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Bio/AlignIO/maf.pm  view on Meta::CPAN

		  unless $line =~ /^##maf/;
	  $self->{seen_header} = 1;
	  # keep in case we parse this later
	  $self->_pushback($line);
    }
	
    my $aln =  Bio::SimpleAlign->new(-source => 'maf');

    my($aline, @slines, $seen_aline);
    while(my $line = $self->_readline()){
	  if ($line =~ /^a\s/xms) {
		# next block?
		if ($seen_aline) {
		  $self->_pushback($line);
		  last;
		}
		$aline = $line;
		$seen_aline++;
	  } elsif ($line =~ /^s\s/xms) {
		push @slines, $line;
	  } else {
		# missed lines
		$self->debug($line);
	  }
    }
	
	# all MAF starts with 'a' line
    return unless $aline;

    my($kvs) = $aline =~ /^a\s+(.+)$/;
    my @kvs  = split /\s+/, $kvs if $kvs;
    my %kv;
    foreach my $kv (@kvs){
	my($k,$v) = $kv =~ /(.+)=(.+)/;
	$kv{$k} = $v;
    }

    $aln->score($kv{score});

    foreach my $sline (@slines){
	my($s,$src,$start,$size,$strand,$srcsize,$text) =
	    split /\s+/, $sline;
	# adjust coordinates to be one-based inclusive
        $start = $start + 1;
    $strand = $strand eq '+' ? 1 : $strand eq '-' ? -1 : 0;
	my $seq = Bio::LocatableSeq->new('-seq'          => $text,
					 '-display_id'   => $src,
					 '-start'        => $strand > 0 ? $start                : ($srcsize-($start+$size-2)),
					 '-end'          => $strand > 0 ? ($start + $size - 1)  : ($srcsize-($start-1)) ,
					 '-strand'       => $strand,
					 '-alphabet'     => $self->alphabet,
					);
	$aln->add_seq($seq);
    }

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

sub write_aln {
  shift->throw_not_implemented
}

1;