diff scripts/TEMP_Insertion.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_Insertion.sh	Mon Apr 25 13:08:56 2016 -0400
@@ -0,0 +1,176 @@
+#!/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_database.fa -t annotated_TEs.bed -m MISMATCH -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     Transposon sequence database in fasta format with full path
+        -t     Annotated TEs in BED6 format with full path. Detected insertions that overlap with annoated TEs will be filtered. 
+        -u     TE families annotations. If supplied detected insertions overlap with annotated TE of the same family will be filtered. Only use with -t.
+        -m     Number of mismatch allowed when mapping to TE concensus sequences. Default is 3
+        -x     The minimum score difference between the best hit and the second best hit for considering a read as uniquely mapped. For BWA mem. 
+        -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 8
+        -h     Show help message
+
+EOF
+echo -en "\e[0m"
+}
+
+# taking options
+while getopts "hi:c:f:m:o:r:s:t:u:x:" OPTION
+do
+        case $OPTION in
+                h)
+                        usage && exit 1
+		;;
+                i)
+                        BAM=$OPTARG
+		;;
+	        f)
+		        INSERT=$OPTARG
+		;;
+	        m)
+		        MM=$OPTARG
+		;;
+                o)
+                        OUTDIR=$OPTARG
+                ;;
+                c)
+                        CPU=$OPTARG
+                ;;
+                s)
+                        BINDIR=$OPTARG
+                ;;
+	        r)
+		        TESEQ=$OPTARG
+		;;
+	        t)
+                        ANNO=$OPTARG
+                ;;
+                u)
+                        FAMI=$OPTARG
+                ;;
+	        x)
+		        SCORE=$OPTARG
+		;;
+                ?)
+                        usage && exit 1
+                ;;
+        esac
+done
+
+if [[ -z $BAM ]] || [[ -z $BINDIR ]] || [[ -z $TESEQ ]]
+then
+        usage && exit 1
+fi
+[ ! -z "${CPU##*[!0-9]*}" ] || CPU=8
+[ ! -z "${INSERT##*[!0-9]*}" ] || INSERT=500
+[ ! -z "${MM##*[!0-9]*}" ] || MM=3
+[ ! -z "${SCORE##*[!0-9]*}" ] || SCORE=0
+[ ! -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"
+
+cp $TESEQ ./
+name=`basename $BAM`
+te=`basename $TESEQ`
+i=${name/.sorted.bam/}
+echo $name
+echo $i
+if [[ ! -s $name ]]
+then
+    cp $BAM ./
+fi
+if [[ ! -s $name.bai ]]
+then cp $BAM.bai ./
+fi
+
+# Get the mate seq of the uniq-unpaired reads
+samtools view -XF 0x2  $name > $i.unpair.sam
+if [[ $SCORE -eq 0 ]]
+then
+    perl $BINDIR/pickUniqPairFastq.pl $i.unpair.sam $i.unpair.uniq
+    perl $BINDIR/pickUniqPos.pl $i.unpair.sam > $i.unpair.uniq.bed
+else
+    perl $BINDIR/pickUniqPairFastq_MEM.pl $i.unpair.sam $i.unpair.uniq $SCORE
+    perl $BINDIR/pickUniqPos_MEM.pl $i.unpair.sam $SCORE > $i.unpair.uniq.bed 
+fi
+
+# Map to transposons
+bwa index -a is $te
+bwa aln -t $CPU -n $MM -l 100 -R 1000 $te $i.unpair.uniq.1.fastq > $i.unpair.uniq.1.sai
+bwa aln -t $CPU -n $MM -l 100 -R 1000 $te $i.unpair.uniq.2.fastq > $i.unpair.uniq.2.sai
+bwa sampe -P $te $i.unpair.uniq.1.sai $i.unpair.uniq.2.sai $i.unpair.uniq.1.fastq $i.unpair.uniq.2.fastq > $i.unpair.uniq.transposons.sam
+
+
+#Summary
+samtools view -hSXF 0x2 $i.unpair.uniq.transposons.sam > $i.unpair.uniq.transposons.unpair.sam
+perl $BINDIR/pickUniqMate.pl $i.unpair.uniq.transposons.unpair.sam $i.unpair.uniq.bed > $i.unpair.uniq.transposons.bed
+cp $i.unpair.uniq.transposons.bed $i.unpair.uniq.transposons.filtered.bed
+
+
+#Prepare for insertion breakpoints identification
+awk -F "\t" -v sample=$i '{OFS="\t"; print $1,$2,$3,sample,$5,$6}' $i.unpair.uniq.transposons.filtered.bed >> tmp
+perl $BINDIR/mergeTagsWithoutGap.pl tmp > $i.uniq.transposons.filtered.woGap.bed
+perl $BINDIR/mergeTagsWithGap.pl $i.uniq.transposons.filtered.woGap.bed $INSERT > $i.uniq.transposons.filtered.wGap.bed
+rm tmp
+perl $BINDIR/get_class.pl $i.uniq.transposons.filtered.wGap.bed $i > $i.uniq.transposons.filtered.wGap.class.bed
+perl $BINDIR/make.bp.bed.pl $i.uniq.transposons.filtered.wGap.class.bed $ANNO $FAMI
+
+#rm $i.unpair.sam $i.unpair.uniq.bed $i.unpair.uniq.?.fastq $i.unpair.uniq.?.sai 
+rm $i.unpair.uniq.transposons.sam $i.unpair.uniq.transposons.unpair.sam $i.uniq.transposons.filtered.woGap.bed $i.uniq.transposons.filtered.wGap.bed
+
+
+#Detect insertion breakpoints using soft-clipping information
+perl $BINDIR/pickClippedFastq.pl $i $te
+perl $BINDIR/refine_breakpoint.in.pl
+
+
+#Estimate insertion frequencies
+perl $BINDIR/pickOverlapPair.in.pl $i.insertion.refined.bp $INSERT > $i.insertion.refined.bp.summary
+
+
+################################
+##End of processing insertions##
+################################
+