Query: bio::alignio::maf
OS: debian
Section: 3pm
Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar
Bio::AlignIO::maf(3pm) User Contributed Perl Documentation Bio::AlignIO::maf(3pm)NAMEBio::AlignIO::maf - Multiple Alignment Format sequence input streamSYNOPSISDo 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, " "; print $aln->length, " "; print $aln->num_residues, " "; print $aln->is_flush, " "; print $aln->num_sequences, " "; $aln->splice_by_seq_pos(1); print $aln->consensus_string(60), " "; print $aln->get_seq_by_pos(1)->seq, " "; print $aln->match_line(), " "; print " "; }DESCRIPTIONThis 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/FAQformatFEEDBACKSupport 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 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 the web: https://redmine.open-bio.org/projects/bioperl/ AUTHORS - Allen Day Email: allenday@ucla.eduAPPENDIXThe rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : my $alignio = Bio::AlignIO->new(-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 : perl v5.14.2 2012-03-02 Bio::AlignIO::maf(3pm)
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