lib/Bio/Tools/Fgenesh.pm

   1 #
   2 # BioPerl module for Bio::Tools::Fgenesh
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Christopher Dwan (chris@dwan.org)
   7 #
   8 # Copied, lock stock & barrel from Genscan.pm
   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::Tools::Fgenesh - parse results of one Fgenesh run
  17
  18 =head1 SYNOPSIS
  19
  20    use Bio::Tools::Fgenesh;
  21
  22    $fgenesh = Bio::Tools::Fgenesh->new(-file => 'result.fgenesh');
  23    # filehandle:
  24    $fgenesh = Bio::Tools::Fgenesh->new( -fh  => \*INPUT );
  25
  26    # parse the results
  27    # note: this class is-a Bio::Tools::AnalysisResult which implements
  28    # Bio::SeqAnalysisParserI, i.e., $fgensh->next_feature() is the same
  29    while($gene = $fgenesh->next_prediction()) {
  30        # $gene is an instance of Bio::Tools::Prediction::Gene, which inherits
  31        # off Bio::SeqFeature::Gene::Transcript.
  32        #
  33        # $gene->exons() returns an array of
  34        # Bio::Tools::Prediction::Exon objects
  35        # all exons:
  36        @exon_arr = $gene->exons();
  37
  38        # initial exons only
  39        @init_exons = $gene->exons('Initial');
  40        # internal exons only
  41        @intrl_exons = $gene->exons('Internal');
  42        # terminal exons only
  43        @term_exons = $gene->exons('Terminal');
  44        # singleton exons:
  45        ($single_exon) = $gene->exons();
  46    }
  47
  48    # essential if you gave a filename at initialization (otherwise the file
  49    # will stay open)
  50    $fgenesh->close();
  51
  52 =head1 DESCRIPTION
  53
  54 The Fgenesh module provides a parser for Fgenesh (version 2) gene structure
  55 prediction output. It parses one gene prediction into a
  56 Bio::SeqFeature::Gene::Transcript- derived object.
  57
  58 This module also implements the L<Bio::SeqAnalysisParserI> interface, and thus
  59 can be used wherever such an object fits.
  60
  61 =head1 FEEDBACK
  62
  63 =head2 Mailing Lists
  64
  65 User feedback is an integral part of the evolution of this and other
  66 Bioperl modules. Send your comments and suggestions preferably to one
  67 of the Bioperl mailing lists.  Your participation is much appreciated.
  68
  69   bioperl-l@bioperl.org                  - General discussion
  70   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  71
  72 =head2 Support
  73
  74 Please direct usage questions or support issues to the mailing list:
  75
  76 I<bioperl-l@bioperl.org>
  77
  78 rather than to the module maintainer directly. Many experienced and
  79 reponsive experts will be able look at the problem and quickly
  80 address it. Please include a thorough description of the problem
  81 with code and data examples if at all possible.
  82
  83 =head2 Reporting Bugs
  84
  85 Report bugs to the Bioperl bug tracking system to help us keep track
  86 the bugs and their resolution.  Bug reports can be submitted via the
  87 web:
  88
  89   https://github.com/bioperl/bioperl-live/issues
  90
  91 =head1 AUTHOR - Chris Dwan
  92
  93 Email chris-at-dwan.org
  94
  95 =head1 APPENDIX
  96
  97 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
  98
  99 =cut
 100
 101
 102 # Let the code begin...
 103
 104
 105 package Bio::Tools::Fgenesh;
 106
 107 use strict;
 108 use Symbol;
 109
 110 use Bio::Root::Root;
 111 use Bio::Tools::Prediction::Gene;
 112 use Bio::Tools::Prediction::Exon;
 113
 114 use base qw(Bio::Tools::AnalysisResult);
 115
 116 my %ExonTags = ('CDSf' => 'Initial',
 117                 'CDSi' => 'Internal',
 118                 'CDSl' => 'Terminal',
 119                 'CDSo' => 'Singleton');
 120
 121 sub _initialize_state {
 122     my ($self,@args) = @_;
 123
 124     # first call the inherited method!
 125     $self->SUPER::_initialize_state(@args);
 126
 127     # our private state variables
 128     $self->{'_preds_parsed'} = 0;
 129     $self->{'_has_cds'} = 0;
 130     # array of pre-parsed predictions
 131     $self->{'_preds'} = [];
 132     # seq stack
 133     $self->{'_seqstack'} = [];
 134 }
 135
 136 =head2 analysis_method
 137
 138  Usage     : $genscan->analysis_method();
 139  Purpose   : Inherited method. Overridden to ensure that the name matches
 140              /genscan/i.
 141  Returns   : String
 142  Argument  : n/a
 143
 144 =cut
 145
 146 #-------------
 147 sub analysis_method {
 148 #-------------
 149     my ($self, $method) = @_;
 150     if($method && ($method !~ /fgenesh/i)) {
 151         $self->throw("method $method not supported in " . ref($self));
 152     }
 153     return $self->SUPER::analysis_method($method);
 154 }
 155
 156 =head2 next_feature
 157
 158  Title   : next_feature
 159  Usage   : while($gene = $fgenesh->next_feature()) {
 160                   # do something
 161            }
 162  Function: Returns the next gene structure prediction of the Fgenesh result
 163            file. Call this method repeatedly until FALSE is returned.
 164
 165            The returned object is actually a SeqFeatureI implementing object.
 166            This method is required for classes implementing the
 167            SeqAnalysisParserI interface, and is merely an alias for
 168            next_prediction() at present.
 169
 170  Example :
 171  Returns : A Bio::Tools::Prediction::Gene object.
 172  Args    :
 173
 174 =cut
 175
 176 sub next_feature {
 177     my ($self,@args) = @_;
 178     # even though next_prediction doesn't expect any args (and this method
 179     # does neither), we pass on args in order to be prepared if this changes
 180     # ever
 181     return $self->next_prediction(@args);
 182 }
 183
 184 =head2 next_prediction
 185
 186  Title   : next_prediction
 187  Usage   : while($gene = $fgenesh->next_prediction()) { ... }
 188  Function: Returns the next gene structure prediction of the Genscan result
 189            file. Call this method repeatedly until FALSE is returned.
 190  Example :
 191  Returns : A Bio::Tools::Prediction::Gene object.
 192  Args    :
 193
 194 =cut
 195
 196 sub next_prediction {
 197     my ($self) = @_;
 198     my $gene;
 199
 200     # if the prediction section hasn't been parsed yet, we do this now
 201     $self->_parse_predictions() unless $self->_predictions_parsed();
 202
 203     # get next gene structure
 204     $gene = $self->_prediction();
 205
 206     if($gene) {
 207         # fill in predicted protein, and if available the predicted CDS
 208         #
 209
 210         # use the seq stack if there's a seq on it
 211         my $seqobj = pop(@{$self->{'_seqstack'}});
 212         my ($id, $seq);
 213         unless ($seqobj) {
 214            ($id, $seq) = $self->_read_fasta_seq();
 215            my $alphabet;
 216            if (($id =~ /mrna/) || ($id =~ /cds/)) { $alphabet = 'dna'; }
 217            else { $alphabet = 'protein'; }
 218            $seqobj = Bio::PrimarySeq->new('-seq'        => $seq,
 219                                           '-display_id' => $id,
 220                                           '-alphabet'   => $alphabet);
 221         }
 222         if ($seqobj) {
 223
 224             # check that prediction number matches the prediction number
 225             # indicated in the sequence id (there may be incomplete gene
 226             # predictions that contain only signals with no associated protein
 227             # prediction.
 228
 229             $gene->primary_tag() =~ /[^0-9]([0-9]+)$/;
 230             my $prednr = $1;
 231             if ($id !~ /_predicted_(\w+)_$prednr/) {
 232                 # this is not our sequence, so push back for next prediction
 233                 push(@{$self->{'_seqstack'}}, $seqobj);
 234             } else {
 235                 if ($1 eq "protein") {
 236                   $gene->predicted_protein($seqobj);
 237                 } elsif (($1 eq "mrna") || ($1 eq "cds")) {
 238                   $self->_has_cds(1);
 239                   $gene->predicted_cds($seqobj);
 240
 241                   # Have to go back in and get the protein...
 242                   ($id, $seq) = $self->_read_fasta_seq();
 243                   if ($id =~ /_cds_/) {
 244                     ($id, $seq) = $self->_read_fasta_seq();
 245                   }
 246
 247                   $seqobj = Bio::PrimarySeq->new('-seq' => $seq,
 248                                                  '-display_id' => $id,
 249                                                  '-alphabet' => "protein");
 250                   $gene->predicted_protein($seqobj);
 251                 }
 252             }
 253         }
 254     }
 255
 256     return $gene;
 257 }
 258
 259 =head2 _parse_predictions
 260
 261  Title   : _parse_predictions()
 262  Usage   : $obj->_parse_predictions()
 263  Function: Parses the prediction section. Automatically called by
 264            next_prediction() if not yet done.
 265  Example :
 266  Returns :
 267
 268 =cut
 269
 270 sub _parse_predictions {
 271     my ($self) = @_;
 272     my $gene;
 273     my $seqname;
 274
 275     while(defined($_ = $self->_readline())) {
 276
 277         if(/^\s*(\d+)\s+([+\-])/) {
 278             my $line = $_;
 279
 280             # exon or signal
 281             my $prednr = $1;
 282             my $strand = ($2 eq '+') ? 1 : -1;
 283
 284             if(! defined($gene)) {
 285                 $gene = Bio::Tools::Prediction::Gene->new(
 286                                        '-primary' => "GenePrediction$prednr",
 287                                        '-source' => 'Fgenesh');
 288             }
 289             # split into fields
 290             chomp();
 291             my @flds = split(/\s+/, ' ' . $line);
 292             ## NB - the above adds leading whitespace before the gene
 293             ## number in case there was none (as quick patch to code
 294             ## below which expects it but it is not present after 999
 295             ## predictions!) This allows >999 predictions to be parsed.
 296
 297             # create the feature object depending on the type of signal
 298             my $predobj;
 299             my $is_exon = grep {$line =~ $_} keys(%ExonTags);
 300             my ($start, $end);
 301             if($is_exon) {
 302                 $predobj = Bio::Tools::Prediction::Exon->new();
 303                 $predobj->score($flds[8]);
 304                 $start   = $flds[5];
 305                 $end     = $flds[7];
 306             } else {
 307                 # PolyA site, or TSS
 308                 $predobj = Bio::SeqFeature::Generic->new();
 309                 $predobj->score($flds[5]);
 310                 $start   = $flds[4];
 311                 $end     = $flds[4];
 312             }
 313             # set common fields
 314             $predobj->source_tag('Fgenesh');
 315             $predobj->strand($strand);
 316
 317 # Following tactical commenting-out made by
 318 # malcolm.cook@stowers-institute.org since coordinate reversal is
 319 # apparently vestigial copy/paste detritus from Genscan.pm origins of
 320 # this module and this is NOT needed for fgenesh (at least in v
 321 # 2.1.4).
 322
 323 #           if($predobj->strand() == 1) {
 324                 $predobj->start($start);
 325                 $predobj->end($end);
 326 #           } else {
 327 #               $predobj->end($start);
 328 #               $predobj->start($end);
 329 #           }
 330
 331             # print STDERR "start $start end $end\n";
 332             # add to gene structure (should be done only when start and end
 333             # are set, in order to allow for proper expansion of the range)
 334             if($is_exon) {
 335                 # first, set fields unique to exons
 336                 $predobj->primary_tag($ExonTags{$flds[4]} . 'Exon');
 337                 $predobj->is_coding(1);
 338                 my $cod_offset;
 339                 if($predobj->strand() == 1) {
 340                     $cod_offset = ($flds[9] - $predobj->start()) % 3;
 341                     # Possible values are -2, -1, 0, 1, 2. -1 and -2 correspond
 342                     # to offsets 2 and 1, resp. Offset 3 is the same as 0.
 343                     $cod_offset += 3 if($cod_offset < 1);
 344                 } else {
 345                     # On the reverse strand the Genscan frame also refers to
 346                     # the first base of the first complete codon, but viewed
 347                     # from forward, which is the third base viewed from
 348                     # reverse.
 349                     $cod_offset = ($flds[11] - $predobj->end()) % 3;
 350                     # Possible values are -2, -1, 0, 1, 2. Due to the reverse
 351                     # situation, {2,-1} and {1,-2} correspond to offsets
 352                     # 1 and 2, resp. Offset 3 is the same as 0.
 353                     $cod_offset -= 3 if($cod_offset >= 0);
 354                     $cod_offset = -$cod_offset;
 355                 }
 356                 # Offsets 2 and 1 correspond to frame 1 and 2 (frame of exon
 357                 # is the frame of the first base relative to the exon, or the
 358                 # number of bases the first codon is missing).
 359                 $predobj->frame(3 - $cod_offset);
 360                 # print STDERR "  frame is " . $predobj->frame() . "\n";
 361                 # then add to gene structure object
 362                 $gene->add_exon($predobj, $ExonTags{$flds[1]});
 363             } elsif($flds[3] eq 'PolA') {
 364                 $predobj->primary_tag("PolyAsite");
 365                 $gene->poly_A_site($predobj);
 366             } elsif($flds[3] eq 'TSS') {
 367                 $predobj->primary_tag("Promoter"); # (hey! a TSS is NOT a promoter... what's going on here?...
 368                 $gene->add_promoter($predobj);
 369                 #I'd like to do this (for now):
 370                 #$predobj->primary_tag("TSS"); #this is not the right model, but, it IS a feature at least.
 371                 #but the followg errs out
 372                 #$gene->add_SeqFeature($predobj); #err: MSG: start is undefined when bounds at Bio::SeqFeature::Generic::add_SeqFeature 671 check since gene has no start yet
 373             }
 374             else {
 375               $self->throw("unrecognized prediction line: " . $line);
 376             }
 377             next;
 378         }
 379
 380         if(/^\s*$/ && defined($gene)) {
 381             # current gene is completed
 382             $gene->seq_id($seqname);
 383             $self->_add_prediction($gene);
 384             $gene = undef;
 385             next;
 386         }
 387
 388         if(/^(FGENESH)\s+([\d\.]+)/) {
 389             $self->analysis_method($1);
 390             $self->analysis_method_version($2);
 391             if (/\s(\S+)\sgenomic DNA/) {
 392               $self->analysis_subject($1);
 393             }
 394             next;
 395         }
 396
 397         if(/^\s*Seq name:\s+(\S+)/) {
 398             $seqname = $1;
 399             next;
 400         }
 401
 402         /^Predicted protein/ && do {
 403             # section of predicted sequences
 404             $self->_pushback($_);
 405             last;
 406         };
 407     }
 408
 409     $self->_predictions_parsed(1);
 410 }
 411
 412 =head2 _prediction
 413
 414  Title   : _prediction()
 415  Usage   : $gene = $obj->_prediction()
 416  Function: internal
 417  Example :
 418  Returns :
 419
 420 =cut
 421
 422 sub _prediction {
 423     my ($self) = @_;
 424
 425     return unless(exists($self->{'_preds'}) && @{$self->{'_preds'}});
 426     return shift(@{$self->{'_preds'}});
 427 }
 428
 429 =head2 _add_prediction
 430
 431  Title   : _add_prediction()
 432  Usage   : $obj->_add_prediction($gene)
 433  Function: internal
 434  Example :
 435  Returns :
 436
 437 =cut
 438
 439 sub _add_prediction {
 440     my ($self, $gene) = @_;
 441
 442     if(! exists($self->{'_preds'})) {
 443         $self->{'_preds'} = [];
 444     }
 445     push(@{$self->{'_preds'}}, $gene);
 446 }
 447
 448 =head2 _predictions_parsed
 449
 450  Title   : _predictions_parsed
 451  Usage   : $obj->_predictions_parsed
 452  Function: internal
 453  Example :
 454  Returns : TRUE or FALSE
 455
 456 =cut
 457
 458 sub _predictions_parsed {
 459     my ($self, $val) = @_;
 460
 461     $self->{'_preds_parsed'} = $val if $val;
 462     if(! exists($self->{'_preds_parsed'})) {
 463         $self->{'_preds_parsed'} = 0;
 464     }
 465     return $self->{'_preds_parsed'};
 466 }
 467
 468 =head2 _has_cds
 469
 470  Title   : _has_cds()
 471  Usage   : $obj->_has_cds()
 472  Function: Whether or not the result contains the predicted CDSs, too.
 473  Example :
 474  Returns : TRUE or FALSE
 475
 476 =cut
 477
 478 sub _has_cds {
 479     my ($self, $val) = @_;
 480
 481     $self->{'_has_cds'} = $val if $val;
 482     if(! exists($self->{'_has_cds'})) {
 483         $self->{'_has_cds'} = 0;
 484     }
 485     return $self->{'_has_cds'};
 486 }
 487
 488 =head2 _read_fasta_seq
 489
 490  Title   : _read_fasta_seq()
 491  Usage   : ($id,$seqstr) = $obj->_read_fasta_seq();
 492  Function: Simple but specialised FASTA format sequence reader. Uses
 493            $self->_readline() to retrieve input, and is able to strip off
 494            the traling description lines.
 495  Example :
 496  Returns : An array of two elements: fasta_id & sequence
 497
 498 =cut
 499
 500 sub _read_fasta_seq {
 501     my ($self) = @_;
 502     my ($id, $seq);
 503     #local $/ = ">";
 504
 505     my $entry = $self->_readline();
 506     # print " ^^ $entry\n";
 507     return unless ($entry);
 508     $entry = $self->_readline() if ($entry =~ /^Predicted protein/);
 509     # print " ^^ $entry\n";
 510
 511     # Pick up the header / id.
 512     if ($entry =~ /^>FGENESH:/) {
 513       if ($entry =~ /^>FGENESH:\s+(\d+)/) {
 514          # print STDERR "  this is a predicted gene\n";
 515          $id  = "_predicted_protein_" . $1;
 516       } elsif ($entry =~ /^>FGENESH:\[mRNA\]\s*(\d+)/) {
 517         # print STDERR "  this is an mRNA\n";
 518          $id  = "_predicted_mrna_" . $1;
 519       } elsif ($entry =~ /^>FGENESH:\[exon\]\s+Gene:\s*(\d+)/) {
 520          $id  = "_predicted_cds_"  . $1;
 521       }
 522       $seq = "";
 523       $entry = $self->_readline();
 524     }
 525
 526     my $done = 0;
 527     while (!$done) {
 528        # print "*** $entry\n";
 529        if (($entry =~ /^>FGENESH:\[exon\]/) && ($id =~ /^_predicted_cds_/)) {
 530          # print STDERR "  -- informed about an exon header...\n";
 531          $entry = $self->_readline();
 532        } else {
 533          $seq .= $entry;
 534          # print STDERR "  Added $entry\n";
 535        }
 536
 537        last unless $entry  = $self->_readline();
 538        if (($entry =~ /^>/) &&
 539            (!(($entry =~ /^>FGENESH:\[exon\]/) && ($id =~ /^_predicted_cds_/)))) {
 540           $self->_pushback($entry); last;
 541        }
 542     }
 543
 544     # id and sequence
 545     $seq =~ s/\s//g; # Remove whitespace
 546     return ($id, $seq);
 547 }
 548
 549 1;