. Default is current directory
+        -r     Annotated transposon positions in the genome (e.g., repeakMask) in bed6 format with full path
+        -t     2bit file for the reference genome (can be downloaded from UCSC Genome Browser)
+        -f     An integer specifying the length of the fragments (inserts) of the library. Default is 500
+        -c     An integer specifying the number of CUPs used. Default is 4
+        -h     Show help message
+
+EOF
+echo -en "\e[0m"
+}
+
+# taking options
+while getopts "hi:c:f:o:r:s:t:" OPTION
+do
+        case $OPTION in
+                h)
+                        usage && exit 1
+		;;
+                i)
+                        BAM=$OPTARG
+		;;
+	        f)
+		        INSERT=$OPTARG
+		;;
+                o)
+                        OUTDIR=$OPTARG
+                ;;
+                c)
+                        CPU=$OPTARG
+                ;;
+                s)
+                        BINDIR=$OPTARG
+                ;;
+	        r)
+		        TEBED=$OPTARG
+		;;
+	        t)
+		        REF=$OPTARG
+		;;
+                ?)
+                        usage && exit 1
+                ;;
+        esac
+done
+
+if [[ -z $BAM ]] || [[ -z $BINDIR ]] || [[ -z $TEBED ]] || [[ -z $REF ]]
+then
+        usage && exit 1
+fi
+[ ! -z "${CPU##*[!0-9]*}" ] || CPU=4
+[ ! -z "${INSERT##*[!0-9]*}" ] || INSERT=500
+[ ! -z $OUTDIR ]  || OUTDIR=$PWD
+
+mkdir -p "${OUTDIR}" || echo -e "\e[1;31mWarning: Cannot create directory ${OUTDIR}. Using the direcory of input fastq file\e[0m"
+cd ${OUTDIR} || echo -e "\e[1;31mError: Cannot access directory ${OUTDIR}... Exiting...\e[0m" || exit 1
+touch ${OUTDIR}/.writting_permission && rm -rf ${OUTDIR}/.writting_permission || echo -e "\e[1;31mError: Cannot write in directory ${OUTDIR}... Exiting...\e[0m" || exit 1
+
+function checkExist {
+        echo -ne "\e[1;32m\"${1}\" is using: \e[0m" && which "$1"
+        [[ $? != 0 ]] && echo -e "\e[1;36mError: cannot find software/function ${1}! Please make sure that you have installed the pipeline correctly.\nExiting...\e[0m" && exit 1
+}
+echo -e "\e[1;35mTesting required softwares/scripts:\e[0m"
+checkExist "echo"
+checkExist "rm"
+checkExist "mkdir"
+checkExist "date"
+checkExist "mv"
+checkExist "sort"
+checkExist "touch"
+checkExist "awk"
+checkExist "grep"
+checkExist "bwa"
+checkExist "samtools"
+echo -e "\e[1;35mDone with testing required softwares/scripts, starting pipeline...\e[0m"
+
+name=`basename $BAM`
+i=${name/.sorted.bam/}
+echo $name
+echo $i
+if [[ ! -s $name ]]
+then
+    cp $BAM ./
+fi
+if [[ ! -s $name.bai ]]
+then cp $BAM.bai ./
+fi
+
+#Detect excision sites
+samtools view -XF 0x2 $name > $i.unpair.sam
+awk -F "\t" '{OFS="\t"; if ($9 != 0) print $0}' $i.unpair.sam > temp1.sam
+perl $BINDIR/pickUniqIntervalPos.pl temp1.sam $INSERT > $i.unproper.uniq.interval.bed
+
+rm temp1.sam $i.unpair.sam
+
+# Sometimes $i.unproper.uniq.interval.bed contains malformed bed entries 
+# These must be removed to prevent the script failing
+awk '{if ($3>=$2 && $3 > 0 && $2 > 0) print $0}' $i.unproper.uniq.interval.bed > $i.unproper.uniq.interval.fixed.bed
+mv $i.unproper.uniq.interval.fixed.bed $i.unproper.uniq.interval.bed
+
+# Map to transposons
+bedtools intersect -a $TEBED -b $i.unproper.uniq.interval.bed -f 1.0 -wo > temp
+perl $BINDIR/filterFalsePositive.ex.pl temp $INSERT $i.final.pairs.rpmk.bed
+bedtools intersect -a $TEBED -b $i.final.pairs.rpmk.bed -f 1.0 -wo > temp2
+
+perl $BINDIR/excision.clustering.pl temp2 $i.excision.cluster.rpmk
+rm temp temp2 $i.unproper.uniq.interval.bed $i.final.pairs.rpmk.bed
+
+# Identify breakpoints using soft-clipping information
+perl $BINDIR/pickSoftClipping.over.pl $i.excision.cluster.rpmk $REF > $i.excision.cluster.rpmk.sfcp
+perl $BINDIR/refine_breakpoint.ex.pl
+
+# Estimate excision sites frequencies
+perl $BINDIR/pickOverlapPair.ex.pl $i.excision.cluster.rpmk.refined.bp > $i.excision.cluster.rpmk.refined.bp.refsup
+perl $BINDIR/summarize_excision.pl