Mercurial > repos > iuc > te_finder

annotate TEfinder @ 0:838fb3a1678f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
author iuc
date Mon, 08 Aug 2022 19:41:18 +0000
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838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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1 #!/usr/bin/env bash
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
iuc
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2
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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3 ##
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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4 ##
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5 ## Authors: Vista Sohrab & Dilay Hazal Ayhan
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6 ## Date: January 15, 2021
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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7 ## Description: TEfinder uses discordant reads to detect novel transposable element insertion events in short read paired-end sample sequencing data.
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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8 ## Software dependencies include bedtools 2.28.0 or later, samtools 1.3 or later, picard 2.0.1 or later
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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9 ## Required inputs include sample alignment file (.bam|.sam), reference genome FASTA (.fa), reference TE annotation in GFF/GTF or GFF3 (.gff|.gtf), and TEs of interest (.txt)
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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10 ##
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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11 ## University of Massachusetts Amherst
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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12 ##
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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13 ##
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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14 ##
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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15 ##
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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17 set -e
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19 margs=4
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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21 # Functions
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22 function example {
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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23 echo -e "example: TEfinder -alignment sample.bam -fa reference.fa -gtf TEs.gtf -te List_of_TEs.txt"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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24 }
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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26 function help {
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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27 echo -e "REQUIRED:"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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28 echo -e " -alignment, --alignmentFile STR sample reads aligned to reference genome (BAM/SAM file)"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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29 echo -e " -fa, --FastaFile STR reference genome FASTA index (FA file)"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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30 echo -e " -gtf, --TransposonsInGenome STR reference genome TE annotation (GFF2/GTF file)"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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31 echo -e " -te, --TransposonsToSearch STR TE names (single column text file)\n"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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32 echo -e "OPTIONAL:"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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33 echo -e " -bamo, --DiscordantReads STR BAM output\n"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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34 echo -e " -bedo, --bTEinsertions STR TEinsertions BED output\n"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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35 echo -e " -gtfo, --gTEinsertions STR TEinsertions GTF output\n"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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36 echo -e " -fis, --FragmentInsertSize INT short-read sequencing fragment insert size [400]"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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37 echo -e " -picard, --pathToPicardjar STR path to picard tools .jar file [picard.jar]"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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38 echo -e " -md, --MaxDistanceForMerge INT maximum distance between reads for bedtools merge [150]"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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39 echo -e " -k, --MaxTSDLength INT maximum TE target site duplication (TSD) length [20]"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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40 echo -e " -maxHeapMem, --MaxHeapMemory INT java maximum heap memory allocation for picard in Mb [2000]"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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41 echo -e " -workingdir, --WorkingDirectory STR working directory name [TEfinder_<Date>]"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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42 echo -e " -out, --OutputFormat STR output format as GTF [BED]"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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43 echo -e " -outname, --OutputName STR output name prefix added to file names [null]"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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44 echo -e " -threads, --Threads INT number of threads for samtools multi-threading [1]"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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45 echo -e " -intermed --IntermediateFiles STR keep intermediate files created by pipeline [no]"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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46 echo -e " -h, --help prints help\n"
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47 example
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48 }
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49
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50 # check if mandatory args are empty
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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51 function margs_check {
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52 if [ $# -lt $margs ]; then
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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53 echo -e "One or more required parameters are missing."
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54 example
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55 exit 1 # error
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56 fi
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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57 }
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58
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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59 # main workflow
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60 #### : comment out
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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61 function pipeline() {
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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62 mkdir ${workingdir}/${line}
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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63 currdir=${workingdir}/${line}
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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64 echo -e $(date) " Transposon analysis for "${line}" has started\n"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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65
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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66 grep -P '[^(\w|\d|\-|\_|\#|\.)]'${line}'[^(\w|\d|\-|\_|\#|\.)]' $gtf > ${currdir}/${line}_TE.gff
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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67 echo -e $(date) " Individual TE GFF has been created for "${line}"\n" ####
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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68
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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69 bedtools intersect -abam ${workingdir}/${outname}Alignments.bam -b ${currdir}/${line}_TE.gff -wa > ${currdir}/${line}_MappedReadsToTE.bam
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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70 echo -e $(date) " Mapped reads to TE via bedtools intersect has been completed for "${line}"\n" ####
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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71 samtools view -@ $threads ${currdir}/${line}_MappedReadsToTE.bam | \
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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72 awk -v Ins=`expr $fis \* 10` '{if (($7 != "=") || ($9 > Ins) || ($9 < -Ins)) print $1}' > ${currdir}/${line}_ReadID.txt
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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73 echo -e $(date) " Identifying discordant read IDs has been completed for "${line}"\n" ####
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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74
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75 # if discordant readID file exists, then continue with remainder of TE analysis
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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76 if [[ -s ${currdir}/${line}_ReadID.txt ]]
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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77 then
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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78 #java $maxHeapMem -jar $picard FilterSamReads I=${workingdir}/${outname}Alignments.bam O=${currdir}/${line}_DiscordantPairs.bam READ_LIST_FILE=${currdir}/${line}_ReadID.txt FILTER=includeReadList WRITE_READS_FILES=false
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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79 $picard $maxHeapMem FilterSamReads -I ${workingdir}/${outname}Alignments.bam -O ${currdir}/${line}_DiscordantPairs.bam -READ_LIST_FILE ${currdir}/${line}_ReadID.txt -FILTER includeReadList -WRITE_READS_FILES false &>/dev/null
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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80 echo -e $(date) " Filtering original alignment based on discordant reads IDs is complete for "${line}"\n" ####
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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81
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82 bedtools merge -d $md -S + -c 1 -o count -i ${currdir}/${line}_DiscordantPairs.bam | \
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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83 awk '{if ($4 > 3) print $0}' > ${currdir}/${line}_plusCluster.bed
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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84 echo -e $(date) " Primary reads from the + strand have been merged if read count greater than 3 for "${line}"\n" ####
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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85
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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86 bedtools merge -d $md -S - -c 1 -o count -i ${currdir}/${line}_DiscordantPairs.bam | \
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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87 awk '{if ($4 > 3) print $0}' > ${currdir}/${line}_minusCluster.bed
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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88 echo -e $(date) " Primary reads from the - strand have been merged if read count greater than 3 for "${line}"\n" ####
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89
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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90 # filtering edges piped into bedtools merge (keeping read counts greater than 3 in the line above)
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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91 ## find the closest minus strand to the plus strand in the cluster
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92 ## filter by the distance between the plus and minus clusters - only retain pairs if reads are 0-100 bases away
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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93 ## if plus strand start is less than minus strand start and plus strand end is less than minus strand end then in proper orientation
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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94 bedtools closest -d -g ${workingdir}/reference.fa.fai -t first -a ${currdir}/${line}_plusCluster.bed -b ${currdir}/${line}_minusCluster.bed | \
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95 awk -v TSD=$k '{if ($9 <= TSD && $9 >= 0) print $0}' | \
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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96 awk '{if ($2 < $6 && $3 < $7) print $0}' > ${currdir}/${line}_plusminus.bed
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97 echo -e $(date) " Filtration of clusters in proper orientation using bedtools closest has been completed for "${line}"\n" ####
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98
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99 # if plus strand end is greater than minus strand start, then report the pair
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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100 awk '{if ($3 > $6) print $1"\t"$6"\t"$3"\t"$0}' ${currdir}/${line}_plusminus.bed > ${currdir}/${line}_plusminus_1.bed
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101 echo -e $(date) " Overlapping reads TE insertions reported for "${line}"\n" ####
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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102
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103 #if plus strand end is less than or equal to minus strand start and the region in between is less than a user-defined value k, report the pair
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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104 awk -v TSD=$k '{if ($3 <= $6 && $6 - $3 < TSD) print $1"\t"$3 - 1"\t"$6 + 1"\t"$0}' ${currdir}/${line}_plusminus.bed > \
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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105 ${currdir}/${line}_plusminus_2.bed
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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106 echo -e $(date) " Non-overlapping reads TE insertions reported for "${line}"\n" ####
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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107
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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108 #combine reported TE insertions
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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109 cat ${currdir}/${line}_plusminus_1.bed ${currdir}/${line}_plusminus_2.bed | \
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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110 awk -v TEname=$line '{$0=TEname"\t"$0}1' | sort -k 1 | sort -k 2 > \
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111 ${currdir}/${line}_insertionRegion.txt
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112
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113
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114 cat ${currdir}/${line}_insertionRegion.txt >> ${workingdir}/insertions.txt
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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115 echo -e $(date) " TE insertions for "${line}" have been reported.\n" ####
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116
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117
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118 echo -e $(date) " Transposon named "${line}" is processed.\n"
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119 else
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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120 echo -e $(date) " Transposon named "${line}" is processed. No discordant reads found.\n"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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121 rm -r ${currdir}
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122 fi
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123 }
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124
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125 # functions end
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126
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127 # get arguments
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128 fa=
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129 alignment=
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130 gtf=
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131 te=
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132 out=
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133 intermed=
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134 bamo="DiscordantReads.bam"
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135 bedo="TEinsertions.bed"
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136 gtfo="TEinsertions.gtf"
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137 outname=""
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138 fis=400
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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139 picard="picard"
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140 maxHeapMem=-Xmx2000m
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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141 md=150
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142 k=20
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143 d=$(date +%Y%m%d%H%M%S)
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144 # workingdir=TEfinder_${d}
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145 workingdir="TEfinder"
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146 threads=1
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147
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148 while [ "$1" != "" ];
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149 do
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150 case $1 in
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151 -fa | --FastaFile )
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152 shift
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153 fa=$1 ;;
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154 -alignment | --alignmentFile )
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155 shift
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156 alignment=$1 ;;
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157 -gtf | --TransposonsInGenome )
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158 shift
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159 gtf=$1 ;;
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160 -te | --TransposonsToSearch )
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161 shift
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162 te=$1 ;;
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163 -fis | --FragmentInsertSize )
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164 shift
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165 fis=$1 ;;
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166 -picard | --pathToPicardjar )
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167 shift
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168 picard=$1 ;;
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169 -md | --MaxDistanceForMerge )
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170 shift
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171 md=$1 ;;
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172 -k | --MaxTSDLength )
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173 shift
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174 k=$1 ;;
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175 -bamo | --DiscordantReads )
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176 shift
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177 bamo=$1 ;;
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178 -bedo | --bTEinsertions )
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179 shift
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180 bedo=$1 ;;
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181 -gtfo | --gTEinsertions )
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182 shift
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183 gtfo=$1 ;;
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184 -maxHeapMem | --MaxHeapMemory )
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185 shift
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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186 maxHeapMem="-Xmx"$1"m" ;;
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187 -workingdir | --WorkingDirectory )
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188 shift
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189 workingdir=$1 ;;
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190 -out | --OutputFormat )
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191 shift
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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192 out=$1 ;;
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193 -outname | --OutputName )
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194 shift
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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195 outname=$1 ;;
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196 -threads | --Threads )
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197 shift
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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198 threads=$1 ;;
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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199 -intermed | --IntermediateFiles )
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200 shift
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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201 intermed=$1 ;;
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202 -h | --help )
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203 help
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204 exit;;
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205 *) # error
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206 echo "TEfinder: illegal option $1"
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207 example
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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208 exit 1 ;;
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209 esac
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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210 shift
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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211 done
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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212 margs_check $fa $alignment $gtf $te
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213
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214 # main
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215
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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216 mkdir ${workingdir}
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217
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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218 # remove empty lines from user provided TE list if present
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219 sed '/^$/d' $te > ${workingdir}"/userTE_noEmptyLines.txt"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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220
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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221 # create output file
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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222 printf "%s\t" "track name=TEfinder" "type=bedDetail" "description=FR:forward read, RR:reverse read, InsRegion:insertion region start and end positions, FILTER:comma separated filters" > ${workingdir}/${outname}TEinsertions.bed
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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223 printf "\n" >> ${workingdir}/${outname}TEinsertions.bed
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224
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225 # create fasta index (fai) file
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226 cp $fa ${workingdir}/reference.fa
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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227 samtools faidx ${workingdir}/reference.fa
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228
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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229 # sort alignment input
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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230 samtools sort -@ $threads -o ${workingdir}/alignmentInput.sorted.bam ${alignment}
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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231 echo -e $(date) " Alignment file sorted successfully.\n"
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232
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233 # remove secondary and supplementary alignments from sorted bam
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234 samtools view -F 2304 -@ $threads -o ${workingdir}/${outname}Alignments.bam ${workingdir}/alignmentInput.sorted.bam
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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235 echo -e $(date) " Alignments are filtered - secondary and supplementary alignments have been removed. \n"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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236
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237 # run pipeline for each TE
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238 while IFS="" read -r line || [ -n "$line" ]
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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239 do
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240 pipeline &
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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241 done < ${workingdir}/userTE_noEmptyLines.txt
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242 wait
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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243 echo -e $(date) " All transposons are processed. Finalizing...\n"
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244
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245 # combine discordant bam files
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246 samtools merge -@ $threads -r ${workingdir}/${outname}DiscordantReads.bam ${workingdir}/*/*_DiscordantPairs.bam
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247 echo -e $(date) " BAM Output: Discordant pair alignment file is now available.\n"
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248 # Sorting by position
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249 samtools sort -@ $threads ${workingdir}/${outname}DiscordantReads.bam | samtools view -h -o ${workingdir}/${outname}DiscordantReads.sam
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250 grep -v '^@PG' ${workingdir}/${outname}DiscordantReads.sam > ${workingdir}/${outname}DiscordantReadsNoPG.sam
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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251 rm ${workingdir}/${outname}DiscordantReads.sam
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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252 samtools view -hb -x "PG" --no-PG --remove-flags "PG" -O BAM ${workingdir}/${outname}DiscordantReadsNoPG.sam -o ${bamo}
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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253 rm ${workingdir}/${outname}DiscordantReadsNoPG.sam
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254
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255 # update output BED file with TEfinder results: organize the starting file
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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256 awk '{print $2"\t"$3"\t"$4"\t"$1"\t"$8+$12"\t.\tFR="$8";RR="$12";InsRegion="$6"-"$11";FILTER="}' ${workingdir}/insertions.txt > ${workingdir}/TEinsertions_putative.bed
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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257 # find the entries in repeat regions for filtering
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258 bedtools intersect -wa -u -a ${workingdir}/TEinsertions_putative.bed -b $gtf > ${workingdir}/TEinsertions_putative_inrepeat.bed
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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259 # filtering process
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260 while IFS="" read -r line || [ -n "$line" ]
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261 do
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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262 #located in repeat region
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263 if (grep -Fxq "$line" "${workingdir}/TEinsertions_putative_inrepeat.bed")
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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264 then
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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265 line=$line"in_repeat,"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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266 fi
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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267
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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268 #weak evidence
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269 readc=$(echo $line | awk '{print $5}')
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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270 if (( $readc < 10 ))
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271 then
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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272 line=$line"weak_evidence,"
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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273 fi
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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274
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275 #strand-biased
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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276 FR=$(echo $line | grep -o 'FR=[[:digit:]]*' | cut -f2 -d'=')
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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277 RR=$(echo $line | grep -o 'RR=[[:digit:]]*' | cut -f2 -d'=')
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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278 var1=$(echo 'e(l('$FR')*1.25)' | bc -l)
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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279 var2=$(echo 'e(l('$FR')*0.8)' | bc -l)
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280
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281 if [ $(echo "$RR > $var1" | bc) -eq 1 ] || [ $(echo "$RR < $var2" | bc) -eq 1 ]
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282 then
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283 line=$line"strand_bias,"
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284 fi
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285
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286 #pass
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287 lastchar=${line: -1}
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288 if [ $lastchar == "," ]
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289 then
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290 line=${line::${#line}-1}
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291 else
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292 line=$line"PASS"
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293 fi
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294
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295 #write to final output
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296 printf "%s\n" "$line" >> ${workingdir}/${outname}TEinsertions.bed
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297
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298 done < ${workingdir}/TEinsertions_putative.bed
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299 wait
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300 echo -e $(date) " BED Output: TEfinder output BED file is now available.\n"
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301 # Sorting
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302 # cp ${workingdir}/${outname}TEinsertions.bed ${outo}
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303 bedtools sort -chrThenSizeA -i ${workingdir}/${outname}TEinsertions.bed > ${bedo}
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304 # cat ${bedo}
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305
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306 # gtf option - create output GTF files with TEfinder results
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307 if [ ! -z "$out" ]
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308 then
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309 awk 'FNR > 1 {print $1"\tTEfinder\tTIP\t"$2 + 1"\t"$3"\t"$5"\t.\t.\tte_name \""$4"\"; tags \""$7"\""}' ${workingdir}/${outname}TEinsertions.bed > ${workingdir}/${outname}TEinsertions.gtf
838fb3a1678f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ commit d86db11ee07ccc379667797b9124185ddfde1948
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310 bedtools sort -chrThenSizeA -i ${workingdir}/${outname}TEinsertions.gtf > ${gtfo}
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311 # awk 'FNR > 1 {print $1"\tTEfinder\tTIP\t"$2 + 1"\t"$3"\t"$5"\t.\t.\tte_name \""$4"\"; tags \""$7"\""}' ${bedo} > ${gtfo}
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312 # Sorting
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313 # cp ${workingdir}/${outname}TEinsertions.gtf ${gtfo}
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314 echo -e "\n\n"
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315 # cat ${gtfo}
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316 # bedtools sort -chrThenSizeA -i ${workingdir}/${outname}TEinsertions.gtf > ${gtfo}
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317 echo -e $(date) " GTF Output: TEfinder output GTF file is now available.\n"
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318 fi
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319
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320 # clean working directory
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321 if [ -z "$intermed" ]
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322 then
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323 rm ${workingdir}/TEinsertions_putative.bed ${workingdir}/TEinsertions_putative_inrepeat.bed ${workingdir}/reference.fa ${workingdir}/reference.fa.fai \
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324 ${workingdir}/alignmentInput.sorted.bam ${workingdir}/insertions.txt ${workingdir}/${outname}Alignments.bam ${workingdir}/userTE_noEmptyLines.txt
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325 rm -r ${workingdir}/*/
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326 fi
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327
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328 if [ `wc -l <${workingdir}/${outname}TEinsertions.bed` -le "1" ]
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329 then
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330 echo -e $(date) " Error: TEfinder run unsuccessful."
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331 else
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332 echo -e $(date) " TE insertion output files have been created. TEfinder completed successfully."
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333 fi