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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;
	$entry =~ /^\/\// && last;
	if($entry !~ /^(\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;


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

	$aln->add_seq($add);
	
    }

#  If $end <= 0, we have either reached the end of
#  file in <> or we have encountered some other error
#
   if ($end <= 0) { undef $aln;}

      return $aln;

}

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

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

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Email: schattner@alum.mit.edu

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