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1 #!/usr/bin/perl
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2
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3
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4 use warnings;
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5 use strict;
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6 use Getopt::Std;
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7
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8 ######################################### USAGE ################################
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9
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10 my $usage=
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11 "$0 file_bowtie_result file_solexa_seq file_chromosome
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12
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13 This is a converter which changes Bowtie output into Blast format.
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14 The input includes three files: a Bowtie result file (default Bowtie
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15 output file), a fasta file consisting of small Reads and a chromosome
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16 fasta file. It outputs the alignments in blast_parsed format.
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17
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18 file_bowtie_result likes:
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19
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20 AtFlower100010_x2 + MIR319c 508 AAGGAGATTCTTTCAGTCCAG IIIIIIIIIIIIIIIIIIIII 0
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21 AtFlower1000188_x1 + MIR2933a 421 TCGGAGAGGAAATTCGTCGGCG IIIIIIIIIIIIIIIIIIIIII 0
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22
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23 file_solexa_seq likes:
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24
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25 >AtFlower100010_x2
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26 AAGGAGATTCTTTCAGTCCAG
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27
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28 file_chromosome contains chromosome seq in fasta format
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29
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30 ";
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31
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32
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33 ####################################### INPUT FILES ############################
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34
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35 my $file_bowtie_result=shift or die $usage;
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36 my $file_short_seq=shift or die $usage;
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37 my $file_chromosome_seq=shift or die $usage;
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38
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39
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40 ##################################### GLOBAL VARIBALES #########################
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41
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42 my %short_seq_length=();
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43 my %chromosome_length=();
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44
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45
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46 ######################################### MAIN #################################
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47
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48 #get the short sequence id and its length
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49 sequence_length($file_short_seq,\%short_seq_length);
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50
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51 #get the chromosome sequence id and its length
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52 sequence_length($file_chromosome_seq,\%chromosome_length);
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53
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54 #convert bowtie result format to blast format;
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55 change_format($file_bowtie_result);
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56
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57 exit;
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58
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59
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60 ##################################### SUBROUTINES ##############################
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61
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62 sub sequence_length{
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63 my ($file,$hash) = @_;
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64 my ($id, $desc, $sequence, $seq_length) = ();
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65
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66 open (FASTA, "<$file") or die "can not open $$file\n";
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67 while (<FASTA>)
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68 {
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69 chomp;
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70 if (/^>(\S+)(.*)/)
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71 {
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72 $id = $1;
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73 $desc = $2;
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74 $sequence = "";
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75 while (<FASTA>){
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76 chomp;
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77 if (/^>(\S+)(.*)/){
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78 $$hash{$id} = length $sequence;
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79 $id = $1;
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80 $desc = $2;
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81 $sequence = "";
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82 next;
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83 }
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84 $sequence .= $_;
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85 }
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86 }
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87 }
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88 $seq_length=length($sequence);
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89 $$hash{$id} = $seq_length;
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90 close FASTA;
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91 }
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92
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93
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94
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95
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96
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97 sub change_format{
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98 #Change Bowtie format into blast format
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99 my $file=shift @_;
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100 open(FILE,"<$file")||die"can not open the bowtie result file:$!\n";
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101 #open(BLASTOUT,">blastout")||die"can not create the blastout file:$!\n";
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102
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103 while(<FILE>){
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104 chomp;
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105 my @tmp=split("\t",$_);
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106 #Clean the reads ID
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107 my @tmp1=split(" ",$tmp[0]);
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108 print "$tmp1[0]"."\t"."$short_seq_length{$tmp1[0]}"."\t"."1".'..'."$short_seq_length{$tmp1[0]}"."\t"."$tmp[2]"."\t"."$chromosome_length{$tmp[2]}"."\t";
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109 if($tmp[1] eq "+"){
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110 my $seq_end=$tmp[3] + $short_seq_length{$tmp1[0]};
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111 my $seq_bg=$tmp[3] + 1;
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112 print "$seq_bg".'..'."$seq_end"."\t"."1e-04"."\t"."1.00"."\t"."42.1"."\t"."Plus / Plus"."\n";
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113 }
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114 if($tmp[1] eq "-"){
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115 my $seq_end=$chromosome_length{$tmp[2]} - $tmp[3];
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116 my $seq_bg=$seq_end - $short_seq_length{$tmp1[0]} + 1;
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117 print "$seq_bg".'..'."$seq_end"."\t"."1e-04"."\t"."1.00"."\t"."42.1"."\t"."Plus / Minus"."\n";
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118 }
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119 }
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120
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121 # close BLASTOUT;
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122
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123 }
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124
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125
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126
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