Bio/SeqIO/lasergene.pm

   1 #-----------------------------------------5~------------------------------------
   2 # PACKAGE : Bio::SeqIO::lasergene
   3 # AUTHOR  : Malcolm Cook <mec@stowers-institute.org>
   4 # CREATED : Feb 16 1999
   5 #
   6 # _History_
   7 #
   8 # This code is based on the Bio::SeqIO::raw module with
   9 # the necessary minor tweaks necessary to get it to read (only)
  10 # Lasergene formatted sequences
  11 #
  12 # Cleaned up by Torsten Seemann June 2006
  13
  14 # POD documentation - main docs before the code
  15
  16 =head1 NAME
  17
  18 Bio::SeqIO::lasergene - Lasergene sequence file input/output stream
  19
  20 =head1 SYNOPSIS
  21
  22 Do not use this module directly.  Use it via the L<Bio::SeqIO> class.
  23
  24 =head1 DESCRIPTION
  25
  26 This object can product Bio::Seq::RichSeq objects from Lasergene sequence files.
  27
  28 IT DOES NOT PARSE ANY ATTRIBUTE VALUE PAIRS IN THE HEADER OF THE LASERGENE FORMATTED FILE.
  29
  30 IT DOES NOT WRITE THESE FILES EITHER.
  31
  32 =head1 REFERENCES
  33
  34   https://www.dnastar.com/products/lasergene.php
  35
  36 =head1 FEEDBACK
  37
  38 =head2 Mailing Lists
  39
  40 User feedback is an integral part of the evolution of this and other
  41 Bioperl modules. Send your comments and suggestions preferably to one
  42 of the Bioperl mailing lists.  Your participation is much appreciated.
  43
  44   bioperl-l@bioperl.org                  - General discussion
  45   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  46
  47 =head2 Support
  48
  49 Please direct usage questions or support issues to the mailing list:
  50
  51 I<bioperl-l@bioperl.org>
  52
  53 rather than to the module maintainer directly. Many experienced and
  54 reponsive experts will be able look at the problem and quickly
  55 address it. Please include a thorough description of the problem
  56 with code and data examples if at all possible.
  57
  58 =head2 Reporting Bugs
  59
  60 Report bugs to the Bioperl bug tracking system to help us keep track
  61 of the bugs and their resolution. Bug reports can be submitted via
  62 the web:
  63
  64   https://github.com/bioperl/bioperl-live/issues
  65
  66 =head1 AUTHORS
  67
  68   Torsten Seemann - torsten.seemann AT infotech.monash.edu.au
  69   Malcolm Cook  - mec AT stowers-institute.org
  70
  71 =head1 APPENDIX
  72
  73 The rest of the documentation details each of the object methods.
  74 Internal methods are usually preceded with a _
  75
  76 =cut
  77
  78
  79 # Let the code begin...
  80
  81 package Bio::SeqIO::lasergene;
  82
  83 use strict;
  84
  85 use base qw(Bio::SeqIO);
  86
  87 =head2 next_seq
  88
  89  Title   : next_seq
  90  Usage   : $seq = $stream->next_seq()
  91  Function: returns the next sequence in the stream
  92  Returns : Bio::Seq object
  93  Args    : none
  94
  95 =cut
  96
  97 use Bio::Seq;
  98 use Bio::Annotation::Collection;
  99 use Bio::Annotation::Comment;
 100
 101 sub next_seq {
 102    my ($self) = @_;
 103
 104    my $state = 0;
 105    my @comment;
 106    my @sequence;
 107
 108    while (my $line = $self->_readline) {
 109      $state = 1 if $state == 0;
 110      chomp $line;
 111      next if $line =~ m/^\s*$/; # skip blank lines
 112
 113      if ($line eq '^^') {  # end of a comment or sequence
 114        $state++;
 115        last if $state > 2; # we have comment and sequence so exit
 116      }
 117      elsif ($state == 1) { # another piece of comment
 118        push @comment, $line;
 119      }
 120      elsif ($state == 2) { # another piece of sequence
 121        push @sequence, $line
 122      }
 123      else {
 124        $self->throw("unreachable state reached, probable bug!");
 125      }
 126    }
 127
 128    # return quietly if there was nothing in the file
 129    return if $state == 0;
 130
 131    # ensure we read some comment and some sequence
 132    if ($state < 2) {
 133      $self->throw("unexpected end of file");
 134    }
 135
 136    my $sequence = join('', @sequence);
 137 #   print STDERR "SEQ=[[$sequence]]\n";
 138    $sequence or $self->throw("empty sequence in lasergene file");
 139    my $seq = Bio::Seq->new(-seq => $sequence);
 140
 141    my $comment = join('; ', @comment);
 142 #   print STDERR "COM=[[$comment]]\n";
 143    my $anno = Bio::Annotation::Collection->new;
 144    $anno->add_Annotation('comment', Bio::Annotation::Comment->new(-text => $comment) );
 145    $seq->annotation($anno);
 146
 147    return $seq;
 148 }
 149
 150 =head2 write_seq (NOT IMPLEMENTED)
 151
 152  Title   : write_seq
 153  Usage   : $stream->write_seq($seq)
 154  Function: writes the $seq object into the stream
 155  Returns : 1 for success and 0 for error
 156  Args    : Array of Bio::PrimarySeqI objects
 157
 158 =cut
 159
 160 sub write_seq {
 161   my ($self, @seq) = @_;
 162   $self->throw("write_seq() is not implemented for the lasergene format.");
 163 }
 164
 165
 166 1;
 167