Bio::AlignIO largemultifasta
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Summary
Bio::AlignIO::largemultifasta - Largemultifasta MSA Sequence
input/output stream
Package variables
No package variables defined.
Included modules
Bio::Seq::LargeLocatableSeq
Bio::Seq::SeqFactory
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
_initialize
No description
Code
next_seqDescriptionCode
next_alnDescriptionCode
write_alnDescriptionCode
Methods description
next_seqcode    nextTop
 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
next_alncodeprevnextTop
 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
write_alncodeprevnextTop
 Title   : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in largemultifasta format
Returns : 1 for success and 0 for error
Args : Bio::Align::AlignI object
Methods code
_initializedescriptionprevnextTop
sub _initialize {
  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);
  if( ! defined $self->sequence_factory ) {
      $self->sequence_factory(Bio::Seq::SeqFactory->new
			      (-verbose => $self->verbose(),
			       -type => 'Bio::Seq::LargeLocatableSeq'));
  }
}
next_seqdescriptionprevnextTop
sub next_seq {
    my ($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;
}
next_alndescriptionprevnextTop
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 $aln->num_sequences;
	return;
}
write_alndescriptionprevnextTop
sub write_aln {
    my ($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
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 - Albert Vilella, Heikki LehvaslaihoTop
Email: avilella-at-gmail-dot-com, heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _