Mercurial > repos > iuc > fasta_stats

annotate fasta-stats.pl @ 2:d7421f5dbb4f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit adc5e3616c1849551c9a712b651b0d1c6b0e88f1"
author iuc
date Mon, 26 Apr 2021 10:01:17 +0000
parents 53c14c29c2fd
children 5b072a9eaa9d
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be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
iuc
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diff changeset
1 #!/usr/bin/env perl
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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3 # fasta-stats
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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4 # written by torsten.seemann@monash.edu
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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5 # oct 2012
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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6
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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7 use strict;
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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8 use warnings;
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9 use List::Util qw(sum min max);
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1
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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12 #Parameters
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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13 my $file = shift;
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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14 my $calc_ng50 = 0;
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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15 my $genome_size = 0;
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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16 if (scalar(@ARGV) > 0){
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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17 $genome_size = $ARGV[0];
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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18 $calc_ng50 = 1;
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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19 }
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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0
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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21 # stat storage
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be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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23 my $n=0;
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24 my $seq = '';
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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25 my %stat;
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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26 my @len;
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be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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28 # MAIN LOOP collecting sequences
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29
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30 #open the file first
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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31 open IN, $file or die{ "Couldn't open $file for reading\n$!" };
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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33 while (my $line = <IN>) {
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be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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34 chomp $line;
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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35 if ($line =~ m/^\s*>/) {
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36 process($seq) if $n;
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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37 $n++;
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38 $seq='';
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39 }
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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40 else {
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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41 $seq .= $line;
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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42 }
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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43 }
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be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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45 process($seq) if $n;
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be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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47 # sort length array
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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48 # (should use hash here for efficiency with huge no of short reads?)
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49
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50 @len = sort { $b <=> $a } @len;
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be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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52 # compute more stats
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be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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54 $stat{'num_seq'} = scalar(@len);
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56 if (@len) {
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57 $stat{'num_bp'} = sum(@len);
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58 $stat{'len_min'} = $len[0];
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59 $stat{'len_max'} = $len[-1];
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60 $stat{'len_median'} = $len[int(@len/2)];
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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61 $stat{'len_mean'} = int( $stat{'num_bp'} / $stat{'num_seq'} );
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62
0
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63 # calculate n50
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64 my $thresh = int 0.5 * $stat{'num_bp'};
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65 ($stat{'len_N50'}, $stat{'L50'}) = &calc_x50(\@len, $thresh);
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67 #calculate NG50
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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68 if ($calc_ng50) {
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69 my $thresh = int 0.5 * $genome_size;
d7421f5dbb4f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit adc5e3616c1849551c9a712b651b0d1c6b0e88f1"
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70 ($stat{'len_NG50'}, $stat{'LG50'}) = &calc_x50(\@len, $thresh);
0
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71 }
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72 }
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74 #calculate GC content
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75 $stat{'num_bp_not_N'} = $stat{'num_G'} + $stat{'num_C'} + $stat{'num_A'} + $stat{'num_T'};
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76 $stat{'GC_content'} = ($stat{'num_G'} + $stat{'num_C'}) / $stat{'num_bp_not_N'}*100;
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78 # print stats as .tsv
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80 for my $name (sort keys %stat) {
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81 if ($name =~ m/GC_content/){
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82 printf "%s\t%0.1f\n", $name, $stat{$name};
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83 } else {
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84 printf "%s\t%s\n", $name, $stat{$name};
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85 }
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86 }
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87
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88 # run for each sequence
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89
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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90 sub process {
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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91 my($s) = @_;
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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92 # base composition
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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93 for my $x (qw(A G T C N)) {
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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94 my $count = $s =~ s/$x/$x/gi;
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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95 $stat{"num_$x"} += $count;
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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96 }
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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97 # keep list of all lengths encountered
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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98 push @len, length($s);
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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99 }
be48db09665c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
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100
1
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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101 # N50/NG50 calculation sub
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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102
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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103 sub calc_x50{
2
d7421f5dbb4f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit adc5e3616c1849551c9a712b651b0d1c6b0e88f1"
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104 my $ref = shift;
d7421f5dbb4f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit adc5e3616c1849551c9a712b651b0d1c6b0e88f1"
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105 my @x = @$ref;
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53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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106 my $thresh = shift;
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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107 my $cum=0;
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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108 for my $i (0 .. $#x) {
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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109 $cum += $x[$i];
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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110 if ($cum >= $thresh) {
2
d7421f5dbb4f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit adc5e3616c1849551c9a712b651b0d1c6b0e88f1"
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111 return $x[$i], $i+1;
1
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112 }
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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113 }
2
d7421f5dbb4f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit adc5e3616c1849551c9a712b651b0d1c6b0e88f1"
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114 return (0,0);
1
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115 }
53c14c29c2fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
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