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comparison scripts/TEMP_Absence.sh @ 12:ca36262102d8 draft

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planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
author portiahollyoak
date Fri, 29 Apr 2016 05:47:54 -0400
parents 28d1a6f8143f
children 9672fe07a232
comparison
equal deleted inserted replaced
11:e19d9742c99b 12:ca36262102d8
24 -s Directory where all the scripts are 24 -s Directory where all the scripts are
25 -o Path to output directory. Default is current directory 25 -o Path to output directory. Default is current directory
26 -r Annotated transposon positions in the genome (e.g., repeakMask) in bed6 format with full path 26 -r Annotated transposon positions in the genome (e.g., repeakMask) in bed6 format with full path
27 -t 2bit file for the reference genome (can be downloaded from UCSC Genome Browser) 27 -t 2bit file for the reference genome (can be downloaded from UCSC Genome Browser)
28 -f An integer specifying the length of the fragments (inserts) of the library. Default is 500 28 -f An integer specifying the length of the fragments (inserts) of the library. Default is 500
29 -c An integer specifying the number of CUPs used. Default is 4 29 -x The minimum score difference between the best hit and the second best hit for considering a read as uniquely mapped. For BWA MEM.
30 -c An integer specifying the number of CPUs used. Default is 4
30 -h Show help message 31 -h Show help message
31 32
32 EOF 33 EOF
33 echo -en "\e[0m" 34 echo -en "\e[0m"
34 } 35 }
35 36
36 # taking options 37 # taking options
37 while getopts "hi:c:f:o:r:s:t:" OPTION 38 while getopts "hi:c:f:o:r:s:t:x:" OPTION
38 do 39 do
39 case $OPTION in 40 case $OPTION in
40 h) 41 h)
41 usage && exit 1 42 usage && exit 1
42 ;; 43 ;;
59 TEBED=$OPTARG 60 TEBED=$OPTARG
60 ;; 61 ;;
61 t) 62 t)
62 REF=$OPTARG 63 REF=$OPTARG
63 ;; 64 ;;
65 x)
66 SCORE=$OPTARG
67 ;;
64 ?) 68 ?)
65 usage && exit 1 69 usage && exit 1
66 ;; 70 ;;
67 esac 71 esac
68 done 72 done
71 then 75 then
72 usage && exit 1 76 usage && exit 1
73 fi 77 fi
74 [ ! -z "${CPU##*[!0-9]*}" ] || CPU=4 78 [ ! -z "${CPU##*[!0-9]*}" ] || CPU=4
75 [ ! -z "${INSERT##*[!0-9]*}" ] || INSERT=500 79 [ ! -z "${INSERT##*[!0-9]*}" ] || INSERT=500
80 [ ! -z "${SCORE##*[!0-9]*}" ] || SCORE=0
76 [ ! -z $OUTDIR ] || OUTDIR=$PWD 81 [ ! -z $OUTDIR ] || OUTDIR=$PWD
77 82
78 mkdir -p "${OUTDIR}" || echo -e "\e[1;31mWarning: Cannot create directory ${OUTDIR}. Using the direcory of input fastq file\e[0m" 83 mkdir -p "${OUTDIR}" || echo -e "\e[1;31mWarning: Cannot create directory ${OUTDIR}. Using the direcory of input fastq file\e[0m"
79 cd ${OUTDIR} || echo -e "\e[1;31mError: Cannot access directory ${OUTDIR}... Exiting...\e[0m" || exit 1 84 cd ${OUTDIR} || echo -e "\e[1;31mError: Cannot access directory ${OUTDIR}... Exiting...\e[0m" || exit 1
80 touch ${OUTDIR}/.writting_permission && rm -rf ${OUTDIR}/.writting_permission || echo -e "\e[1;31mError: Cannot write in directory ${OUTDIR}... Exiting...\e[0m" || exit 1 85 touch ${OUTDIR}/.writting_permission && rm -rf ${OUTDIR}/.writting_permission || echo -e "\e[1;31mError: Cannot write in directory ${OUTDIR}... Exiting...\e[0m" || exit 1
91 checkExist "mv" 96 checkExist "mv"
92 checkExist "sort" 97 checkExist "sort"
93 checkExist "touch" 98 checkExist "touch"
94 checkExist "awk" 99 checkExist "awk"
95 checkExist "grep" 100 checkExist "grep"
101 checkExist "twoBitToFa"
96 checkExist "bwa" 102 checkExist "bwa"
97 checkExist "samtools" 103 checkExist "samtools"
98 echo -e "\e[1;35mDone with testing required softwares/scripts, starting pipeline...\e[0m" 104 echo -e "\e[1;35mDone with testing required softwares/scripts, starting pipeline...\e[0m"
99 105
100 name=`basename $BAM` 106 name=`basename $BAM`
132 # Identify breakpoints using soft-clipping information 138 # Identify breakpoints using soft-clipping information
133 perl $BINDIR/pickSoftClipping.over.pl $i.excision.cluster.rpmk $REF > $i.excision.cluster.rpmk.sfcp 139 perl $BINDIR/pickSoftClipping.over.pl $i.excision.cluster.rpmk $REF > $i.excision.cluster.rpmk.sfcp
134 perl $BINDIR/refine_breakpoint.ex.pl 140 perl $BINDIR/refine_breakpoint.ex.pl
135 141
136 # Estimate excision sites frequencies 142 # Estimate excision sites frequencies
137 perl $BINDIR/pickOverlapPair.ex.pl $i.excision.cluster.rpmk.refined.bp > $i.excision.cluster.rpmk.refined.bp.refsup 143 if [[ $SCORE -eq 0 ]]
144 then
145 perl $BINDIR/pickOverlapPair.ex.pl $i.excision.cluster.rpmk.refined.bp > $i.excision.cluster.rpmk.refined.bp.refsup
146 else
147 perl $BINDIR/pickOverlapPair.ex_MEM.pl $i.excision.cluster.rpmk.refined.bp $SCORE > $i.excision.cluster.rpmk.refined.bp.refsup
148 fi
149
138 perl $BINDIR/summarize_excision.pl 150 perl $BINDIR/summarize_excision.pl