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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:47:24 +0000
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1 package CPT::GBK2GFF3;
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2 use strict;
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3 use warnings;
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4 use CPT;
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5 use Data::Dumper;
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6 use autodie;
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7 use Bio::SeqIO;
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8 use Moose;
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9
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10 has data => (
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11 is => 'rw',
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12 isa => 'ArrayRef',
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13 default => sub { [] },
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14 );
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15 has header => (
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16 is => 'rw',
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17 isa => 'ArrayRef',
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18 );
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19 has sequence => (
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20 is => 'rw',
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21 isa => 'Str',
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22 );
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23 has seqid => (
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24 is => 'rw',
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25 isa => 'Str',
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26 );
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27 has genbank => (
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28 is => 'rw',
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29 isa => 'Str',
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30 );
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31 has is_circular => (
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32 is => 'rw',
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33 isa => 'Str',
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34 );
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35 has id_prefix => ( is => 'rw', isa => 'Str' );
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36 has global_feat_idx => ( is => 'rw', isa => 'Int', default => sub { 0 } );
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37 has source => ( is => 'rw', isa => 'ArrayRef');
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38
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39 my %feat_type_count;
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40 my %reserved_keys = map { $_ => 1 }
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41 qw/ID Name Alias Parent Target Gap Derives_from Note Dbxref Ontology_term/;
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42
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43 use CPT::Bio;
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44 my $bio = CPT::Bio->new();
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45 my %key_mapping = (
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46 "-" => [ "located_sequence_feature", "SO:0000110" ],
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47 "-10_signal" => [ "minus_10_signal", "SO:0000175" ],
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48 "-35_signal" => [ "minus_35_signal", "SO:0000176" ],
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49 "3'UTR" => [ "three_prime_UTR", "SO:0000205" ],
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50 "3'clip" => [ "three_prime_clip", "SO:0000557" ],
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51 "5'UTR" => [ "five_prime_UTR", "SO:0000204" ],
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52 "5'clip" => [ "five_prime_clip", "SO:0000555" ],
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53 "CAAT_signal" => [ "CAAT_signal", "SO:0000172" ],
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54 "CDS" => [ "CDS", "SO:0000316" ],
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55 "D-loop" => [ "D_loop", "SO:0000297" ],
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56 "D_segment" => [ "D_gene", "SO:0000458" ],
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57 "GC_signal" => [ "GC_rich_region", "SO:0000173" ],
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58 "LTR" => [ "long_terminal_repeat", "SO:0000286" ],
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59 "RBS" => [ "ribosome_entry_site", "SO:0000139" ],
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60 "STS" => [ "STS", "SO:0000331" ],
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61 "TATA_signal" => [ "TATA_box", "SO:0000174" ],
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62 "attenuator" => [ "attenuator", "SO:0000140" ],
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63 "enhancer" => [ "enhancer", "SO:0000165" ],
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64 "exon" => [ "exon", "SO:0000147" ],
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65 "gap" => [ "gap", "SO:0000730" ],
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66 "gene" => [ "gene", "SO:0000704" ],
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67 "iDNA" => [ "iDNA", "SO:0000723" ],
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68 "intron" => [ "intron", "SO:0000188" ],
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69 "mRNA" => [ "mRNA", "SO:0000234" ],
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70 "mat_peptide" => [ "mature_protein_region", "SO:0000419" ],
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71 "misc_RNA" => [ "transcript", "SO:0000673" ],
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72 "misc_binding" => [ "binding_site", "SO:0000409" ],
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73 "misc_difference" => [ "sequence_difference", "SO:0000413" ],
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74 "misc_feature" => [ "region", "SO:0000001" ],
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75 "misc_recomb" => [ "recombination_feature", "SO:0000298" ],
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76 "misc_signal" => [ "regulatory_region", "SO:0005836" ],
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77 "misc_structure" => [ "sequence_secondary_structure", "SO:0000002" ],
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78 "modified_base" => [ "modified_DNA_base", "SO:0000305" ],
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79 "operon" => [ "operon", "SO:0000178" ],
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80 "oriT" => [ "origin_of_transfer", "SO:0000724" ],
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81 "polyA_signal" => [ "polyA_signal_sequence", "SO:0000551" ],
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82 "polyA_site" => [ "polyA_site", "SO:0000553" ],
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83 "precursor_RNA" => [ "primary_transcript", "SO:0000185" ],
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84 "prim_transcript" => [ "primary_transcript", "SO:0000185" ],
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85 "primer_bind" => [ "primer_binding_site", "SO:0005850" ],
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86 "promoter" => [ "promoter", "SO:0000167" ],
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87 "protein_bind" => [ "protein_binding_site", "SO:0000410" ],
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88 "rRNA" => [ "rRNA", "SO:0000252" ],
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89 "repeat_region" => [ "repeat_region", "SO:0000657" ],
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90 "repeat_unit" => [ "repeat_unit", "SO:0000726" ],
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91 "satellite" => [ "satellite_DNA", "SO:0000005" ],
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92 "scRNA" => [ "scRNA", "SO:0000013" ],
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93 "sig_peptide" => [ "signal_peptide", "SO:0000418" ],
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94 "snRNA" => [ "snRNA", "SO:0000274" ],
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95 "snoRNA" => [ "snoRNA", "SO:0000275" ],
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96 "source" => [ "contig", "SO:0000149" ], # manually modified
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97 "stem_loop" => [ "stem_loop", "SO:0000313" ],
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98 "tRNA" => [ "tRNA", "SO:0000253" ],
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99 "terminator" => [ "terminator", "SO:0000141" ],
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100 "transit_peptide" => [ "transit_peptide", "SO:0000725" ],
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101 "variation" => [ "sequence_variant", "SO:0000109" ],
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102 );
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103
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104
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105 sub get_gff3_file {
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106 my ($self) = @_;
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107 my @output;
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108 for my $header_line ( @{ $self->header() } ) {
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109 push( @output, $header_line );
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110 }
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111 push( @output, join( "\t", @{ $self->get_source } ) );
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112 for my $data_line ( @{ $self->data() }) {
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113 push( @output, join( "\t", @{$data_line} ) );
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114 }
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115 push( @output, '##FASTA' );
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116 push( @output, '>' . $self->seqid() );
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117 my $seq = $self->sequence();
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118 $seq =~ s/(.{80})/$1\n/g;
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119 push( @output, $seq );
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120 return join( "\n", @output );
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121 }
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122
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123 sub escape {
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124 my ($self, $str) = @_;
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125 $str =~ s/,/%2C/g;
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126 $str =~ s/=/%3D/g;
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127 $str =~ s/;/%3B/g;
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128 $str =~ s/\t/%09/g;
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129 return $str;
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130 }
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131
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132 sub FT_SO_map {
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133 my ( $self, $key ) = @_;
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134 if ( $key_mapping{$key} ) {
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135 my @result = @{ $key_mapping{$key} };
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136 return $result[0];
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137 }
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138 else {
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139 return 'region';
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140 }
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141 }
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142
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143 sub source_map {
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144 my ( $self, $type ) = @_;
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145 if ( $self->{'override_source'} ) {
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146 return $self->{'override_source'};
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147 }
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148 if ( $self->{'annotation_software'}{$type} ) {
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149 return $self->{'annotation_software'}{$type};
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150 }
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151 else {
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152 return '.';
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153 }
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154 }
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155
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156 sub get_attrs {
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157 my ( $self, %data ) = @_;
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158 my $feature = $data{'feat'};
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159 my $parents_ref = $data{'parents'};
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160
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161 my %attrs = ();
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162 $attrs{'ID'} =
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163 $self->id_prefix() . '.' . ($self->global_feat_idx());
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164
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165 $self->global_feat_idx($self->global_feat_idx()+1);
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166
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167 # Handle Identifier
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168 my $identifier = $bio->_getIdentifier($feature);
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169 if ( $identifier ne 'ERROR' ) {
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170 $attrs{'Name'} = $identifier . '.' . $feature->primary_tag;
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171 }
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172
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173 # Handle parents, if there are any
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174 if ($parents_ref) {
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175 if ( ref($parents_ref) eq 'ARRAY' ) {
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176 $attrs{'Parent'} = $parents_ref;
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177 }
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178 else {
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179 $attrs{'Parent'} = [$parents_ref];
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180 }
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181 }
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182
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183 # These are otherwise "Special" keys that need to be handled differently.
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184 if ( $feature->has_tag('note') ) {
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185 my @notes = $feature->get_tag_values('note');
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186 $attrs{'Note'} = \@notes;
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187 }
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188 if ( $feature->has_tag('db_xref') ) {
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189 my @dbxref = $feature->get_tag_values('db_xref');
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190 $attrs{'Dbxref'} = \@dbxref;
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191 }
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192
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193 # Do the rest
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194 for my $tag ( $feature->get_all_tags() ) {
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195
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196 # If not one of the specially handled ones
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197 if ( $tag ne 'name' && $tag ne 'note' && $tag ne 'db_xref' ) {
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198
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199 # If not a reserved_key
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200 if ( !$reserved_keys{$tag} ) {
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201 my @vals = $feature->get_tag_values($tag);
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202 $attrs{lc($tag)} = \@vals;
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203 }
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204 else {
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205 warn
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206 "Trying to set a reserved key $tag with value $attrs{$tag}";
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207 }
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208 }
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209 }
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210 my %response = (
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211 id => $attrs{'ID'},
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212 attr_str => $self->post_process_attribute_string(%attrs),
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213 );
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214 return %response;
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215 }
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216
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217 sub post_process_attribute_string {
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218 my ($self,%attrs) = @_;
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219 my @parts = ();
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220 for my $k ( keys %attrs ) {
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221
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222 # IGNORED TAGS
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223 if ( $k ne 'translation' && $k ne 'product' ) {
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224 my $joined =
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225 $self->escape_and_join_attribute_subpart( $attrs{$k} );
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226 push @parts, "$k=$joined";
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227 }
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228 }
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229
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230 #print STDERR join("\t",@parts),"\n";
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231 return join( ";", @parts );
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232
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233 }
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234
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235 sub escape_and_join_attribute_subpart {
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236 my ($self,$ref) = @_;
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237 if ( ref($ref) eq 'ARRAY' ) {
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238 my @attrs = @{$ref};
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239 return join( ",", map { $self->escape($_) } @attrs );
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240 }
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241 else { #scalar
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242 return $self->escape($ref);
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243 }
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244 }
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245
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246 sub get_source {
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247 my ($self) = @_;
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248 if ( !$self->source() ) {
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249 $self->auto_source();
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250 }
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251 return $self->source();
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252 }
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253
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254 sub auto_source {
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255
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256 # Auto generate a source feature, in case there isn't one.
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257 my ($self) = @_;
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258 my @region = (
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259 $self->seqid(),
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260 ( $self->genbank() ? 'Genbank' : 'Assembly' ),
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261 'contig',
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262 1,
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263 $self->get_length,
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264 '.',
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265 '.',
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266 '.',
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267 sprintf( "ID=%s;Name=%s", $self->seqid(), $self->seqid() )
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268 . ( $self->is_circular() ? ";Is_circular=True" : "" )
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269 );
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270 $self->source(\@region);
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271 }
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272
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273 sub add_feature {
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274 my ( $self, $feat ) = @_;
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275 my $primary_tag = $feat->primary_tag;
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276 if ( $primary_tag eq 'CDS' ) {
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277 my ( $id, $data_0 ) = $self->_add_gene( feat => $feat, );
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278 my ($data_1) = $self->_add_feature(
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279 feat => $feat,
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280 parent => $id,
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281 );
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282 $self->_low_level_add_feature($data_0);
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283 $self->_low_level_add_feature($data_1);
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284 }
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285 elsif ( $primary_tag eq 'source' ) {
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286 my ($data) = $self->_add_feature( feat => $feat, );
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287
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288 # YUCK.
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289 my @z = @{$data};
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290 my $seqid = $self->seqid();
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291 $z[8] =~ s/ID=[^;]*;/ID=$seqid;/g;
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292 $self->source( \@z );
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293 }
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294 elsif ( $primary_tag ne 'gene' ) {
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295 my ($data) = $self->_add_feature( feat => $feat, );
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296 $self->_low_level_add_feature($data);
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297 }
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298
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299 }
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300
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301 sub _low_level_add_feature {
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302 my ( $self, $data ) = @_;
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303 push( @{ $self->data() }, $data );
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304 }
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305
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306 sub _add_feature {
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307 my ( $self, %data ) = @_;
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308 my %attrs =
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309 $self->get_attrs( feat => $data{feat}, parents => $data{parent} );
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310 my @data = (
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311 $self->seqid(),
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312 $self->source_map( $data{feat}->primary_tag ),
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313 $self->FT_SO_map( $data{feat}->primary_tag ),
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314 $data{feat}->start,
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315 $data{feat}->end,
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316 '.',
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317 ( $data{feat}->strand == 1 ? '+' : '-' ),
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318 '.',
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319 $attrs{attr_str}
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320 );
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321
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322 #$self->_low_level_add_feature(\@data);
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323 return \@data;
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324 }
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325
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326 sub _add_gene {
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327 my ( $self, %data ) = @_;
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328 my $id = $self->id_prefix() . '.' . ( $self->global_feat_idx());
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329 $self->global_feat_idx($self->global_feat_idx()+1);
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330 my $gene_count = ++$feat_type_count{'gene'};
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331 my @data = (
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332 $self->seqid(),
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333 $self->source_map( $data{feat}->primary_tag ),
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334 $self->FT_SO_map('gene'),
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335 $data{feat}->start,
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336 $data{feat}->end,
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337 '.',
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338 ( $data{feat}->strand == 1 ? '+' : '-' ),
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339 '.',
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340 "ID=$id;Name=Gene$gene_count"
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341 );
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342
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343 #$self->_low_level_add_feature(\@data);
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344 return ( $id, \@data );
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345 }
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346
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347 no Moose;
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348 1;
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349
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350 __END__
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351
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352 =pod
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353
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354 =encoding UTF-8
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355
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356 =head1 NAME
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357
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358 CPT::GBK2GFF3
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359
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360 =head1 VERSION
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361
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362 version 1.99.4
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363
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364 =head1 AUTHOR
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365
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366 Eric Rasche <rasche.eric@yandex.ru>
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367
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368 =head1 COPYRIGHT AND LICENSE
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369
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370 This software is Copyright (c) 2014 by Eric Rasche.
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371
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372 This is free software, licensed under:
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373
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374 The GNU General Public License, Version 3, June 2007
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375
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376 =cut