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

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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

DESCRIPTION

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

FEEDBACK

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Support

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.

Reporting Bugs

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/

AUTHORS - Peter Schattner

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Email: schattner@alum.mit.edu

APPENDIX

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

next_aln

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

write_aln

 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    : L<Bio::Align::AlignI> object
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::AlignIO::pfam

#   based on the Bio::SeqIO:: modules
#       by Ewan Birney <birney@ebi.ac.uk>
#       and Lincoln Stein  <lstein@cshl.org>
#
#       and the SimpleAlign.pm module of Ewan Birney
#
# Copyright Peter Schattner
#
# You may distribute this module under the same terms as perl itself
# _history
# September 5, 2000
# POD documentation - main docs before the code


# Let the code begin...

package Bio::AlignIO::pfam;
use strict;

use Bio::SimpleAlign;
use base qw(Bio::AlignIO);


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;