Bio::AlignIO xmfa
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Summary
Bio::AlignIO::xmfa - XMFA MSA Sequence input/output stream
Package variables
No package variables defined.
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 from
XMFA flat file databases. For more information, see:
  http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-output-file-formats.html
This module is based on the AlignIO::fasta parser written by
Peter Schattner
Methods
next_alnDescriptionCode
write_alnDescriptionCode
_get_lenDescriptionCode
widthDescriptionCode
_process_seq
No description
Code
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 xmfa 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 ($name, $tempname, $seqchar);
    my $aln = Bio::SimpleAlign->new();
    my $seqs = 0;
    # alignments
while (defined (my $entry = $self->_readline) ) { chomp $entry; if ( index($entry, '=') == 0 ) { if (defined $name && $seqchar) { my $seq = $self->_process_seq($name, $seqchar); $aln->add_seq($seq); } if ($aln && $entry =~ m{score\s*=\s*(\d+)}) { $aln->score($1); } $seqchar = ''; undef $name; last; } elsif ( $entry =~ m{^>.+$}xms) { if ( defined $name ) { my $seq = $self->_process_seq($name, $seqchar); $aln->add_seq($seq); } $seqchar = ''; $name = $entry; } else { $seqchar .= $entry; } } # this catches last sequence if '=' is not present (Mauve)
if ( defined $name ) { my $seq = $self->_process_seq($name, $seqchar); $aln->add_seq($seq); } $aln->num_sequences ? return $aln : return;
}
write_alndescriptionprevnextTop
sub write_aln {
    my ($self,@aln) = @_;
    my $width = $self->width;
    my ($seq,$desc,$rseq,$name,$count,$length,$seqsub,$start,$end,$strand,$id);

    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);
#}
my $seqct = 1; foreach $rseq ( $aln->each_seq() ) { ($start, $end, $strand, $id) = ($rseq->start, $rseq->end, $rseq->strand || 0, $rseq->display_id); $strand = ($strand == 1) ? '+' : ($strand == -1) ? '-' : ''; $name = sprintf("%d:%d-%d %s %s",$seqct,$start,$end,$strand,$id); $seq = $rseq->seq(); $desc = $rseq->description || ''; $self->_print (">$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) || return 0; $seqct++; } my $alndesc = ''; $alndesc = "score = ".$aln->score if ($aln->score); $self->_print("= $alndesc\n") || return 0; } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1;
}
_get_lendescriptionprevnextTop
sub _get_len {
    my ($self,$seq) = @_;
    $seq =~ s/[^A-Z]//gi;
    return CORE::length($seq);
}
widthdescriptionprevnextTop
sub width {
    my $self = shift;

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

####### PRIVATE #######
}
_process_seqdescriptionprevnextTop
sub _process_seq {
    my ($self, $entry, $seq) = @_;
    my ($start, $end, $strand, $seqname, $desc, $all);
    # put away last name and sequence
if ( $entry =~ m{^>\s*\d+:(\d+)-(\d+)\s([+-]{1})(?:\s+(\S+)\s*(\S\.*)?)?} ) { ($start, $end, $seqname, $desc) = ($1, $2, $4, $5); $strand = ($3 eq '+') ? 1 : -1; } else { $self->throw("Line does not comform to XMFA format:\n$entry"); } my $seqobj = Bio::LocatableSeq->new( -nowarnonempty => 1, -strand => $strand, -seq => $seq, -display_id => $seqname, -description => $desc || $all, -start => $start, -end => $end, -alphabet => $self->alphabet, ); $self->debug("Reading $seqname\n"); return $seqobj; } 1;
}
General documentation
TODOTop
Finish write_aln(), clean up code, allow LargeLocatableSeq (ie for
very large sequences a'la Mauve)
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
Chris Fields
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _