Bio::AlignIO::maf - Multipla Alignment Format sequence input stream 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"; } 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://hgwdev-sugnet.cse.ucsc.edu/cgi-bin/hgGateway?org=human

Reporting Bugs
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/ Email: allenday@ucla.edu The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $alignio = new Bio::AlignIO(-format => 'maf' -file => '>file', -idlength => 10, -idlinebreak => 1); Function: Initialize a new L<Bio::AlignIO::maf> reader Returns : L<Bio::AlignIO> object Args :

next_aln
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 : L<Bio::SimpleAlign> object Args :