Public Member Functions
public	fset2transcript ()

public	fset2transcript_guess_phases ()

public	fset2transcript_3frame ()

public	fset2transcript_with_seq ()

Detailed Description

Synopsis

use Bio::EnsEMBL::TranscriptFactory;
 
&Bio::EnsEMBL::TranscriptFactory::fset2transcript($fset_id);

Description

Module containing the subroutines fset2transcript*, 
which create transcripts from features (formally housed in
Bio::EnsEMBL::DBSQL::Utils).

Definition at line 21 of file TranscriptFactory.pm.

Member Function Documentation

◆ fset2transcript()

public Bio::EnsEMBL::TranscriptFactory::fset2transcript ( )

Undocumented method

Code:

click to view

◆ fset2transcript_3frame()

public Bio::EnsEMBL::TranscriptFactory::fset2transcript_3frame ( )

Undocumented method

Code:

click to view

sub fset2transcript_3frame {
  my ($fset,$contig) = @_;
 
  my @f = $fset->sub_SeqFeature;
  
  if ($f[0]->strand == 1) {
    @f = sort {$a->start <=> $b->start} @f;
  } else {
    @f = sort {$b->start <=> $a->start} @f;
  }
 
  my @transcripts;
 
  my $startphase = 0;
 
  while ($startphase < 3) {
    my $endphase = $startphase;
 
    my $transcript = new Bio::EnsEMBL::Transcript;
 
    push(@transcripts,$transcript);
 
    $transcript->temporary_id($contig->id . "." . $endphase);
 
    my $count    = 1;
    my @exons;
 
   
    foreach my $f (@f) {
      #print "exon seqname = ".$f->seqname."\n";
      my $exon  = new Bio::EnsEMBL::Exon;
      #print STDERR "exon ".$f->gffstring."\n";
      push(@exons,$exon);
      $exon->seqname($f->seqname);
      $exon->temporary_id ($contig->id . ".$count");
      $exon->contig   ($contig);
      $exon->start    ($f->start);
      $exon->end      ($f->end  );
      $exon->strand   ($f->strand);
      $exon->slice($contig);
      $exon->phase    ($endphase);
      $exon->end_phase( ($exon->phase + $exon->length)%3 );
      #$exon->score    ($f->score);
#      $exon->p_value  ($f->p_value);
      $endphase = $exon->end_phase;
 
      $transcript->add_Exon($exon);
      $count++;
 
      #print STDERR "Added exon start " . $exon->start . " end " . $exon->end . " strand " . $exon->strand . " score " . $exon->score . " pvalue " . $exon->p_value . "\n";
    }
       
    my $translation = new Bio::EnsEMBL::Translation;
 
    my $contig_id = "";
    my $fset_id   = "";
 
    if (defined($contig->id)) {
       $contig_id = $contig->id;
    }
    if (defined($fset->id)) {
       $fset_id = $fset->id;
    }
 
    $translation->temporary_id($contig_id . "." . $fset_id);
    $translation->start        (1);
    $translation->end          ($exons[$#exons]->end - $exons[$#exons]->start + 1);
    $translation->start_Exon($exons[0]);
    $translation->end_Exon  ($exons[$#exons]);
    $transcript->translation($translation);
 
 #  print STDERR "Phase $startphase " . $transcript->translate->seq . "\n";
 
    $startphase++;
  }
  #print "finshed  fset2transcript_3frame\n";
  return @transcripts;
}

◆ fset2transcript_guess_phases()

public Bio::EnsEMBL::TranscriptFactory::fset2transcript_guess_phases ( )

Undocumented method

Code:

click to view

◆ fset2transcript_with_seq()

public Bio::EnsEMBL::TranscriptFactory::fset2transcript_with_seq ( )

Undocumented method

Code:

click to view

The documentation for this class was generated from the following file:

ensembl/modules/Bio/EnsEMBL/TranscriptFactory.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ fset2transcript()

◆ fset2transcript_3frame()

◆ fset2transcript_guess_phases()

◆ fset2transcript_with_seq()