Bio::SeqIO lasergene
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Summary
Bio::SeqIO::lasergene - Lasergene sequence file input/output stream
Package variables
No package variables defined.
Included modules
Bio::Annotation::Collection
Bio::Annotation::Comment
Bio::Seq
Inherit
Bio::SeqIO
Synopsis
Do not use this module directly. Use it via the Bio::SeqIO class.
Description
This object can product Bio::Seq::RichSeq objects from Lasergene sequence files.
IT DOES NOT PARSE ANY ATTIBUTE VALUE PAIRS IN THE HEADER OF THE LASERGENE FORMATTED FILE.
IT DOES NOT WRITE THESE FILES EITHER.
Methods
next_seqDescriptionCode
write_seqDescriptionCode
Methods description
next_seqcode    nextTop
 Title   : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args : none
write_seq (NOT IMPLEMENTED)codeprevnextTop
 Title   : write_seq
Usage : $stream->write_seq($seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Array of Bio::PrimarySeqI objects
Methods code
next_seqdescriptionprevnextTop
sub next_seq {
   my ($self) = @_;

   my $state = 0;
   my @comment;
   my @sequence;

   while (my $line = $self->_readline) {
     $state = 1 if $state == 0;
     chomp $line;
     next if $line =~ m/^\s*$/; # skip blank lines

if ($line eq '^^') { # end of a comment or sequence
$state++;
last if $state > 2; # we have comment and sequence so exit
} elsif ($state == 1) { # another piece of comment
push @comment, $line; } elsif ($state == 2) { # another piece of sequence
push @sequence, $line } else { $self->throw("unreachable state reached, probable bug!"); } } # return quietly if there was nothing in the file
return if $state == 0; # ensure we read some comment and some sequence
if ($state < 2) { $self->throw("unexpected end of file"); } my $sequence = join('', @sequence); # print STDERR "SEQ=[[$sequence]]\n";
$sequence or $self->throw("empty sequence in lasergene file"); my $seq = Bio::Seq->new(-seq => $sequence); my $comment = join('; ', @comment); # print STDERR "COM=[[$comment]]\n";
my $anno = Bio::Annotation::Collection->new; $anno->add_Annotation('comment', Bio::Annotation::Comment->new(-text => $comment) ); $seq->annotation($anno); return $seq;
}
write_seqdescriptionprevnextTop
sub write_seq {
  my ($self, @seq) = @_;
  $self->throw("write_seq() is not implemented for the lasergene format.");
}


1;
}
General documentation
REFERENCESTop
  https://www.dnastar.com/products/lasergene.php
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORSTop
  Torsten Seemann - torsten.seemann AT infotech.monash.edu.au
Malcolm Cook - mec AT stowers-institute.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _