Bio::AlignIO fasta
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Summary
Bio::AlignIO::fasta - fasta MSA Sequence input/output stream
Package variables
No package variables defined.
Included modules
Bio::LocatableSeq
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
fasta flat file databases. This is for the fasta alignment format, not
for the FastA sequence analysis program. To process the alignments from
FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO module.
Methods
next_alnDescriptionCode
write_alnDescriptionCode
_get_lenDescriptionCode
widthDescriptionCode
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 - returns 0 on end of file
or on error
Args : -width => optional argument to specify the width sequence
will be written (60 chars by default)
See Bio::Align::AlignI
write_alncodeprevnextTop
 Title   : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in fasta format
Returns : 1 for success and 0 for error
Args : Bio::Align::AlignI object
See Bio::Align::AlignI
_get_lencodeprevnextTop
 Title   : _get_len
Usage :
Function: determine number of alphabetic chars
Returns : integer
Args : sequence string
widthcodeprevnextTop
 Title   : width
Usage : $obj->width($newwidth)
$width = $obj->width;
Function: Get/set width of alignment
Returns : integer value of width
Args : on set, new value (a scalar or undef, optional)
Methods code
next_alndescriptionprevnextTop
sub next_aln {
	my $self = shift;
	my ($width) = $self->_rearrange([qw(WIDTH)],@_);
	$self->width($width || $WIDTH);

	my ($start, $end, $name, $seqname, $seq, $seqchar, $entry, 
		 $tempname, $tempdesc, %align, $desc, $maxlen);
	my $aln = Bio::SimpleAlign->new();

	while (defined ($entry = $self->_readline) ) {
	    chomp $entry;
	    if ( $entry =~ s/^>\s*(\S+)\s*// ) {
		$tempname  = $1;
		chomp($entry);
		$tempdesc = $entry;
		if ( defined $name ) {
		    $seqchar =~ s/\s//g;
				# put away last name and sequence
if ( $name =~ /(\S+)\/(\d+)-(\d+)/ ) { $seqname = $1; $start = $2; $end = $3; } else { $seqname = $name; $start = 1; $end = $self->_get_len($seqchar); } $seq = Bio::LocatableSeq->new ( '-seq' => $seqchar, '-display_id' => $seqname, '-description' => $desc, '-start' => $start, '-end' => $end, '-alphabet' => $self->alphabet, ); $aln->add_seq($seq); $self->debug("Reading $seqname\n"); } $desc = $tempdesc; $name = $tempname; $desc = $entry; $seqchar = ""; next; } # removed redundant symbol validation
# this is already done in Bio::PrimarySeq
$seqchar .= $entry; } # Next two lines are to silence warnings that
# otherwise occur at EOF when using <$fh>
$name = "" if (!defined $name); $seqchar="" if (!defined $seqchar); $seqchar =~ s/\s//g; # Put away last name and sequence
if ( $name =~ /(\S+)\/(\d+)-(\d+)/ ) { $seqname = $1; $start = $2; $end = $3; } else { $seqname = $name; $start = 1; $end = $self->_get_len($seqchar); } # This logic now also reads empty lines at the
# end of the file. Skip this is seqchar and seqname is null
unless ( length($seqchar) == 0 && length($seqname) == 0 ) { $seq = Bio::LocatableSeq->new ('-seq' => $seqchar, '-display_id' => $seqname, '-description' => $desc, '-start' => $start, '-end' => $end, '-alphabet' => $self->alphabet, ); $aln->add_seq($seq); $self->debug("Reading $seqname\n"); } my $alnlen = $aln->length; foreach my $seq ( $aln->each_seq ) { if ( $seq->length < $alnlen ) { my ($diff) = ($alnlen - $seq->length); $seq->seq( $seq->seq() . "-" x $diff); } } # no sequences means empty alignment (possible EOF)
return $aln if $aln->num_sequences;
}
write_alndescriptionprevnextTop
sub write_aln {
    my ($self,@aln) = @_;
    my $width = $self->width;
    my ($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;
	}
	if( $self->force_displayname_flat ) {
	    $aln->set_displayname_flat(1);
	}
	foreach $rseq ( $aln->each_seq() ) {
	    $name = $aln->displayname($rseq->get_nse());
	    $seq  = $rseq->seq();
	    $desc = $rseq->description || '';
		$desc = ' '.$desc if $desc;
	    $self->_print (">$name$desc\n") or return;	
	    $count = 0;
	    $length = length($seq);
	    if(defined $seq && $length > 0) {
		$seq =~ s/(.{1,$width})/$1\n/g;
	    } else {
		$seq = "\n";
	    }
	    $self->_print($seq);
	}
    }
    $self->flush if $self->_flush_on_write && defined $self->_fh;
    return 1;
}
_get_lendescriptionprevnextTop
sub _get_len {
	my ($self,$seq) = @_;
	my $chars = $Bio::LocatableSeq::GAP_SYMBOLS.$Bio::LocatableSeq::FRAMESHIFT_SYMBOLS;
	$seq =~ s{[$chars]+}{}gi;
	return CORE::length($seq);
}
widthdescriptionprevnextTop
sub width {
    my $self = shift;

    return $self->{'_width'} = shift if @_;
    return $self->{'_width'} || $WIDTH;
}

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/
AUTHORSTop
Peter Schattner
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _