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annotate lib/CPT/Writer/Genomic.pm @ 1:8691c1c61a8e draft default tip

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:48:47 +0000
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1
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1 package CPT::Writer::Genomic;
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2 use Moose;
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3 with 'CPT::Writer';
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4
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5 # Specific format of genomic writer
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6 has 'format' => ( is => 'rw', isa => 'Str', default => 'Genbank');
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7
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8 sub process {
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9 my ($self) = @_;
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10 $self->processed_data( $self->data );
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11 $self->processing_complete(1);
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12 return 1;
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13 }
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14
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15 sub write {
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16 my ($self) = @_;
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17 if ( $self->processing_complete ) {
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18 $self->OutputFilesClass->extension( $self->suffix() );
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19 my $next_output_file = $self->OutputFilesClass->get_next_file();
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20 open( my $filehandle, '>', $next_output_file );
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21
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22 require Bio::SeqIO;
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23 my $obj_type = ref $self->processed_data();
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24 if(substr($obj_type,0,10) eq 'Bio::Seq::'){
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25 my $outseq = Bio::SeqIO->new(
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26 -fh => $filehandle,
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27 -format => $self->format(),
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28 );
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29 $outseq->write_seq( $self->processed_data );
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30 }elsif(substr($obj_type,0,10) eq 'Bio::SeqIO'){
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31 my $outseq = Bio::SeqIO->new(
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32 -fh => $filehandle,
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33 -format => $self->format(),
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34 );
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35 while (my $inseq = $self->processed_data()->next_seq()) {
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36 $outseq->write_seq($inseq);
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37 }
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38 }elsif(substr($obj_type,0,8) eq 'Bio::Seq'){
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39 my $outseq = Bio::SeqIO->new(
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40 -fh => $filehandle,
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41 -format => $self->format(),
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42 );
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43 $outseq->write_seq( $self->processed_data );
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44 }elsif(ref $self->processed_data eq 'ARRAY'){
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45 # Assume array of genomes
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46 my $outseq = Bio::SeqIO->new(
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47 -fh => $filehandle,
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48 -format => $self->format(),
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49 );
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50 foreach my $inseq(@{$self->processed_data}){
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51 $outseq->write_seq($inseq);
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52 }
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53 }else{
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54 print $filehandle $self->processed_data();
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55 }
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56 close($filehandle);
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57 }
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58 else {
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59 warn
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60 "Write called but processing was not marked as complete. Not writing";
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61 }
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62 }
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63
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64 sub suffix {
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65 my ($self) = @_;
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66 my %suffix_map = (
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67 'abi' => 'abi',
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68 'ace' => 'ace',
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69 'agave' => 'agave',
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70 'alf' => 'alf',
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71 'asciitree' => 'txt',
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72 'bsml' => 'bsml',
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73 'bsml_sax' => 'bsml',
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74 'chadoxml' => 'xml',
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75 'chaos' => 'chaos',
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76 'chaosxml' => 'xml',
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77 'ctf' => 'ctf',
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78 'embl' => 'emb',
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79 'entrezgene' => 'asn1',
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80 'excel' => 'xls',
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81 'exp' => 'exp',
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82 'fasta' => 'fa',
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83 'fastq' => 'fastq',
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84 'game' => 'xml',
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85 'gcg' => 'gcg',
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86 'genbank' => 'gbk',
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87 'interpro' => 'xml',
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88 'kegg' => 'kegg',
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89 'largefasta' => 'lfa',
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90 'lasergene' => 'lasergene',
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91 'locuslink' => 'll_tmpl',
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92 'phd' => 'phred',
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93 'pir' => 'pir',
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94 'pln' => 'pln',
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95 'qual' => 'phred',
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96 'raw' => 'txt',
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97 'scf' => 'scf',
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98 'seqxml' => 'xml',
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99 'strider' => 'strider',
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100 'swiss' => 'sp',
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101 'tab' => 'tsv',
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102 'tigr' => 'xml',
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103 'tigrxml' => 'xml',
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104 'tinyseq' => 'xml',
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105 'ztr' => 'ztr',
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106 );
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107
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108 if($suffix_map{lc($self->format())}){
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109 return $suffix_map{lc($self->format())};
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110 }else{
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111 return 'unknown';
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112 }
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113 }
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114
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115 no Moose;
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116 1;
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117
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118 __END__
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119
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120 =pod
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121
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122 =encoding UTF-8
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123
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124 =head1 NAME
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125
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126 CPT::Writer::Genomic
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127
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128 =head1 VERSION
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129
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130 version 1.99.4
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131
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132 =head1 AUTHOR
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133
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134 Eric Rasche <rasche.eric@yandex.ru>
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135
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136 =head1 COPYRIGHT AND LICENSE
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137
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138 This software is Copyright (c) 2014 by Eric Rasche.
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139
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140 This is free software, licensed under:
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141
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142 The GNU General Public License, Version 3, June 2007
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143
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144 =cut