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Summary

Bio::AlignIO::pfam - pfam sequence input/output stream

Package variables

Included modules

Inherit

Bio::AlignIO

Synopsis

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

Description

This object can transform Bio::SimpleAlign objects to and from pfam flat
file databases.

Methods

Methods description

 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream
 Returns : Bio::Align::AlignI object
 Args    : NONE

 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::Align::AlignI object

Methods code

sub next_aln {

    my $self = shift;
    my $entry;
    my $name;
    my $start;
    my $end;
    my $seq;
    my $add;
    my $acc;
    my %names;

    my $aln =  Bio::SimpleAlign->new(-source => 'pfam');

    while( $entry = $self->_readline) {
	chomp $entry;
	$entry =~ m{^//} && last;
	if($entry !~ m{^(\S+)/(\d+)-(\d+)\s+(\S+)\s*} ) {
	    $self->throw("Found a bad line [$_] in the pfam format alignment");
	    next;
	}

	$name = $1;
	$start = $2;
	$end = $3;
	$seq = $4;


	$add = Bio::LocatableSeq->new('-seq'         => $seq,
				      '-display_id'  => $name,
				      '-start'       => $start,
				      '-end'         => $end,
				      '-alphabet'    => $self->alphabet,
			    );

	$aln->add_seq($add);

    }

#  If $end <= 0, we have either reached the end of
#  file in <> or we have encountered some other error
#

	return $aln if $aln->num_sequences;
	return;

}

sub write_aln {

   my ($self,@aln) = @_;
   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"); }
   my $aln = shift @aln;
   if( ! $aln || ! $aln->isa('Bio::Align::AlignI')  ) {
       $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
       next;
   }
   my ($namestr,$seq,$add);
   my ($maxn);
   $maxn = $aln->maxdisplayname_length();

   foreach $seq ( $aln->each_seq() ) {
       $namestr = $aln->displayname($seq->get_nse());
       $add = $maxn - length($namestr) + 2;
       $namestr .= " " x $add;
	  $self->_print (sprintf("%s  %s\n",$namestr,$seq->seq())) or return;
   }
   $self->flush() if $self->_flush_on_write && defined $self->_fh;
   return 1;
}

1;

}

General documentation

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.

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:

  https://redmine.open-bio.org/projects/bioperl/

Email: schattner@alum.mit.edu

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