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1 package subgroups;
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2
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3 use strict;
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4 use warnings;
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5 use Exporter;
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6 our @ISA = qw( Exporter );
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7 our @EXPORT_OK = qw( &subgroups );
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8
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9 use POSIX;
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10 use FindBin;
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11 use lib $FindBin::Bin;
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12 use align qw ( get_hash_alignment );
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13
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14 sub subgroups
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15 {
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16 my ($fin, $dir, $mis, $mis_TE, $proc, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $exons, $TE, $min_si, $max_si, $min_pi, $max_pi, $report ) = @_;
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17 my (@files, $sum, $pie, $repar, %ismapped, %isjunk, %repartition, @junk_ref, @all_ref );
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18
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20
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19 srand();
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20 print $report "----------------------------\n";
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21 print $report "Create subgroups:\nfastq_in: $fin\ndirectory_out: $dir\nmismatches: $mis\nmismatches TE: $mis_TE\n";
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22
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23 mkdir $dir;
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24 $dir = $dir.'/' unless $dir =~ /(.*)\/$/;
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25
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26 my $accept_miRNas = $dir.'miRNAs.fastq';
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27 my $reject_miRNAs = $dir.'miRNAs_rejected.fastq';
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28 my $sam_miRNAs = $dir.'miRNAs.sam';
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29 my @tmp = get_hash_alignment($miRNAs, $mis, 1, 1, $accept_miRNas, $reject_miRNAs, $fin, $proc, 'miRNAs',$sam_miRNAs, $report);
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30 my $mi = $tmp[0];
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31 $repartition{'miRNAs'} = $mi;
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32
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33 my $sam = new String::Random;
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34 $sam = $sam->randpattern("CCcccccc");
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35 my $reject_rRNAs = $dir.'rRNAs_rejected.fastq';
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36 @tmp = get_hash_alignment($rRNAs, $mis, 0, 1, 'NA', $reject_rRNAs, $reject_miRNAs, $proc, 'rRNAs', $sam, $report);
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37 $repartition{'rRNAs'} = $tmp[0];
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38 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
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39
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40 $sam = new String::Random;
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41 $sam = $sam->randpattern("CCcccccc");
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42 my $reject_tRNAs = $dir.'tRNAs_rejected.fastq';
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43 @tmp = get_hash_alignment($tRNAs, $mis, 0, 1, 'NA', $reject_tRNAs, $reject_rRNAs, $proc, 'tRNAs', $sam, $report);
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44 $repartition{'tRNAs'} = $tmp[0];
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45 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
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46
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47 $sam = new String::Random;
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48 $sam = $sam->randpattern("CCcccccc");
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49 my $bonafide = $dir.'bonafide_reads.fastq';
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50 @tmp = get_hash_alignment($snRNAs, $mis, 0, 1, 'NA', $bonafide, $reject_tRNAs, $proc, 'snRNAs', $sam, $report);
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51 $repartition{'snRNAs'} = $tmp[0];
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52 my $bo = $tmp[1];
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53 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
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54
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55 my $sam_exons = $dir.'exons.sam';
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56 my $reject_exons = $dir.'rejected_exons.fastq';
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57 @tmp = get_hash_alignment($exons, $mis, 0, 1, 'NA', $reject_exons, $bonafide, $proc, 'exons', $sam_exons, $report, $dir.'exons.fai');
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58 $repartition{'exons'} = $tmp[0];
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59
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60
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61 my $sam_TEs = $dir.'TEs.sam';
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62 my $reject_TEs = $dir.'rejected.fastq';
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63 @tmp = get_hash_alignment($TE, $mis_TE, 0, 1, 'NA', $reject_TEs, $reject_exons, $proc, 'TEs', $sam_TEs, $report, $dir.'TEs.fai' );
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64 $repartition{'TEs'} = $tmp[0] ; $repartition{'others'} = $tmp[1];
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65 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
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66 unlink $reject_exons;
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67 unlink $reject_rRNAs;
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68 unlink $reject_miRNAs;
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69 unlink $reject_tRNAs;
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70
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71 #create repartition
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72 my $pi = fastqSubgroups($bonafide, $dir, $min_si, $max_si, $min_pi, $max_pi );
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73
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74 open (my $re, '>'.$dir.'repartition.txt') || die "cannot open $dir repartition.txt $!\n";
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75 print $re "type\tnumber\tpercentage\n";
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76 $sum += $_ foreach values %repartition;
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77 foreach my $k ( sort keys %repartition )
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78 {
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79 my $prct = 0;
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80 $prct = $repartition{$k} / $sum * 100 if $sum != 0;
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81 print $re "$k\t$repartition{$k}\t"; printf $re "%.2f\n",$prct;
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82 }
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83 return ( $bo, $mi, $pi);
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84 }
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85
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86 sub fastqSubgroups
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87 {
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88 my ( $fastq, $output_directory, $min_si, $max_si, $min_pi, $max_pi ) = @_;
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89 my $fastq_siRNA = $output_directory."siRNAs.fastq";
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90 my $fastq_piRNA = $output_directory."piRNAs.fastq";
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91
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92 open my $fic, '<', $fastq || die "cannot open input file $! \n";
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93 open my $si, '>', $fastq_siRNA || die "cannot open siRNA.fastq $! \n";
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94 open my $pi, '>', $fastq_piRNA || die "cannot open piRNA.fastq $! \n";
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95
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96 my ($length, $cmp, $type, $siRNA_number, $miRNA_h_number, $piRNA_number, $not_pi_number) = (0,0,0,0,0,0,0);
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97 my (@fastq) =(); my $seq_name;
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98 my $out;
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99 while(<$fic>)
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100 {
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101 chomp $_;
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102 $cmp++;
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103 if ($cmp == 1)
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104 {
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105 die "file do not contain a @ at line $cmp\n" unless ($_ =~ /^\@/ );
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106 $type = 0; @fastq = ();
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107 if ($_ =~ /^\@(.*)\s.*/) { $seq_name = $1;}
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108 elsif ($_ =~ /^\@(.*)/) {$seq_name = $1;}
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109 push(@fastq,$_);
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110 }
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111 elsif ($cmp == 2)
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112 {
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113 #die "unrecognized symbol at line $cmp\n" unless $_ =~ /[atcgATCGnN]+/;
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114 push(@fastq,$_);
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115 $length = length($_);
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116 $type = 0;
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117 if ( $length >= $min_si && $length <= $max_si )
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118 {
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119 $type = 2;
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120 $siRNA_number++;
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121 }
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122 if ($length >= $min_pi && $length <= $max_pi )
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123 {
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124 $type += 4;
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125 $piRNA_number++;
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126 }
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127 }
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128 elsif ($cmp == 3 )
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129 {
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130 die "file do not contain a + at line $cmp\n" unless $_ =~ /^\+/;
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131 push(@fastq,$_);
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132 }
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133 elsif ($cmp == 4 )
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134 {
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135 push(@fastq,$_);
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136 $cmp = 0;
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137 if ($type != 0)
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138 {
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139 if ($type & 4 ) { foreach my $t (@fastq) { print $pi $t."\n";} }
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140 if ($type & 2 ) { foreach my $t (@fastq) { print $si $t."\n";} }
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141 }
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142 }
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143 }
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144 close $fic;
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145 close $si; close $pi;
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146 return ($piRNA_number);
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147 }
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148
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149 1;
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