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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::Bio;
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2 use Moose;
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3 use strict;
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4 use warnings;
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5 use autodie;
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6 use CPT::FiletypeDetector;
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7 use CPT::BioData;
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8 my $bd = CPT::BioData->new();
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9
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10 my $filetype = CPT::FiletypeDetector->new();
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11
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12 has 'var_translate' => ( is => 'rw', isa => 'Bool');
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13 has 'var_header' => ( is => 'rw', isa => 'Bool');
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14 has codonTable => (
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15 is => 'rw',
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16 isa => 'Any',
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17 default => sub {
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18 $bd->getTranslationTable(11)
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19 },
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20 );
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21
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22 sub set_codon_table {
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23 my ($self, $num) = @_;
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24 $self->codonTable($bd->getTranslationTable($num));
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25 }
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26
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27
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28 sub _getFeatureTag {
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29 my ( $self, $feat, $tag ) = @_;
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30 if(! defined($feat)){
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31 warn "Undefined feature";
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32 }
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33 return $feat->has_tag($tag)
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34 ? ( join( ',', $feat->get_tag_values($tag) ) )
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35 : '';
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36 }
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37
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38 sub _getIdentifier {
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39 my ( $self, $feat ) = @_;
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40 my $line;
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41 if ( ref $feat eq 'Bio::Seq::RichSeq' || ref $feat eq 'Bio::Seq' ) {
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42 return $feat->display_id;
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43 }
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44 else {
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45 my $locus_tag = $self->_getFeatureTag( $feat, 'locus_tag' );
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46 if ($locus_tag) {
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47 return $locus_tag;
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48 }
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49 my $gene = $self->_getFeatureTag( $feat, 'gene' );
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50 if ($gene) {
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51 return $gene;
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52 }
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53 my $product = $self->_getFeatureTag( $feat, 'product' );
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54 if ($product) {
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55 return $product;
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56 }
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57 }
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58 return sprintf("%s_%s_%s", $feat->start(), $feat->end(), ($feat->strand() == 1 ? 'sense':'antisense'));
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59 }
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60
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61
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62 sub requestCopy {
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63 my ( $self, %data ) = @_;
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64 use Bio::SeqIO;
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65 if ($data{'file'} ) {
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66 my ($guessed_type) = $filetype->detect( $data{'file'} );
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67 my $seqio = Bio::SeqIO->new(
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68 -file => $data{'file'},
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69 -format => $guessed_type
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70 );
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71 my @results;
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72 while ( my $seqobj = $seqio->next_seq() ) {
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73 return \$seqobj;
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74 }
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75 }
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76 else {
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77 die "No file specified";
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78 }
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79 }
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80
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81
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82 sub getSeqIO {
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83 my ( $self, $file ) = @_;
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84 use Bio::SeqIO;
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85 if ($file ) {
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86 my ($guessed_type) = $filetype->detect( $file );
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87 my $seqio = Bio::SeqIO->new(
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88 -file => $file,
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89 -format => $guessed_type
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90 );
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91 return $seqio;
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92 }
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93 else {
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94 die "No file specified";
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95 }
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96 }
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97
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98
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99 sub parseFile {
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100 my ( $self, %data ) = @_;
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101 use Bio::SeqIO;
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102
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103 my ($guessed_type) = $filetype->detect( $data{'file'} );
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104 my $seqio = Bio::SeqIO->new(
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105 -file => $data{'file'},
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106 -format => $guessed_type
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107 );
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108
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109 # Are we to translate this
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110 $self->var_translate(defined($data{translate}) && $data{translate});
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111 $self->var_header(defined($data{header}) && $data{header});
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112
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113 my @results;
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114 if ( not defined $data{'subset'} ) {
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115 $data{'subset'} = 'all';
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116 }
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117 while ( my $seqobj = $seqio->next_seq() ) {
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118 if (
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119 (ref $data{'subset'} ne 'ARRAY'
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120 && $data{'subset'} eq 'whole' ) # Want the whole thing for a richseq
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121 ||
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122 (ref $seqobj eq 'Bio::Seq' || ref $seqobj eq 'Bio::Seq::fasta')
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123 # or it's a fasta type sequence
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124 )
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125 {
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126 push( @results, $self->handle_seq($seqobj));
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127 }
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128 else #data subset eq sometag
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129 {
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130 my %wanted_tags;
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131 if ( ref $data{'subset'} eq 'ARRAY' ) {
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132 %wanted_tags =
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133 map { $_ => 1 } @{ $data{'subset'} };
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134 }
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135 else {
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136 $wanted_tags{ $data{'subset'} }++;
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137 }
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138 foreach my $feat ( $seqobj->get_SeqFeatures ) {
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139 if (
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140 $wanted_tags{ $feat->primary_tag }
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141 || ( $wanted_tags{'all'}
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142 && $feat->primary_tag ne
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143 "source" )
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144 )
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145 {
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146 push( @results, $self->handle_seq($feat));
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147 }
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148 }
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149 }
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150 }
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151 if ( $data{'callback'} ) {
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152 $data{'callback'}->( \@results );
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153 }
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154 else {
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155 return \@results;
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156 }
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157 }
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158
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159 sub handle_seq {
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160 my ($self, $obj) = @_;
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161
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162 my @line;
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163 if ( $self->var_header() ){
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164 $line[0] = '>' . $self->_getIdentifier($obj);
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165 }
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166
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167 # Get our sequence
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168 $line[1] = $self->intelligent_get_seq($obj);
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169
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170 if ( $self->var_translate() ) {
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171 $line[1] = $self->translate($line[1]);
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172 }
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173 return \@line;
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174 }
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175
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176 sub intelligent_get_seq {
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177 my ($self, $obj, %extra) = @_;
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178 # Top level, e.g., fasta/gbk file, "extra" doesn't apply to these
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179 if ( ref $obj eq 'Bio::Seq::RichSeq' || ref $obj eq 'Bio::Seq' ) {
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180 return $obj->seq;
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181 }else{
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182 return $self->get_seq_from_feature($obj, %extra);
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183 }
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184 }
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185 sub get_seq_from_feature {
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186 my ($self, $feat, %extra) = @_;
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187 my $seq;
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188 my $l;
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189 if($extra{parent}){
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190 $l = $extra{parent}->length();
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191 }
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192
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193 if($extra{upstream}){
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194 if($feat->strand < 0){
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195 my $y = $feat->end + 1;
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196 my $z = $feat->end + $extra{upstream};
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197 if($y < $l){
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198 if($z > $l){
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199 $z = $l;
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200 }
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201 $seq .= $extra{parent}->trunc($y, $z)->revcom->seq;
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202 }
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203 }else{
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204 my $y = $feat->start - $extra{upstream};
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205 my $z = $feat->start - 1;
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206 if($z > 0){
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207 if($y < 1){
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208 $y = 1;
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209 }
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210 $seq .= $extra{parent}->trunc($y, $z)->seq;
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211 }
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212 }
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213 }
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214 if(ref($feat->location) eq 'Bio::Location::Simple'){
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215 $seq .= $feat->seq->seq();
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216 }else{
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217 $seq .= $feat->spliced_seq->seq();
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218 }
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219 if($extra{downstream}){
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220 if($feat->strand < 0){
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221 my $y = $feat->start - $extra{downstream};
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222 my $z = $feat->start - 1;
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223 if($z > 0){
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224 if($y < 1){
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225 $y = 1;
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226 }
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227 $seq .= $extra{parent}->trunc($y, $z)->revcom->seq;
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228 }
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229 }else{
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230 my $y = $feat->end + 1;
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231 my $z = $feat->end + $extra{downstream};
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232 if($y < $l){
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233 if($z > $l){
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234 $z = $l;
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235 }
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236 $seq .= $extra{parent}->trunc($y, $z)->seq;
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237 }
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238 }
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239 }
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240
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241 return $seq;
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242 }
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243
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244
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245 sub translate {
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246 my ($self, $seq) = @_;
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247 if($seq =~ /^[ACTGN]+$/){
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248 my %ct = %{$self->codonTable};
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249 $seq = join( '' , map { if($ct{$_}){ $ct{$_} }else{ () } } unpack("(A3)*", $seq));
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250 }
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251 return $seq;
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252 }
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253
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254 no Moose;
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255 1;
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256
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257 __END__
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258
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259 =pod
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260
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261 =encoding UTF-8
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262
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263 =head1 NAME
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264
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265 CPT::Bio
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266
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267 =head1 VERSION
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268
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269 version 1.99.4
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270
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271 =head2 _getFeatureTag
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272
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273 my $tag = $libCPT->_getFeatureTag($feature,'note');
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274
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275 returns all values of the given tag, joined with ','.
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276
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277 =head2 requestCopy
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278
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279 my $seqobj = $libCPT->requestCopy('file'=>'test.gbk');
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280
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281 requests a 'copy' of a given Bio::SeqIO file, which allows for addition of features before writing out to file.
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282
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283 =head2 getSeqIO
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284
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285 my $seqio = $libCPT->getSeqIO('file'=>'test.gbk');
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286
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287 requests a 'copy' of a given Bio::SeqIO file, which allows for addition of features before writing out to file.
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288
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289 =head2 parseFile
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290
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291 $libCPT->parseFile(
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292 'file' => $options{'file'},
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293 'callback' => \&func,
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294 'translate' => 1,
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295 'header' => 1,
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296 'subset' => ['CDS', $options{'tag'}],
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297 );
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298
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299 Arguably the most important function in this library, wraps a lot of functionality in a clean wrapper, since most of the scripts we have are written around data munging.
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300
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301 =over 4
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302
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303 =item *
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304
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305 file - the Bio::SeqIO file to process
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306
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307 =item *
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308
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309 callback - the function to send our data to. Done all at once, in an array
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310
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311 =item *
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312
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313 translate - should we translate the sequence to amino acids if it's not already.
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314
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315 =item *
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316
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317 subset - either "whole", a valid tag, or an array of valid tags
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318
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319 =item *
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320
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321 header - Do we want a header (FASTA) with our result set
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322
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323 =back
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324
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325 =head1 AUTHOR
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326
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327 Eric Rasche <rasche.eric@yandex.ru>
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328
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329 =head1 COPYRIGHT AND LICENSE
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330
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331 This software is Copyright (c) 2014 by Eric Rasche.
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332
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333 This is free software, licensed under:
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334
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335 The GNU General Public License, Version 3, June 2007
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336
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337 =cut