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1 #!/usr/bin/perl -w
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2 #Filename:
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3 #Author: Tian Dongmei
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4 #Email: tiandm@big.ac.cn
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5 #Date: 2013/7/19
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6 #Modified:
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7 #Description:
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8 my $version=1.00;
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9
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10 use strict;
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11 use Getopt::Long;
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12
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13 my %opts;
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14 GetOptions(\%opts,"i=s","g=s","index:s","v:i","p:i","r:s","o=s","time:s","h");
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15 if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
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16 &usage;
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17 }
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18
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19 my $filein=$opts{'i'};
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20 my $fileout=$opts{'o'};
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21 unless ($fileout=~/\/$/) {$fileout.="/";}
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22 my $genome=$opts{'g'};
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23 my $mis=defined $opts{'v'}? $opts{'v'} : 0;
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24 my $hits=defined $opts{'r'}? $opts{'r'} : 25;
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25 my $index=defined $opts{'index'} ? $opts{'index'} : "";
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26 my $threads=defined $opts{'p'} ? $opts{'p'} : 1;
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27
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28
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29 my $time=&Time();
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30 if (defined $opts{'time'}) {
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31 $time=$opts{'time'};
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32 }
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33
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34 my $mapdir=$fileout."/genome_match_".$time;
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35 if(not -d $mapdir){
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36 mkdir $mapdir;
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37 }
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38 chdir $mapdir;
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39 ###check genome index
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40 if (-s $index.".1.ebwt") {
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41 }else{
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42 `bowtie-build $genome $genome`;
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43 $index="$genome";
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44 }
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45
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46 ### genome mapping
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47 `bowtie -v $mis -f -p $threads -m $hits -a --best --strata $index $filein --al genome_mapped.fa --un genome_not_mapped.fa --max genome_mapped_Mlimit.fa > genome_mapped.bwt`;
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48
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49 #`convert_bowtie_to_blast.pl genome_mapped.bwt genome_mapped.fa $genome > genome_mapped.bst`;
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50
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51 sub Time{
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52 my $time=time();
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53 my ($sec,$min,$hour,$day,$month,$year) = (localtime($time))[0,1,2,3,4,5,6];
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54 $month++;
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55 $year+=1900;
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56 if (length($sec) == 1) {$sec = "0"."$sec";}
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57 if (length($min) == 1) {$min = "0"."$min";}
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58 if (length($hour) == 1) {$hour = "0"."$hour";}
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59 if (length($day) == 1) {$day = "0"."$day";}
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60 if (length($month) == 1) {$month = "0"."$month";}
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61 #print "$year-$month-$day $hour:$min:$sec\n";
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62 return("$year-$month-$day-$hour-$min-$sec");
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63 }
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64
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65 sub usage{
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66 print <<"USAGE";
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67 Version $version
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68 Usage:
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69 $0 -i -o
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70 options:
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71 -i input file# input reads fasta/fastq file
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72 -g input file# genome file
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73 -index file-prefix #(must be indexed by bowtie-build) The parameter
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74 string must be the prefix of the bowtie index. For instance, if
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75 the first indexed file is called 'h_sapiens_37_asm.1.ebwt' then
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76 the prefix is 'h_sapiens_37_asm'.##can be null
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77 -v <int> report end-to-end hits w/ <=v mismatches; ignore qualities,default 0;
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78
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79 -p/--threads <int> number of alignment threads to launch (default: 1)
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80
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81 -r int a read is allowed to map up to this number of positions in the genome
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82 default is 25
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83
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84 -o output directory
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85
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86 -h help
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87 USAGE
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88 exit(1);
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89 }
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90
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