Bio::AlignIO pfam
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Summary
Bio::AlignIO::pfam - pfam sequence input/output stream
Package variables
No package variables defined.
Included modules
Bio::SimpleAlign
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
next_alnDescriptionCode
write_alnDescriptionCode
Methods description
next_alncode    nextTop
 Title   : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream
Returns : Bio::Align::AlignI object
Args : NONE
write_alncodeprevnextTop
 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
next_alndescriptionprevnextTop
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 $aln->num_sequences; return;
}
write_alndescriptionprevnextTop
sub write_aln {
   my ($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
FEEDBACKTop
Support Top
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 BugsTop
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 SchattnerTop
Email: schattner@alum.mit.edu
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _