Do not use this module directly. Use it via the Bio::AlignIO class.
use Bio::AlignIO;
my $alignio = Bio::AlignIO->new(-fh => \*STDIN, -format => 'maf');
while(my $aln = $alignio->next_aln()){
my $match_line = $aln->match_line;
print $aln, "\n";
print $aln->length, "\n";
print $aln->no_residues, "\n";
print $aln->is_flush, "\n";
print $aln->no_sequences, "\n";
$aln->splice_by_seq_pos(1);
print $aln->consensus_string(60), "\n";
print $aln->get_seq_by_pos(1)->seq, "\n";
print $aln->match_line(), "\n";
print "\n";
}
sub _initialize
{ my($self,@args) = @_;
$self->SUPER::_initialize(@args);
1; } | sub next_aln
{ my $self = shift;
if(!$seen_header){
my $line = $self->_readline;
$self->throw("This doesn't look like a MAF file. First line should start with ##maf, but it was: ".$line)
unless $line =~ /^##maf/;
$seen_header = 1;
}
my $aln = Bio::SimpleAlign->new(-source => 'maf');
my($aline, @slines);
while(my $line = $self->_readline()){
$aline = $line if $line =~ /^a/;
push @slines, $line if $line =~ /^s /;
last if $line !~ /\S/;
}
return undef 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;
my $seq = new Bio::LocatableSeq('-seq' => $text,
'-id' => $src,
'-start' => $start,
'-end' => $start + $size,
);
$aln->add_seq($seq);
}
return $aln;} | Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/