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annotate cpt_genbank2circosk.pl @ 1:f093e08f21f3 draft default tip

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:47:24 +0000
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1
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1 #!/usr/bin/perl
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2 #
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3 # Code written by Eric Rasche
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4 # mailto:rasche.eric@yandex.ru
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5 # tel:404.692.2048
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6 # http://eric.rasche.co.uk
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7 # for
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8 # Center for Phage Technology
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9 #
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10
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11 use strict;
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12 use warnings;
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13
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14 use CPT::GalaxyGetOpt;
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15 use Data::Dumper;
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16
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17 my $ggo = CPT::GalaxyGetOpt->new();
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18 my %colors = map { $_ => $_ } qw(red orange yellow green blue gray black white);
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19 my %intensity = map { $_ => $_ } qw (vvvvl vvvl vvl vl vd vvd vvvd vvvvd);
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20
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21 my $options = $ggo->getOptions(
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22 'options' => [
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23 [
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24 'file',
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25 'Input file',
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26 {
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27 required => 1,
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28 validate => 'File/Input',
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29 file_format => ['genbank', 'embl', 'txt'],
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30 }
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31 ],
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32 [
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33 'chromosome' => 'Name for the
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34 chromosome inside Circos',
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35 {
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36 required => 1,
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37 validate => 'String'
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38 }
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39 ],
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40 [
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41 'color' => 'Color to use for Circos plot',
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42 {
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43 required => 1,
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44 validate => 'Option',
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45 options => \%colors,
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46 }
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47 ],
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48 [
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49 'intensity' => 'Circos color intensity. ',
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50 {
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51 validate => 'Option',
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52 options => \%intensity,
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53 }
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54 ],
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55 ],
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56 'outputs' => [
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57 [
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58 'circosk',
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59 'Circos Karyotype File',
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60 {
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61 validate => 'File/Output',
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62 required => 1,
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63 default => 'karyotype',
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64 data_format => 'text/plain',
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65 default_format => 'TXT'
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66 }
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67 ],
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68 ],
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69 'defaults' => [
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70 'appname' => 'Genbank2CircosK',
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71 'appid' => 'Genbank2CircosK',
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72 'appvers' => '1.94',
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73 'appdesc' =>
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74 'Convert genbank files to Circos Karyotype configuration files',
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75 ],
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76 'tests' => [
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77 {
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78 test_name => "Default",
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79 params => {
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80 'file' => 'test-data/inputs/multi.gbk',
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81 'chromosome' => 'test',
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82 'color' => 'red',
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83 'intensity' => 'vvvl',
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84 },
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85 outputs => {
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86 'circosk' => ['karyotype.txt', 'test-data/outputs/circosk.conf'],
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87 }
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88 },
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89 ],
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90 );
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91
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92 use CPT::Bio;
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93 my $bio = CPT::Bio->new();
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94
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95 my @results;
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96 my $c = 0;
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97 my $seqio = $bio->requestCopyIO( file => $options->{file} );
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98
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99 while(my $seqobj = $seqio->next_seq()){
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100 foreach my $feat ( $seqobj->get_SeqFeatures () ) {
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101
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102 #band test 12 CDS__test_1gbk 5715 6335 red]
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103 next if ( $feat->primary_tag ne 'CDS' );
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104 my $id = $bio->_getIdentifier($feat);
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105 $id =~ s/\s+/_/g;
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106 push(
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107 @results,
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108 join(
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109 ' ',
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110 (
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111 'band',
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112 $options->{'chromosome'},
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113 $c++,
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114 $id,
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115 $feat->start,
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116 $feat->end,
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117 (defined $options->{'intensity'} ? $options->{'intensity'} : '') . $options->{'color'}
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118 )
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119 )
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120 );
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121 }
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122 }
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123
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124 my $z = join( "\n", @results );
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125
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126 use CPT::OutputFiles;
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127 my $output = CPT::OutputFiles->new(
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128 name => 'circosk',
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129 GGO => $ggo,
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130 );
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131 $output->CRR(data => $z);