annotate scripts/TEMP_Insertion.sh @ 12:ca36262102d8 draft

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author portiahollyoak
date Fri, 29 Apr 2016 05:47:54 -0400
parents 28d1a6f8143f
children e7d3dc3e0ec9
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1 #!/bin/bash -x
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2 # TEMP (Transposable Element Movement present in a Population)
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3 # 2013-06-14
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4 # Jiali Zhuang(jiali.zhuang@umassmed.edu)
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5 # Zhiping Weng Lab
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6 # Programs in Bioinformatics and Integrative Biology
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7 # University of Massachusetts Medical School
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9 #usage function
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10 usage() {
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11 echo -en "\e[1;36m"
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12 cat <<EOF
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13
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14 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
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16 TEMP is a software package for detecting transposable elements (TEs)
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17 insertions and excisions from pooled high-throughput sequencing data.
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18 Please send questions, suggestions and bug reports to:
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19 jiali.zhuang@umassmed.edu
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21 Options:
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22 -i Input file in bam format with full path. Please sort and index the file before calling this program.
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23 Sorting and indexing can be done by 'samtools sort' and 'samtools index'
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24 -s Directory where all the scripts are
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25 -o Path to output directory. Default is current directory
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26 -r Transposon sequence database in fasta format with full path
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27 -t Annotated TEs in BED6 format with full path. Detected insertions that overlap with annoated TEs will be filtered.
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28 -u TE families annotations. If supplied detected insertions overlap with annotated TE of the same family will be filtered. Only use with -t.
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29 -m Number of mismatch allowed when mapping to TE concensus sequences. Default is 3
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30 -x The minimum score difference between the best hit and the second best hit for considering a read as uniquely mapped. For BWA mem.
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31 -f An integer specifying the length of the fragments (inserts) of the library. Default is 500
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32 -c An integer specifying the number of CPUs used. Default is 8
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33 -h Show help message
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34
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35 EOF
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36 echo -en "\e[0m"
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37 }
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38
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39 # taking options
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40 while getopts "hi:c:f:m:o:r:s:t:u:x:" OPTION
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41 do
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42 case $OPTION in
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43 h)
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44 usage && exit 1
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45 ;;
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46 i)
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47 BAM=$OPTARG
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48 ;;
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49 f)
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50 INSERT=$OPTARG
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51 ;;
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52 m)
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53 MM=$OPTARG
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54 ;;
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55 o)
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56 OUTDIR=$OPTARG
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57 ;;
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58 c)
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59 CPU=$OPTARG
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60 ;;
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61 s)
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62 BINDIR=$OPTARG
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63 ;;
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64 r)
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65 TESEQ=$OPTARG
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66 ;;
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67 t)
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68 ANNO=$OPTARG
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69 ;;
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70 u)
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71 FAMI=$OPTARG
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72 ;;
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73 x)
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74 SCORE=$OPTARG
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75 ;;
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76 ?)
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77 usage && exit 1
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78 ;;
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79 esac
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80 done
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81
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82 if [[ -z $BAM ]] || [[ -z $BINDIR ]] || [[ -z $TESEQ ]]
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83 then
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84 usage && exit 1
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85 fi
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86 [ ! -z "${CPU##*[!0-9]*}" ] || CPU=8
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87 [ ! -z "${INSERT##*[!0-9]*}" ] || INSERT=500
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88 [ ! -z "${MM##*[!0-9]*}" ] || MM=3
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89 [ ! -z "${SCORE##*[!0-9]*}" ] || SCORE=0
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90 [ ! -z $OUTDIR ] || OUTDIR=$PWD
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91
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92 mkdir -p "${OUTDIR}" || echo -e "\e[1;31mWarning: Cannot create directory ${OUTDIR}. Using the direcory of input fastq file\e[0m"
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93 cd ${OUTDIR} || echo -e "\e[1;31mError: Cannot access directory ${OUTDIR}... Exiting...\e[0m" || exit 1
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94 touch ${OUTDIR}/.writting_permission && rm -rf ${OUTDIR}/.writting_permission || echo -e "\e[1;31mError: Cannot write in directory ${OUTDIR}... Exiting...\e[0m" || exit 1
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95
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96 function checkExist {
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97 echo -ne "\e[1;32m\"${1}\" is using: \e[0m" && which "$1"
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98 [[ $? != 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
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99 }
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100 echo -e "\e[1;35mTesting required softwares/scripts:\e[0m"
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101 checkExist "echo"
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102 checkExist "rm"
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103 checkExist "mkdir"
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104 checkExist "date"
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105 checkExist "mv"
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106 checkExist "sort"
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107 checkExist "touch"
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108 checkExist "awk"
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109 checkExist "grep"
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110 checkExist "bwa"
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111 checkExist "samtools"
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112 echo -e "\e[1;35mDone with testing required softwares/scripts, starting pipeline...\e[0m"
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113
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114 cp $TESEQ ./
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115 name=`basename $BAM`
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116 te=`basename $TESEQ`
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117 i=${name/.sorted.bam/}
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118 echo $name
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119 echo $i
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120 if [[ ! -s $name ]]
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121 then
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122 cp $BAM ./
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123 fi
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124 if [[ ! -s $name.bai ]]
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125 then cp $BAM.bai ./
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126 fi
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127
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128 # Get the mate seq of the uniq-unpaired reads
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129 samtools view -XF 0x2 $name > $i.unpair.sam
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130 if [[ $SCORE -eq 0 ]]
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131 then
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132 perl $BINDIR/pickUniqPairFastq.pl $i.unpair.sam $i.unpair.uniq
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133 perl $BINDIR/pickUniqPos.pl $i.unpair.sam > $i.unpair.uniq.bed
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134 else
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135 perl $BINDIR/pickUniqPairFastq_MEM.pl $i.unpair.sam $i.unpair.uniq $SCORE
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136 perl $BINDIR/pickUniqPos_MEM.pl $i.unpair.sam $SCORE > $i.unpair.uniq.bed
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137 fi
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138
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139 # Map to transposons
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140 bwa index -a is $te
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141 bwa aln -t $CPU -n $MM -l 100 -R 1000 $te $i.unpair.uniq.1.fastq > $i.unpair.uniq.1.sai
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142 bwa aln -t $CPU -n $MM -l 100 -R 1000 $te $i.unpair.uniq.2.fastq > $i.unpair.uniq.2.sai
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143 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
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144
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145
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146 #Summary
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147 samtools view -hSXF 0x2 $i.unpair.uniq.transposons.sam > $i.unpair.uniq.transposons.unpair.sam
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148 perl $BINDIR/pickUniqMate.pl $i.unpair.uniq.transposons.unpair.sam $i.unpair.uniq.bed > $i.unpair.uniq.transposons.bed
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149 cp $i.unpair.uniq.transposons.bed $i.unpair.uniq.transposons.filtered.bed
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150
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151
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152 #Prepare for insertion breakpoints identification
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153 awk -F "\t" -v sample=$i '{OFS="\t"; print $1,$2,$3,sample,$5,$6}' $i.unpair.uniq.transposons.filtered.bed >> tmp
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154 perl $BINDIR/mergeTagsWithoutGap.pl tmp > $i.uniq.transposons.filtered.woGap.bed
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155 perl $BINDIR/mergeTagsWithGap.pl $i.uniq.transposons.filtered.woGap.bed $INSERT > $i.uniq.transposons.filtered.wGap.bed
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156 rm tmp
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157 perl $BINDIR/get_class.pl $i.uniq.transposons.filtered.wGap.bed $i > $i.uniq.transposons.filtered.wGap.class.bed
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158 perl $BINDIR/make.bp.bed.pl $i.uniq.transposons.filtered.wGap.class.bed $ANNO $FAMI
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159
12
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160 rm $i.unpair.sam $i.unpair.uniq.bed $i.unpair.uniq.?.fastq $i.unpair.uniq.?.sai
0
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161 rm $i.unpair.uniq.transposons.sam $i.unpair.uniq.transposons.unpair.sam $i.uniq.transposons.filtered.woGap.bed $i.uniq.transposons.filtered.wGap.bed
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162
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163
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164 #Detect insertion breakpoints using soft-clipping information
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165 perl $BINDIR/pickClippedFastq.pl $i $te
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166 perl $BINDIR/refine_breakpoint.in.pl
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167
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168
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169 #Estimate insertion frequencies
12
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170 #if [[ $SCORE -eq 0 ]]
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171 #then
0
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172 perl $BINDIR/pickOverlapPair.in.pl $i.insertion.refined.bp $INSERT > $i.insertion.refined.bp.summary
12
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173 #else
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174 # perl $BINDIR/pickOverlapPair.ex_MEM.pl $i.insertion.refined.bp $INSERT $SCORE > $i.insertion.refined.bp.summary
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175 #fi
0
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176
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177 ################################
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178 ##End of processing insertions##
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179 ################################
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180