Bio::SeqIO::lasergene - Lasergene sequence file input/output stream

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::SeqIO::lasergene - Lasergene sequence file input/output stream

SYNOPSIS

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Do not use this module directly. Use it via the Bio::SeqIO class.

DESCRIPTION

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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.

REFERENCES

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  https://www.dnastar.com/products/lasergene.php

FEEDBACK

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Mailing Lists

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

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 Bugs

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/

AUTHORS

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  Torsten Seemann - torsten.seemann AT infotech.monash.edu.au
  Malcolm Cook  - mec AT stowers-institute.org

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

next_seq

 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)

 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
BioPerl documentation Contained in the BioPerl distribution. 
#-----------------------------------------5~------------------------------------
# PACKAGE : Bio::SeqIO::lasergene
# AUTHOR  : Malcolm Cook <mec@stowers-institute.org>
# CREATED : Feb 16 1999
#
# _History_
#
# This code is based on the Bio::SeqIO::raw module with
# the necessary minor tweaks necessary to get it to read (only)
# Lasergene formatted sequences
#
# Cleaned up by Torsten Seemann June 2006

# POD documentation - main docs before the code



# Let the code begin...

package Bio::SeqIO::lasergene;

use strict;

use base qw(Bio::SeqIO);


use Bio::Seq;
use Bio::Annotation::Collection;
use Bio::Annotation::Comment;

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;
}


sub write_seq {
  my ($self, @seq) = @_;
  $self->throw("write_seq() is not implemented for the lasergene format.");
}


1;