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Bio::AlignIO::maf.3pm
Langue: en
Version: 2010-05-19 (ubuntu - 24/10/10)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::AlignIO::maf - Multiple Alignment Format sequence input streamSYNOPSIS
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
FEEDBACK
Support
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:http://bugzilla.open-bio.org/
AUTHORS - Allen Day
Email: allenday@ucla.eduAPPENDIX
The 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 :
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