Mercurial > repos > cpt > cpt_psm_plotter
annotate lib/CPT/FiletypeDetector.pm @ 1:8691c1c61a8e draft default tip
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author | cpt |
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date | Mon, 05 Jun 2023 02:48:47 +0000 |
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1 package CPT::FiletypeDetector; |
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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 Data::Dumper; |
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6 use autodie; |
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7 |
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8 # ABSTRACT: an incredibly basic filetype detection library for genomic data |
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9 |
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10 |
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11 sub head { |
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12 my ($self, $filename) = @_; |
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13 # We're only going to focus on detecting a few types |
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14 open( my $file, '<', $filename ); |
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15 my @lines; |
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16 my $c = 0; |
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17 while (<$file>) { |
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18 # Read ten lines |
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19 if ( $c++ < 10 ) { |
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20 chomp $_; |
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21 push( @lines, $_ ); |
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22 } |
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23 # Then exit |
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24 else { |
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25 last; |
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26 } |
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27 } |
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28 close($file); |
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29 return @lines; |
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30 } |
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31 |
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32 sub detect { |
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33 my ( $self, $filename ) = @_; |
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34 |
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35 my @lines = $self->head($filename); |
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36 |
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37 use CPT::Filetype::gff3; |
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38 use CPT::Filetype::gbk; |
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39 use CPT::Filetype::embl; |
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40 use CPT::Filetype::fasta; |
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41 |
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42 my @scorers = ( |
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43 CPT::Filetype::gff3->new(lines => \@lines, file => $filename), |
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44 CPT::Filetype::gbk->new(lines => \@lines, file => $filename), |
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45 CPT::Filetype::embl->new(lines => \@lines, file => $filename), |
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46 CPT::Filetype::fasta->new(lines => \@lines, file => $filename), |
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47 ); |
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48 |
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49 my $best_score = 0; |
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50 my $best_name = ""; |
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51 foreach(@scorers){ |
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52 my $score = $_->score(); |
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53 # "1 indicating ... to the exclusion [of others] |
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54 if($score == 1){ |
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55 return $_->name(); |
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56 } |
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57 |
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58 # Otherwise check if better |
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59 if($score > $best_score){ |
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60 $best_name = $_->name(); |
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61 } |
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62 } |
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63 |
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64 return $best_name; |
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65 |
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66 # if(defined $string){ |
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67 # return 'fasta' if( $string =~ /\.(fasta|fast|seq|fa|fsa|nt|aa)$/i); |
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68 # return 'genbank' if( $string =~ /\.(gb|gbank|genbank|gbk)$/i); |
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69 # return 'scf' if( $string =~ /\.scf$/i); |
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70 # return 'pir' if( $string =~ /\.pir$/i); |
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71 # return 'embl' if( $string =~ /\.(embl|ebl|emb|dat)$/i); |
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72 # return 'raw' if( $string =~ /\.(txt)$/i); |
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73 # return 'gcg' if( $string =~ /\.gcg$/i); |
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74 # return 'ace' if( $string =~ /\.ace$/i); |
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75 # return 'bsml' if( $string =~ /\.(bsm|bsml)$/i); |
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76 # return 'swiss' if( $string =~ /\.(swiss|sp)$/i); |
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77 # return 'phd' if( $string =~ /\.(phd|phred)$/i); |
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78 # return 'gff' if( $string =~ /\.(gff|gff3)$/i); |
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79 # return 'blastxml' if( $string =~ /\.(xml)$/i); |
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80 # die "File type detection failure"; |
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81 # } |
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82 # else{ |
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83 # die "File type detection failure"; |
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84 # } |
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85 |
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86 } |
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87 |
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88 no Moose; |
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89 1; |
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90 |
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91 __END__ |
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92 |
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93 =pod |
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94 |
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95 =encoding UTF-8 |
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96 |
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97 =head1 NAME |
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98 |
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99 CPT::FiletypeDetector - an incredibly basic filetype detection library for genomic data |
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100 |
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101 =head1 VERSION |
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102 |
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103 version 1.99.4 |
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104 |
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105 =head1 AUTHOR |
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106 |
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107 Eric Rasche <rasche.eric@yandex.ru> |
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108 |
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109 =head1 COPYRIGHT AND LICENSE |
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110 |
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111 This software is Copyright (c) 2014 by Eric Rasche. |
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112 |
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113 This is free software, licensed under: |
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115 The GNU General Public License, Version 3, June 2007 |
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116 |
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117 =cut |