Mercurial > repos > rnateam > rnacode

annotate breakMAF.pl @ 2:f9a7dc68d6cf draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit 3abc213e109bb564de7dee75d71d90eb1bf78c7e
author rnateam
date Thu, 15 Nov 2018 01:15:35 -0500
parents 0554fa091710
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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1 #!/usr/bin/perl -w
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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3 use strict;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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4 use Getopt::Long;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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5 use POSIX qw(ceil floor);
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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7 my $maxLength = 400;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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8 my $desiredLength = 200;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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9 my $help = 0;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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11 GetOptions(
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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12 "maxLength:i" => \$maxLength,
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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13 "desiredLength:i" => \$desiredLength,
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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14 "help" => \$help,
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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15 "h" => \$help
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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16 );
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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18 if ($help) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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19 print STDERR "\nbreakMAF [options] < input.maf > output.maf\n\n";
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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20 print STDERR "Options:\n";
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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21 print STDERR " maxLength: Break all blocks longer than that (default: 400 columns)\n";
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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22 print STDERR " desiredLength: Try to create blocks of this size (default: 200 columns)\n";
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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23 exit(1);
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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24 }
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26 $/ = 'a score=';
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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28 while ( my $block = <> ) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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30 $block = 'a score=' . $block;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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32 my $currAln = readMAF($block)->[0];
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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34 next if not defined($currAln);
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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36 my $length = length( $currAln->[0]->{seq} );
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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38 if ( $length > $maxLength ) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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40 my $breakN = int( $length / $desiredLength );
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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41 my $chunkLength = ceil( $length / $breakN );
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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43 my $from = 0;
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45 while (1) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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46 my $to = $from + $chunkLength;
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48 if ( $to > $length ) {
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49 $to = $length;
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50 }
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52 my $slice = sliceAlnByColumn( $currAln, $from, $to );
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54 print formatAln( $slice, 'maf' ), "\n";
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56 $from = $to;
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57
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58 last if $from == $length;
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59 }
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61 } else {
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62 print formatAln( $currAln, 'maf' ), "\n";
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63 }
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64 }
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65
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66 ######################################################################
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67 #
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68 # readMAF($string)
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69 #
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70 # Converts the MAF in string to internal alignment format. Returns
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71 # list of usual array references.
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72 #
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73 ######################################################################
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75 sub readMAF {
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77 my $string = shift;
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78
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79 return [] if $string eq '';
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81 my @input = split( "\n", $string );
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82
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83 #open(FILE,"<$file") || die("Could not read $file ($!)");
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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84
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85 my @outAlns = ();
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86 my @aln = ();
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87
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88 foreach my $i ( 0 .. $#input ) {
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89
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90 $_ = $input[$i];
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91
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92 next if (/^\s?\#/);
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
rnateam
parents:
diff changeset
93 next if (/^\s?a/);
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
rnateam
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diff changeset
94
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
rnateam
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diff changeset
95 if (/^\s?s/) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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96 ( my $dummy, my $name, my $start, my $length, my $strand, my $fullLength, my $seq ) = split;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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97
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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98 my $end = $start + $length;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
rnateam
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diff changeset
99
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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100 ( my $org, my $chrom ) = split( /\./, $name );
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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101
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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102 push @aln, {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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103 name => $name,
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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104 org => $org,
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
rnateam
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diff changeset
105 chrom => $chrom,
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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106 start => $start,
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
rnateam
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diff changeset
107 end => $end,
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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108 seq => $seq,
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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109 strand => $strand
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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110 };
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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111 }
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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112
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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113 if ( /^\s?$/ and @aln ) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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114 push @outAlns, [@aln];
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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115 @aln = ();
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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116 }
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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117 if ( ( not defined $input[ $i + 1 ] ) and (@aln) ) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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118 push @outAlns, [@aln];
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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119 @aln = ();
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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120 }
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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121 }
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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122 return \@outAlns;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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123 }
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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124
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125 sub formatAln {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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126
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127 my @aln = @{ $_[0] };
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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128
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129 my $format = $_[1];
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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130
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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131 $format = lc($format);
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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132
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133 my @alnSeqs = ();
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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134 my @alnNames = ();
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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135
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136 my $counter = 1;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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137
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138 foreach my $row (@aln) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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139
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140 my $name = "seq$counter";
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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141 $counter++;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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142 if ( $row->{name} ) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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143 $name = ( $row->{name} );
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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144 } elsif ( $row->{org} and $row->{chrom} ) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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145 $name = "$row->{org}.$row->{chrom}";
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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146 }
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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147
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148 my $start = $row->{start};
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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149 my $end = $row->{end};
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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150 my $strand = $row->{strand};
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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151
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152 my $pos = '';
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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153
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diff changeset
154 if ( defined $start
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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diff changeset
155 and defined $end
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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diff changeset
156 and defined $strand
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
rnateam
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157 and ( $format ne 'phylip' ) ) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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158 ( $start, $end ) = ( $end, $start ) if ( $strand eq '-' );
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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159 $pos = "/$start-$end";
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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160 }
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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161
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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162 push @alnNames, "$name$pos";
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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163 push @alnSeqs, $row->{seq};
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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164
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165 }
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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166
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167 my $output = '';
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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168
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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169 if ( $format eq 'clustal' ) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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170
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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171 $output = "CLUSTAL W(1.81) multiple sequence alignment\n\n\n";
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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172 my $maxName = 0;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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173
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174 foreach my $name (@alnNames) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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175 $maxName = ( $maxName < length($name) ) ? length($name) : $maxName;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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176 }
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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177
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178 for my $i ( 0 .. $#alnNames ) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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179 my $buffer = " " x ( ( $maxName + 6 ) - length( $alnNames[$i] ) );
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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180 $alnNames[$i] .= $buffer;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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181 }
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
rnateam
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182 my $columnWidth = 60;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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183 my $currPos = 0;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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184 my $length = length( $alnSeqs[0] );
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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185
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186 while ( $currPos < $length ) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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187 for my $i ( 0 .. $#alnNames ) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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188 $output .= $alnNames[$i];
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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189 $output .= substr( $alnSeqs[$i], $currPos, $columnWidth );
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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190 $output .= "\n";
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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191 }
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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192 $output .= "\n\n";
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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193 $currPos += $columnWidth;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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194 }
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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195 } elsif ( $format eq 'fasta' ) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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196 foreach my $i ( 0 .. $#alnNames ) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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197 my $name = $alnNames[$i];
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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198 my $seq = $alnSeqs[$i];
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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199 $seq =~ s/(.{60})/$1\n/g;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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200 $output .= ">$name\n$seq\n";
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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201 }
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202 } elsif ( $format eq 'phylip' ) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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203 my $length = length( $alnSeqs[0] );
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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204 my $N = @alnSeqs;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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205 $output .= " $N $length\n";
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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206 foreach my $i ( 0 .. $#alnNames ) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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207 my $name = $alnNames[$i];
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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208 my $seq = $alnSeqs[$i];
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209 $seq =~ s/(.{60})/$1\n/g;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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210 $output .= "$name\n$seq\n";
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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211 }
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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212 } elsif ( $format eq 'maf' ) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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213 $output .= "a score=0\n";
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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214 foreach my $row (@aln) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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215 my $length = $row->{end} - $row->{start};
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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216 $output .= "s $row->{org}.$row->{chrom} $row->{start} $length $row->{strand} 0 $row->{seq}\n";
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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217 }
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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218 }
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219 return $output;
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220
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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221 }
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222
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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223 ######################################################################
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224 #
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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225 # sliceAlnByColumn(\@aln ref-to-alignment, $start int, $end int)
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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226 #
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227 # Returns slice of alignment specified by alignment column.
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228 #
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229 # \@aln ... alignment in list of hash format
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230 # $start, $end ... slice to cut
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231 #
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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232 # Returns reference to alignment in list of hash format. This is a new
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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233 # alignment, i.e. the input is not sliced in place
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234 #
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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235 ######################################################################
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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236
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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237 sub sliceAlnByColumn {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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238
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239 my @aln = @{ $_[0] };
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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240 shift;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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241 ( my $start, my $end ) = @_;
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242
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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243 # correct ends without warning if outside of valid range
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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244 $start = 0 if ( $start < 0 );
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245 $end = length( $aln[0]->{seq} ) if ( $end > length( $aln[0]->{seq} ) );
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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246
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247 #my @newAln=@aln;
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248
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249 # make deep copy of list of hash
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250 my @newAln = ();
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251 foreach (@aln) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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252 push @newAln, { %{$_} };
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253 }
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254
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255 foreach my $i ( 0 .. $#newAln ) {
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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256
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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257 my $oldStart = $newAln[$i]->{start};
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258 my $oldEnd = $newAln[$i]->{end};
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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259
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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260 $newAln[$i]->{start} = alnCol2genomePos( $newAln[$i]->{seq}, $oldStart, $start );
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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261 $newAln[$i]->{end} = alnCol2genomePos( $newAln[$i]->{seq}, $oldStart, $end - 1 ) + 1;
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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262 $newAln[$i]->{seq} = substr( $newAln[$i]->{seq}, $start, $end - $start );
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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263
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264 }
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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265
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266 return ( [@newAln] );
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267
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268 }
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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269
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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270 ######################################################################
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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271 #
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272 # alnCol2genomePos($seq string, $start int, $col int)
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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273 #
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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274 # Calculates the genomic position corresponding to a column in an
0554fa091710 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit b6d3800e260cdfcbe99e5f056344c3df101dad00
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275 # alignment.
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276 #
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277 # $seq ... sequence from alignment (i.e. letters with gaps)
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278 # $start ... Genomic position of first letter in $seq
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279 # $col ... column in the alignment that is to be mapped
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280 #
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281 # Returns genomic position. No error handling, so $col must be a valid
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282 # column of the string $seq.
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283 #
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284 #######################################################################
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285
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286 sub alnCol2genomePos {
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287
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288 ( my $seq, my $start, my $col ) = @_;
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289
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290 $seq =~ s/\./-/g; #Convert all gaps to "-"
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291
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292 my $newPos = $start;
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293
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294 # if gap only...
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295 return $start if ( $seq =~ /^-+$/ );
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296
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297 ( my $tmp ) = $seq =~ /(-*)[^-]/;
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298
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299 my $leadingGaps = length($tmp);
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300
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301 # if column is in gap before first letter,
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302 # return position of the first letter
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303 return $start if ( $col < $leadingGaps );
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304
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305 $newPos = $start - 1;
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306
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307 for my $i ( $leadingGaps .. $col ) {
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308 $newPos++ if ( ( my $t = substr( $seq, $i, 1 ) ) ne '-' );
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309 }
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310 return $newPos;
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311 }
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312