changes all issue tracking in preparation for switch to github issues
[bioperl-live.git] / Bio / AlignIO / prodom.pm
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2 # BioPerl module for Bio::AlignIO::prodom
4 # based on the Bio::SeqIO::prodom module
5 # by Ewan Birney <birney@ebi.ac.uk>
6 # and Lincoln Stein <lstein@cshl.org>
8 # and the SimpleAlign.pm module of Ewan Birney
10 # Copyright Peter Schattner
12 # You may distribute this module under the same terms as perl itself
13 # _history
14 # September 5, 2000
15 # POD documentation - main docs before the code
17 =head1 NAME
19 Bio::AlignIO::prodom - prodom sequence input/output stream
21 =head1 SYNOPSIS
23 Do not use this module directly. Use it via the L<Bio::AlignIO> class.
25 =head1 DESCRIPTION
27 This object can transform L<Bio::Align::AlignI> objects to and from prodom flat
28 file databases.
30 =head1 FEEDBACK
32 =head2 Support
34 Please direct usage questions or support issues to the mailing list:
36 I<bioperl-l@bioperl.org>
38 rather than to the module maintainer directly. Many experienced and
39 reponsive experts will be able look at the problem and quickly
40 address it. Please include a thorough description of the problem
41 with code and data examples if at all possible.
43 =head2 Reporting Bugs
45 Report bugs to the Bioperl bug tracking system to help us keep track
46 the bugs and their resolution. Bug reports can be submitted via the
47 web:
49 https://github.com/bioperl/bioperl-live/issues
51 =head1 AUTHORS - Peter Schattner
53 Email: schattner@alum.mit.edu
56 =head1 APPENDIX
58 The rest of the documentation details each of the object
59 methods. Internal methods are usually preceded with a _
61 =cut
63 # Let the code begin...
65 package Bio::AlignIO::prodom;
66 use strict;
69 use base qw(Bio::AlignIO);
71 =head2 next_aln
73 Title : next_aln
74 Usage : $aln = $stream->next_aln()
75 Function: returns the next alignment in the stream.
76 Returns : L<Bio::Align::AlignI> object
77 Args : NONE
79 =cut
81 sub next_aln {
82 my $self = shift;
83 my $entry;
84 my ($acc, $fake_id, $start, $end, $seq, $add, %names);
86 my $aln = Bio::SimpleAlign->new(-source => 'prodom');
88 while( $entry = $self->_readline) {
90 if ($entry =~ /^AC\s+(\S+)\s*$/) { #ps 9/12/00
91 $aln->id( $1 );
93 elsif ($entry =~ /^AL\s+(\S+)\|(\S+)\s+(\d+)\s+(\d+)\s+\S+\s+(\S+)\s*$/){ #ps 9/12/00
94 $acc=$1;
95 $fake_id=$2; # Accessions have _species appended
96 $start=$3;
97 $end=$4;
98 $seq=$5;
100 $names{'fake_id'} = $fake_id;
102 $add = Bio::LocatableSeq->new('-seq' => $seq,
103 '-id' => $acc,
104 '-start' => $start,
105 '-end' => $end,
106 '-alphabet' => $self->alphabet,
109 $aln->add_seq($add);
111 elsif ($entry =~ /^CO/) {
112 # the consensus line marks the end of the alignment part of the entry
113 last;
117 return $aln if $aln->num_sequences;
118 return;
123 =head2 write_aln
125 Title : write_aln
126 Usage : $stream->write_aln(@aln)
127 Function: writes the $aln object into the stream in prodom format ###Not yet implemented!###
128 Returns : 1 for success and 0 for error
129 Args : L<Bio::Align::AlignI> object
132 =cut
134 sub write_aln {
135 my ($self,@aln) = @_;
136 $self->throw_not_implemented();