Bio::AlignIO maf
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Summary
Bio::AlignIO::maf - Multiple Alignment Format sequence input stream
Package variables
No package variables defined.
Included modules
Bio::SimpleAlign
Inherit
Bio::AlignIO
Synopsis
 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->num_residues, "\n"; print $aln->is_flush, "\n"; print $aln->num_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"; }
Description
This class constructs Bio::SimpleAlign objects from an MAF-format
multiple alignment file.
Writing in MAF format is currently unimplemented.
Spec of MAF format is here:
http://genome.ucsc.edu/FAQ/FAQformat
Methods
_initialize
No description
Code
next_alnDescriptionCode
write_aln
No description
Code
Methods description
next_alncode    nextTop
 Title   : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream.
Throws an exception if trying to read in PHYLIP
sequential format.
Returns : Bio::SimpleAlign object
Args :
Methods code
_initializedescriptionprevnextTop
sub _initialize {
  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);

  1;
}
next_alndescriptionprevnextTop
sub next_aln {
    my $self = shift;

	# check beginning of file for proper header
if(!$self->{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/; $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' => $start, '-end' => $start + $size - 1, '-strand' => $strand, '-alphabet' => $self->alphabet, ); $aln->add_seq($seq); } return $aln if $aln->num_sequences; return;
}
write_alndescriptionprevnextTop
sub write_aln {
  shift->throw_not_implemented
}

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 - Allen DayTop
Email: allenday@ucla.edu
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
newTop
 Title   : new
Usage : my $alignio = Bio::AlignIO->new(-format => 'maf'
-file => '>file',
-idlength => 10,
-idlinebreak => 1);
Function: Initialize a new Bio::AlignIO::maf reader
Returns : Bio::AlignIO object
Args :