2 # BioPerl module for Bio::AlignIO::pfam
4 # based on the Bio::SeqIO:: modules
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::pfam - pfam sequence input/output stream
23 Do not use this module directly. Use it via the L<Bio::AlignIO> class.
27 This object can transform Bio::SimpleAlign objects to and from pfam 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://github.com/bioperl/bioperl-live/issues
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
::pfam
;
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
92 my $aln = Bio
::SimpleAlign
->new(-source
=> 'pfam');
94 while( $entry = $self->_readline) {
96 $entry =~ m{^//} && last;
97 if($entry !~ m{^(\S+)/(\d+)-(\d+)\s+(\S+)\s*} ) {
98 $self->throw("Found a bad line [$_] in the pfam format alignment");
108 $add = Bio
::LocatableSeq
->new('-seq' => $seq,
109 '-display_id' => $name,
112 '-alphabet' => $self->alphabet,
119 # If $end <= 0, we have either reached the end of
120 # file in <> or we have encountered some other error
123 return $aln if $aln->num_sequences;
132 Usage : $stream->write_aln(@aln)
133 Function: writes the $aln object into the stream
134 Returns : 1 for success and 0 for error
135 Args : L<Bio::Align::AlignI> object
141 my ($self,@aln) = @_;
142 if( @aln > 1 ) { $self->warn("Only the 1st pfam alignment will be output since the format does not support multiple alignments in the same file"); }
143 my $aln = shift @aln;
144 if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) {
145 $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
148 my ($namestr,$seq,$add);
150 $maxn = $aln->maxdisplayname_length();
152 foreach $seq ( $aln->each_seq() ) {
153 $namestr = $aln->displayname($seq->get_nse());
154 $add = $maxn - length($namestr) + 2;
155 $namestr .= " " x
$add;
156 $self->_print (sprintf("%s %s\n",$namestr,$seq->seq())) or return;
158 $self->flush() if $self->_flush_on_write && defined $self->_fh;