Summary

Bio::AlignIO::prodom - prodom 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 prodom flat
file databases.

Methods

Methods description

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

 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in prodom format  ###Not yet implemented!###
 Returns : 1 for success and 0 for error
 Args    : Bio::SimpleAlign object

Methods code

sub next_aln {

    my $self = shift;
    my $entry;
    my ($acc, $fake_id, $start, $end, $seq, $add, %names);

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

    while( $entry = $self->_readline) {

       if ($entry =~ /^AC\s+(\S+)\s*$/) {         #ps 9/12/00
	   $aln->id( $1 );
       }
       elsif ($entry =~ /^AL\s+(\S+)\|(\S+)\s+(\d+)\s+(\d+)\s+\S+\s+(\S+)\s*$/){    #ps 9/12/00
	   $acc=$1;
	   $fake_id=$2;  # Accessions have _species appended
	   $start=$3;
	   $end=$4;
	   $seq=$5;
	
	   $names{'fake_id'} = $fake_id;

	   $add = new Bio::LocatableSeq('-seq'=>$seq,
			       '-id'=>$acc,
			       '-start'=>$start,
			       '-end'=>$end,
			       );
	
	   $aln->add_seq($add);
       }
       elsif ($entry =~ /^CO/) {
	   # the consensus line marks the end of the alignment part of the entry
	   last;
       }
   }

#  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) = @_;

    $self->throw("Sorry: prodom-format output, not yet implemented! /n");

}

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://bio.perl.org/bioperl-bugs/

Email: schattner@alum.mit.edu

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