[Bioperl-l] microbug in Bio::SeqIO::fasta::next_primary_seq

[Karger, Amir]

Hi.

The following code is from Bio/SeqIO/fasta.pm (from bioperl 0.7.0):

-------------------
sub next_primary_seq {
  my( $self, $as_next_seq ) = @_;
  my $seq;
  my $moltype;
  local $/ = "\n>";

  return unless my $entry = $self->_readline;

  if ($entry eq '>')  {  # very first one
    return unless $entry = $self->_readline;
  }

  my ($top,$sequence) = $entry =~ /^(.+?)\n([^>]*)/s
    or $self->throw("Can't parse entry");
  my ($id,$fulldesc) = $top =~ /^\s*(\S+)\s*(.*)/
    or $self->throw("Can't parse fasta header");
  $id =~ s/^>//;
--------------------

>From what I can tell, the very first entry will not be '>'. It will be the
entire first entry plus a '\n>'. Why? Because '>' doesn't match $/ = '\n>'.
So this condition will never be true.

It's a microbug because it doesn't actually change anything. The $id=~s/^>//
later on removes it. But I'm sure you'd appreciate the opportunity to remove
four lines from the bioperl source code :)

Amir Karger
Curagen Corporation