Bio/SeqIO/kegg.pm

   1 #
   2 # BioPerl module for Bio::SeqIO::kegg
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Allen Day <allenday@ucla.edu>
   7 #
   8 # Copyright Allen Day
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::SeqIO::kegg - KEGG sequence input/output stream
  17
  18 =head1 SYNOPSIS
  19
  20   # It is probably best not to use this object directly, but
  21   # rather go through the SeqIO handler system. Go:
  22
  23   use Bio::SeqIO;
  24
  25   $stream = Bio::SeqIO->new(-file => $filename, -format => 'KEGG');
  26
  27   while ( my $seq = $stream->next_seq() ) {
  28         # do something with $seq
  29   }
  30
  31 =head1 DESCRIPTION
  32
  33 This class transforms KEGG gene records into Bio::Seq objects.
  34
  35 =head2 Mapping of record properties to object properties
  36
  37 This section is supposed to document which sections and properties of
  38 a KEGG databank record end up where in the Bioperl object model. It
  39 is far from complete and presently focuses only on those mappings
  40 which may be non-obvious. $seq in the text refers to the
  41 Bio::Seq::RichSeqI implementing object returned by the parser for each
  42 record.
  43
  44 =over 4
  45
  46 =item 'ENTRY'
  47
  48  $seq->primary_id
  49
  50 =item 'NAME'
  51
  52  $seq->display_id
  53
  54 =item 'DEFINITION'
  55
  56  $seq->annotation->get_Annotations('description');
  57
  58 =item 'ORTHOLOG'
  59
  60  grep {$_->database eq 'KO'} $seq->annotation->get_Annotations('dblink')
  61
  62 =item 'CLASS'
  63
  64  grep {$_->database eq 'PATH'}
  65           $seq->annotation->get_Annotations('dblink')
  66
  67 =item 'POSITION'
  68
  69 FIXME, NOT IMPLEMENTED
  70
  71 =item 'PATHWAY'
  72
  73  for my $pathway ( $seq->annotation->get_Annotations('pathway') ) {
  74     #
  75  }
  76
  77 =item 'DBLINKS'
  78
  79  $seq->annotation->get_Annotations('dblink')
  80
  81 =item 'CODON_USAGE'
  82
  83 FIXME, NOT IMPLEMENTED
  84
  85 =item 'AASEQ'
  86
  87  $seq->translate->seq
  88
  89 =item 'NTSEQ'
  90
  91  $seq-E<gt>seq
  92
  93 =back
  94
  95 =head1 FEEDBACK
  96
  97 =head2 Mailing Lists
  98
  99 User feedback is an integral part of the evolution of this and other
 100 Bioperl modules. Send your comments and suggestions preferably to one
 101 of the Bioperl mailing lists.  Your participation is much appreciated.
 102
 103   bioperl-l@bioperl.org                  - General discussion
 104   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 105
 106 =head2 Support
 107
 108 Please direct usage questions or support issues to the mailing list:
 109
 110 I<bioperl-l@bioperl.org>
 111
 112 rather than to the module maintainer directly. Many experienced and
 113 reponsive experts will be able look at the problem and quickly
 114 address it. Please include a thorough description of the problem
 115 with code and data examples if at all possible.
 116
 117 =head2 Reporting Bugs
 118
 119 Report bugs to the Bioperl bug tracking system to help us keep track
 120 the bugs and their resolution. Bug reports can be submitted via the web:
 121
 122   https://github.com/bioperl/bioperl-live/issues
 123
 124 =head1 AUTHOR - Allen Day
 125
 126 Email allenday@ucla.edu
 127
 128 =head1 APPENDIX
 129
 130 The rest of the documentation details each of the object
 131 methods. Internal methods are usually preceded with a _
 132
 133 =cut
 134
 135 # Let the code begin...
 136
 137 package Bio::SeqIO::kegg;
 138 use strict;
 139
 140 use Bio::SeqFeature::Generic;
 141 use Bio::Species;
 142 use Bio::Seq::SeqFactory;
 143 use Bio::Annotation::Collection;
 144 use Bio::Annotation::Comment;
 145 use Bio::Annotation::DBLink;
 146
 147 use base qw(Bio::SeqIO);
 148
 149 sub _initialize {
 150         my($self,@args) = @_;
 151
 152         $self->SUPER::_initialize(@args);
 153         # hash for functions for decoding keys.
 154         $self->{'_func_ftunit_hash'} = {};
 155         if( ! defined $self->sequence_factory ) {
 156                 $self->sequence_factory(Bio::Seq::SeqFactory->new
 157                                                                                 (-verbose => $self->verbose(),
 158                                                                                  -type => 'Bio::Seq::RichSeq'));
 159         }
 160 }
 161
 162 =head2 next_seq
 163
 164  Title   : next_seq
 165  Usage   : $seq = $stream->next_seq()
 166  Function: returns the next sequence in the stream
 167  Returns : Bio::Seq::RichSeq object
 168  Args    :
 169
 170 =cut
 171
 172 sub next_seq {
 173         my ($self,@args) = @_;
 174         my $builder = $self->sequence_builder();
 175         my $seq;
 176         my %params;
 177
 178         my $buffer;
 179         my (@acc, @features);
 180         my ($display_id, $annotation);
 181         my $species;
 182
 183         # initialize; we may come here because of starting over
 184         @features = ();
 185         $annotation = undef;
 186         @acc = ();
 187         $species = undef;
 188         %params = (-verbose => $self->verbose); # reset hash
 189         local($/) = "///\n";
 190
 191         $buffer = $self->_readline();
 192
 193         return if( !defined $buffer ); # end of file
 194         $buffer =~ /^ENTRY/ ||
 195           $self->throw("KEGG stream with bad ENTRY line. Not KEGG in my book. Got $buffer'");
 196
 197         my %FIELDS;
 198         my @chunks = split /\n(?=\S)/, $buffer;
 199
 200         foreach my $chunk (@chunks){
 201                 my($key) = $chunk =~ /^(\S+)/;
 202                 $FIELDS{$key} = $chunk;
 203         }
 204
 205         # changing to split method to get entry_ids that include
 206         # sequence version like Whatever.1
 207         my(undef,$entry_id,$entry_seqtype,$entry_species) =
 208           split(' ',$FIELDS{ENTRY});
 209
 210         my($name);
 211         if ($FIELDS{NAME}) {
 212           ($name) = $FIELDS{NAME} =~ /^NAME\s+(.+)$/;
 213         }
 214
 215         my( $definition, $aa_length, $aa_seq, $nt_length, $nt_seq );
 216
 217         if(( exists $FIELDS{DEFINITION} ) and ( $FIELDS{DEFINITION} =~ /^DEFINITION/ )) {
 218           ($definition) = $FIELDS{DEFINITION} =~ /^DEFINITION\s+(.+)$/s;
 219           $definition =~ s/\s+/ /gs;
 220         }
 221         if(( exists $FIELDS{AASEQ} ) and ( $FIELDS{AASEQ} =~ /^AASEQ/ )) {
 222           ($aa_length,$aa_seq) = $FIELDS{AASEQ} =~ /^AASEQ\s+(\d+)\n(.+)$/s;
 223           $aa_seq =~ s/\s+//g;
 224         }
 225         if(( exists  $FIELDS{NTSEQ} ) and ( $FIELDS{NTSEQ} =~ /^NTSEQ/ )) {
 226           ($nt_length,$nt_seq) = $FIELDS{NTSEQ} =~ /^NTSEQ\s+(\d+)\n(.+)$/s;
 227           $nt_seq =~ s/\s+//g;
 228         }
 229
 230         $annotation = Bio::Annotation::Collection->new();
 231
 232         $annotation->add_Annotation('description',
 233                                                 Bio::Annotation::Comment->new(-text => $definition));
 234
 235         $annotation->add_Annotation('aa_seq',
 236                                                 Bio::Annotation::Comment->new(-text => $aa_seq));
 237
 238         my($ortholog_db,$ortholog_id,$ortholog_desc);
 239         if ($FIELDS{ORTHOLOG}) {
 240                 ($ortholog_db,$ortholog_id,$ortholog_desc) = $FIELDS{ORTHOLOG}
 241                   =~ /^ORTHOLOG\s+(\S+):\s+(\S+)\s+(.*?)$/;
 242
 243         $annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new(
 244                      -database => $ortholog_db,
 245                      -primary_id => $ortholog_id,
 246                      -comment => $ortholog_desc) );
 247   }
 248
 249   if($FIELDS{MOTIF}){
 250      $FIELDS{MOTIF} =~ s/^MOTIF\s+//;
 251      while($FIELDS{MOTIF} =~/\s*?(\S+):\s+(.+?)$/mg){
 252          my $db = $1;
 253          my $ids = $2;
 254          foreach my $id (split(/\s+/, $ids)){
 255
 256      $annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new(
 257               -database =>$db,
 258               -primary_id => $id,
 259               -comment => "")   );
 260         }
 261      }
 262   }
 263
 264   if($FIELDS{PATHWAY}) {
 265      $FIELDS{PATHWAY} =~ s/^PATHWAY\s+//;
 266      while($FIELDS{PATHWAY} =~ /\s*PATH:\s+(.+)$/mg){
 267         $annotation->add_Annotation('pathway',
 268            Bio::Annotation::Comment->new(-text => "$1"));
 269      }
 270   }
 271
 272   if($FIELDS{POSITION}) {
 273     $FIELDS{POSITION} =~ s/^POSITION\s+//;
 274     $annotation->add_Annotation('position',
 275       Bio::Annotation::Comment->new(-text => $FIELDS{POSITION}));
 276   }
 277
 278   if ($FIELDS{CLASS}) {
 279       $FIELDS{CLASS} =~ s/^CLASS\s+//;
 280       $FIELDS{'CLASS'} =~ s/\n//g;
 281       while($FIELDS{CLASS} =~ /(.*?)\[(\S+):(\S+)\]/g){
 282           my ($pathway,$db,$id) = ($1,$2,$3);
 283           $pathway =~ s/\s+/ /g;
 284           $pathway =~ s/\s$//g;
 285           $pathway =~ s/^\s+//;
 286           $annotation->add_Annotation('pathway',
 287                   Bio::Annotation::Comment->new(-text => $pathway));
 288
 289           $annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new(
 290                       -database => $db, -primary_id => $id));
 291       }
 292   }
 293
 294   if($FIELDS{DBLINKS}) {
 295       $FIELDS{DBLINKS} =~ s/^DBLINKS/       /;
 296       while($FIELDS{DBLINKS} =~ /\s+(\S+):\s+(\S+)\n?/gs){ ### modified
 297            $annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new(
 298                     -database => $1, -primary_id => $2)) if $1;
 299       }
 300   }
 301
 302   $params{'-alphabet'}         = 'dna';
 303   $params{'-seq'}              = $nt_seq;
 304   $params{'-display_id'}       = $name;
 305   $params{'-accession_number'} = $entry_id;
 306   $params{'-species'}          = Bio::Species->new(
 307                                                                                           -common_name => $entry_species);
 308   $params{'-annotation'}       = $annotation;
 309
 310   $builder->add_slot_value(%params);
 311   $seq = $builder->make_object();
 312
 313   return $seq;
 314 }
 315
 316 =head2 write_seq
 317
 318  Title   : write_seq
 319  Note    : write_seq() is not implemented for KEGG format output.
 320
 321 =cut
 322
 323 sub write_seq {
 324     shift->throw("write_seq() not implemented for KEGG format output.");
 325 }
 326
 327 1;