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::clustalw(3pm) User Contributed Perl Documentation Bio::AlignIO::clustalw(3pm) NAME
Bio::AlignIO::clustalw - clustalw sequence input/output stream SYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class. DESCRIPTION
This object can transform Bio::Align::AlignI objects to and from clustalw files. 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 one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHORS - Peter Schattner Email: schattner@alum.mit.edu APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : $alignio = Bio::AlignIO->new(-format => 'clustalw', -file => 'filename'); Function: returns a new Bio::AlignIO object to handle clustalw files Returns : Bio::AlignIO::clustalw object Args : -verbose => verbosity setting (-1, 0, 1, 2) -file => name of file to read in or to write, with ">" -fh => alternative to -file param - provide a filehandle to read from or write to -format => alignment format to process or produce -percentages => display a percentage of identity in each line of the alignment (clustalw only) -linelength=> alignment output line length (default 60) next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream Returns : Bio::Align::AlignI object Args : NONE See Bio::Align::AlignI for details write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the clustalw-format object (.aln) into the stream Returns : 1 for success and 0 for error Args : Bio::Align::AlignI object percentages Title : percentages Usage : $obj->percentages($newval) Function: Set the percentages flag - whether or not to show percentages in each output line Returns : value of percentages Args : newvalue (optional) line_length Title : line_length Usage : $obj->line_length($newval) Function: Set the alignment output line length Returns : value of line_length Args : newvalue (optional) perl v5.14.2 2012-03-02 Bio::AlignIO::clustalw(3pm)