bio::alignio::mega(3pm) [debian man page]
Bio::AlignIO::mega(3pm) User Contributed Perl Documentation Bio::AlignIO::mega(3pm) NAME
Bio::AlignIO::mega - Parse and Create MEGA format data files SYNOPSIS
use Bio::AlignIO; my $alignio = Bio::AlignIO->new(-format => 'mega', -file => 't/data/hemoglobinA.meg'); while( my $aln = $alignio->next_aln ) { # process each alignment or convert to another format like NEXUS } DESCRIPTION
This object handles reading and writing data streams in the MEGA format (Kumar and Nei). FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists 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 of the bugs and their resolution. Bug reports can be submitted the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Jason Stajich Email jason-at-bioperl.org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Supports the following MEGA format features: - The file has to start with '#mega' - Reads in the name of the alignment from a comment (anything after '!TITLE: ') . - Reads in the format parameters datatype Returns : L<Bio::Align::AlignI> object - returns 0 on end of file or on error Args : NONE write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in MEGA format Returns : 1 for success and 0 for error Args : L<Bio::Align::AlignI> object perl v5.14.2 2012-03-02 Bio::AlignIO::mega(3pm)
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Bio::AlignIO::largemultifasta(3pm) User Contributed Perl Documentation Bio::AlignIO::largemultifasta(3pm) NAME
Bio::AlignIO::largemultifasta - Largemultifasta MSA Sequence input/output stream SYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class. DESCRIPTION
This object can transform Bio::SimpleAlign objects to and from largemultifasta flat file databases. This is for the fasta sequence format NOT FastA analysis program. To process the pairwise alignments from a FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO module. Reimplementation of Bio::AlignIO::fasta modules so that creates temporary files instead of keeping the whole sequences in memory. 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: https://redmine.open-bio.org/projects/bioperl/ AUTHORS - Albert Vilella, Heikki Lehvaslaiho Email: avilella-at-gmail-dot-com, heikki-at-bioperl-dot-org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream while taking care of the length Returns : Bio::Seq object Args : NONE next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Returns : L<Bio::Align::AlignI> object - returns 0 on end of file or on error Args : NONE write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in largemultifasta format Returns : 1 for success and 0 for error Args : L<Bio::Align::AlignI> object perl v5.14.2 2012-03-02 Bio::AlignIO::largemultifasta(3pm)