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
15 # POD documentation - main docs before the code
19 Bio::AlignIO::prodom - prodom sequence input/output stream
23 Do not use this module directly. Use it via the L<Bio::AlignIO> class.
27 This object can transform L<Bio::Align::AlignI> objects to and from prodom flat
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.
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
49 https://redmine.open-bio.org/projects/bioperl/
51 =head1 AUTHORS - Peter Schattner
53 Email: schattner@alum.mit.edu
58 The rest of the documentation details each of the object
59 methods. Internal methods are usually preceded with a _
63 # Let the code begin...
65 package Bio
::AlignIO
::prodom
;
69 use base
qw(Bio::AlignIO);
74 Usage : $aln = $stream->next_aln()
75 Function: returns the next alignment in the stream.
76 Returns : L<Bio::Align::AlignI> object
84 my ($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*$/) { #ps 9/12/00
93 elsif ($entry =~ /^AL\s+(\S+)\|(\S+)\s+(\d+)\s+(\d+)\s+\S+\s+(\S+)\s*$/){ #ps 9/12/00
95 $fake_id=$2; # Accessions have _species appended
100 $names{'fake_id'} = $fake_id;
102 $add = Bio
::LocatableSeq
->new('-seq' => $seq,
106 '-alphabet' => $self->alphabet,
111 elsif ($entry =~ /^CO/) {
112 # the consensus line marks the end of the alignment part of the entry
117 return $aln if $aln->num_sequences;
126 Usage : $stream->write_aln(@aln)
127 Function: writes the $aln object into the stream in prodom format ###Not yet implemented!###
128 Returns : 1 for success and 0 for error
129 Args : L<Bio::Align::AlignI> object
135 my ($self,@aln) = @_;
136 $self->throw_not_implemented();