Mercurial > repos > jvolkening > b2b_fq_deinterleave

annotate summarize_run.pl @ 0:b42eb9ff6a8c draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
author jvolkening
date Fri, 08 Mar 2024 00:47:53 +0000
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0
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
jvolkening
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1 #!/usr/bin/perl
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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2
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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3 use strict;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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4 use warnings;
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5
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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6 use Getopt::Long;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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7 use BioX::Seq::Stream;
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8 use List::Util qw/sum/;
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9
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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10 my $fn_raw1;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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11 my $fn_raw2;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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12 my $fn_filt1;
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13 my $fn_filt2;
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14 my $fn_bedgraph;
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15 my $fn_qc1;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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16 my $fn_qc2;
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17 my $fn_consensus;
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18 my $fn_out;
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19 my $n_threads = 1;
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20
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21 GetOptions(
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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22 'raw_1=s' => \$fn_raw1,
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23 'raw_2=s' => \$fn_raw2,
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24 'filt_1=s' => \$fn_filt1,
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25 'filt_2=s' => \$fn_filt2,
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26 'bedgraph=s' => \$fn_bedgraph,
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27 'fastqc_1=s' => \$fn_qc1,
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28 'fastqc_2=s' => \$fn_qc2,
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29 'consensus=s' => \$fn_consensus,
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30 'out=s' => \$fn_out,
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31 'threads=i' => \$n_threads,
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32 );
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33
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34 my @counts;
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35 for ($fn_raw1, $fn_raw2, $fn_filt1, $fn_filt2) {
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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36 open my $in, '-|', 'wc', '-l', $_;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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37 my $ret = <$in>;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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38 close $in;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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39 chomp $ret;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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40 my ($count, $fn) = split ' ', $ret;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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41 die "line length not multiple of four for $_\n"
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42 if ($count % 4);
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43 push @counts, $count/4;
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44 }
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45
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46
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47 die "raw pair count mismatch\n" if ($counts[0] != $counts[1]);
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48 die "filtered pair count mismatch\n" if ($counts[2] != $counts[3]);
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49
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50 # read fragment stats from STDIN
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51 my @lens;
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52 while (<STDIN>) {
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53 chomp $_;
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54 push @lens, $_;
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55 }
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56
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57 my $frag_mean = int( sum(@lens)/scalar(@lens)+0.5 );
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58 my $frag_sd = int( sqrt( sum( map {($_ - $frag_mean)**2} @lens)/(scalar(@lens)-1) )+0.5 );
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59
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60 # extract FastQC data
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61 #warn "extracting FastQC stats...\n";
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62
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63 my @five_nums;
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64 for my $fn ($fn_qc1, $fn_qc2) {
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65 open my $in, '<', $fn;
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66
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67 my $in_data = 0;
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68 my @data;
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69 LINE:
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70 while (my $line = <$in>) {
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71 chomp $line;
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72 if ($in_data) {
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73 if ($line =~ /^>>END_MODULE/) {
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74 last LINE;
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75 }
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76 next if ($line =~ /^#/);
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77 my ($score, $count) = split ' ', $line;
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78 push @data, [$score,$count];
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79 }
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80 elsif ($line =~ /^>>Per sequence quality scores/) {
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81 $in_data = 1;
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82 }
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83 }
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84
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85 push @five_nums, data_to_5( @data );
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86 }
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87
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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88 # Count contigs
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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89
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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90 my $p = BioX::Seq::Stream->new($fn_consensus);
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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91 my %n_contigs;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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92 my @names;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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93 while (my $seq = $p->next_seq) {
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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94
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95 my $id = $seq->id;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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96 push @names, $id;
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97 while ($seq =~ /[^Nn]+/g) {
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98 ++$n_contigs{$id};
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99 }
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100 }
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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101
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102 # Parse assembly depth info
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103 #warn "calculating coverage stats...\n";
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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104
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105 open my $in, '<', $fn_bedgraph;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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106
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107 my %cov_5nums;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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108 my %counts;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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109 my $last_end;
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110 my $last_contig;
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111 my $head = <$in>;
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112 while (my $line = <$in>) {
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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113 chomp $line;
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114 my ($contig,$start,$end,$depth) = split "\t", $line;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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115 $last_contig //= $contig;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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116 if ($contig ne $last_contig) {
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117
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118 my @depths = sort {$a <=> $b} keys %counts;
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119 my @data;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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120 for (@depths) {
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121 push @data, [$_, $counts{$_}];
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122 }
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123 $cov_5nums{$last_contig} = data_to_5( @data );
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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124 $last_contig = $contig;
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125 %counts = ();
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126 $last_end = undef;
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127 }
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128
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129 if (defined($last_end) && $last_end < $start) {
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130 $counts{0} += $start - $last_end;
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131 }
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132 $counts{$depth} += $end - $start;
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133 $last_end = $end;
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134 }
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135 my @depths = sort {$a <=> $b} keys %counts;
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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136 my @data;
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137 for (@depths) {
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138 push @data, [$_, $counts{$_}];
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139 }
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140 $cov_5nums{$last_contig} = data_to_5( @data );
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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141
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142 open my $out, '>', $fn_out;
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143 print {$out} join("\t",
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144 '#id',
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145 'raw_read_pairs',
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146 'filt_read_pairs',
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147 'frag_len_mean',
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148 'frag_len_sd',
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149 'forward_qual',
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150 'reverse_qual',
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151 'n_contigs',
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152 'coverage_depth',
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153 ), "\n";
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154 for my $id (@names) {
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155 print {$out} join("\t",
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156 $id,
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157 $counts[0],
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158 $counts[2],
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159 $frag_mean,
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160 $frag_sd,
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161 $five_nums[0],
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162 $five_nums[1],
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163 $n_contigs{$id},
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164 $cov_5nums{$id},
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165 ), "\n";
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166 }
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167 close $out;
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168
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169 exit;
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170
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171
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172 sub data_to_5 {
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173
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174 my (@data) = @_;
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175 my $total = sum map {$_->[1]} @data;
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176 my @five_num;
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177 my $curr = 0;
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178 for my $i (0..$#data) {
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179 $curr += $data[$i]->[1];
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180 for my $j (0..4) {
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181 next if (defined $five_num[$j]);
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182 my $quant = $j/4;
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183 if ($curr/$total > $quant) {
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184 $five_num[$j] = $data[$i]->[0];
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185 }
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186 elsif ($curr/$total == $quant) {
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187 $five_num[$j] = $i < $#data
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188 ? int(($data[$i]->[0]+$data[$i+1]->[0])/2)
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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189 : $data[$i]->[0];
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190 }
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191 }
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192 }
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193 return join('|',@five_num);
b42eb9ff6a8c planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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194
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195 }