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Summary

Bio::AlignIO::largemultifasta - Largemultifasta MSA Sequence
input/output stream

Package variables

Included modules

Inherit

Bio::AlignIO Bio::SeqIO Bio::SimpleAlign

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
largemultifasta flat file databases. This is for the fasta sequence
format NOT FastA analysis program. To process the pairwise alignments
from a FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO
module.
Reimplementation of Bio::AlignIO::fasta modules so that creates
temporary files instead of keeping the whole sequences in memory.

Methods

Methods description

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream while taking care
           of the length
 Returns : Bio::Seq object
 Args    : NONE

 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream.
 Returns : Bio::Align::AlignI object - returns 0 on end of file
	    or on error
 Args    : NONE

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

Methods code

sub _initialize {

  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);
  if( ! defined $self->sequence_factory ) {
      $self->sequence_factory(Bio::Seq::SeqFactory->new
			      (-verbose => $self->verbose(),
			       -type => 'Bio::Seq::LargeLocatableSeq'));
  }

}

sub next_seq {

    my ($self) = @_;
    my $largeseq = $self->sequence_factory->create(-alphabet=>$self->alphabet);
    my ($id,$fulldesc,$entry);
    my $count = 0;
    my $seen = 0;
    while( defined ($entry = $self->_readline) ) {
	if( $seen == 1 && $entry =~ /^\s*>/ ) {
	    $self->_pushback($entry);
	    return $largeseq;
	}
	if ( ($entry eq '>')  ) { $seen = 1; next; }
	elsif( $entry =~ /\s*>(.+?)$/ ) {
	    $seen = 1;
	    ($id,$fulldesc) = ($1 =~ /^\s*(\S+)\s*(.*)$/)
		or $self->warn("Can't parse fasta header");
	    $largeseq->display_id($id);
	    $largeseq->primary_id($id);
	    $largeseq->desc($fulldesc);
	} else {
	    $entry =~ s/\s+//g;
	    $largeseq->add_sequence_as_string($entry);
	}
	(++$count % 1000 == 0 && $self->verbose() > 0) && print "line $count\n";
    }
    if( ! $seen ) { return; }
    return $largeseq;

}

sub next_aln {

    my $self = shift;
    my $largeseq;
    my $aln =  Bio::SimpleAlign->new();
    while (defined ($largeseq = $self->next_seq) ) {
        $aln->add_seq($largeseq);
        $self->debug("sequence readed\n");
    }

    my $alnlen = $aln->length;
    foreach my $largeseq ( $aln->each_seq ) {
	if( $largeseq->length < $alnlen ) {
	    my ($diff) = ($alnlen - $largeseq->length);
	    $largeseq->seq("-" x $diff);
	}
    }

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

}

sub write_aln {

    my ($self,@aln) = @_;
    my ($seq,$desc,$rseq,$name,$count,$length,$seqsub);

    foreach my $aln (@aln) {
	if( ! $aln || ! $aln->isa('Bio::Align::AlignI')  ) {
	    $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
	    next;
	}
	foreach $rseq ( $aln->each_seq() ) {
	    $name = $aln->displayname($rseq->get_nse());
	    $seq  = $rseq->seq();
	    $desc = $rseq->description || '';
	    $self->_print (">$name $desc\n") or return ;
	    $count =0;
	    $length = length($seq);
	    while( ($count * 60 ) < $length ) {
		$seqsub = substr($seq,$count*60,60);
		$self->_print ("$seqsub\n") or return ;
		$count++;
	    }
	}
    }
    $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: avilella-at-gmail-dot-com, heikki-at-bioperl-dot-org

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