Mercurial > repos > jdv > b2b_summarize_run

annotate summarize_run.pl @ 1:10c319d654df draft default tip

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"planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
author jdv
date Tue, 28 Sep 2021 06:13:50 +0000
parents bd599efae04d
children
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bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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1 #!/usr/bin/perl
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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2
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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3 use strict;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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4 use warnings;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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5
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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6 use Getopt::Long;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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7 use BioX::Seq::Stream;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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8 use List::Util qw/sum/;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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9
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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10 my $fn_raw1;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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11 my $fn_raw2;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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12 my $fn_filt1;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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13 my $fn_filt2;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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14 my $fn_bedgraph;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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15 my $fn_qc1;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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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
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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21 GetOptions(
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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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,
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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25 'filt_2=s' => \$fn_filt2,
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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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,
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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29 'consensus=s' => \$fn_consensus,
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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30 'out=s' => \$fn_out,
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31 'threads=i' => \$n_threads,
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32 );
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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33
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35 my @counts;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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36 for ($fn_raw1, $fn_raw2, $fn_filt1, $fn_filt2) {
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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37 open my $in, '-|', 'wc', '-l', $_;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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38 my $ret = <$in>;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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39 close $in;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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40 chomp $ret;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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41 my ($count, $fn) = split ' ', $ret;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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42 die "line length not multiple of four for $_\n"
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43 if ($count % 4);
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44 push @counts, $count/4;
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45 }
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47
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48 die "raw pair count mismatch\n" if ($counts[0] != $counts[1]);
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49 die "filtered pair count mismatch\n" if ($counts[2] != $counts[3]);
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50
1
10c319d654df "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
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51 # read fragment stats from STDIN
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52 my @lens;
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53 while (<STDIN>) {
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54 chomp $_;
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55 push @lens, $_;
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56 }
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57
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58 my $frag_mean = int( sum(@lens)/scalar(@lens)+0.5 );
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59 my $frag_sd = int( sqrt( sum( map {($_ - $frag_mean)**2} @lens)/(scalar(@lens)-1) )+0.5 );
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60
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61 # extract FastQC data
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62 #warn "extracting FastQC stats...\n";
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63
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64 my @five_nums;
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65 for my $fn ($fn_qc1, $fn_qc2) {
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66 open my $in, '<', $fn;
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67
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68 my $in_data = 0;
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69 my @data;
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70 LINE:
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71 while (my $line = <$in>) {
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72 chomp $line;
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73 if ($in_data) {
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74 if ($line =~ /^>>END_MODULE/) {
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75 last LINE;
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76 }
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77 next if ($line =~ /^#/);
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78 my ($score, $count) = split ' ', $line;
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79 push @data, [$score,$count];
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80 }
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81 elsif ($line =~ /^>>Per sequence quality scores/) {
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82 $in_data = 1;
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83 }
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84 }
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85
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86 push @five_nums, data_to_5( @data );
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87 }
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88
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89 # Count contigs
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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90
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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91 my $p = BioX::Seq::Stream->new($fn_consensus);
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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92 my %n_contigs;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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93 my @names;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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94 while (my $seq = $p->next_seq) {
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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95
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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96 my $id = $seq->id;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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97 push @names, $id;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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98 while ($seq =~ /[^Nn]+/g) {
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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99 ++$n_contigs{$id};
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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100 }
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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101 }
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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102
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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103 # Parse assembly depth info
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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104 #warn "calculating coverage stats...\n";
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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105
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106 open my $in, '<', $fn_bedgraph;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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107
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108 my %cov_5nums;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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109 my %counts;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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110 my $last_end;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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111 my $last_contig;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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112 my $head = <$in>;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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113 while (my $line = <$in>) {
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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114 chomp $line;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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115 my ($contig,$start,$end,$depth) = split "\t", $line;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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116 $last_contig //= $contig;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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117 if ($contig ne $last_contig) {
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118
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119 my @depths = sort {$a <=> $b} keys %counts;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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120 my @data;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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121 for (@depths) {
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122 push @data, [$_, $counts{$_}];
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123 }
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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124 $cov_5nums{$last_contig} = data_to_5( @data );
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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125 $last_contig = $contig;
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126 %counts = ();
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127 $last_end = undef;
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128 }
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129
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130 if (defined($last_end) && $last_end < $start) {
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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131 $counts{0} += $start - $last_end;
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132 }
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133 $counts{$depth} += $end - $start;
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134 $last_end = $end;
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135 }
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136 my @depths = sort {$a <=> $b} keys %counts;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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137 my @data;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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138 for (@depths) {
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139 push @data, [$_, $counts{$_}];
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140 }
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141 $cov_5nums{$last_contig} = data_to_5( @data );
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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142
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143 open my $out, '>', $fn_out;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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144 print {$out} join("\t",
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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145 '#id',
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146 'raw_read_pairs',
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147 'filt_read_pairs',
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148 'frag_len_mean',
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149 'frag_len_sd',
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150 'forward_qual',
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151 'reverse_qual',
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152 'n_contigs',
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153 'coverage_depth',
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154 ), "\n";
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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155 for my $id (@names) {
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156 print {$out} join("\t",
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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157 $id,
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158 $counts[0],
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159 $counts[2],
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160 $frag_mean,
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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161 $frag_sd,
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162 $five_nums[0],
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163 $five_nums[1],
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164 $n_contigs{$id},
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165 $cov_5nums{$id},
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166 ), "\n";
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167 }
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168 close $out;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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169
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170 exit;
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171
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172
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173 sub data_to_5 {
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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174
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175 my (@data) = @_;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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176 my $total = sum map {$_->[1]} @data;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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177 my @five_num;
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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178 my $curr = 0;
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179 for my $i (0..$#data) {
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180 $curr += $data[$i]->[1];
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181 for my $j (0..4) {
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182 next if (defined $five_num[$j]);
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183 my $quant = $j/4;
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184 if ($curr/$total > $quant) {
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185 $five_num[$j] = $data[$i]->[0];
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186 }
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187 elsif ($curr/$total == $quant) {
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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188 $five_num[$j] = $i < $#data
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189 ? int(($data[$i]->[0]+$data[$i+1]->[0])/2)
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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190 : $data[$i]->[0];
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191 }
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192 }
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193 }
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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194 return join('|',@five_num);
bd599efae04d planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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195
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196 }