bio::alignio::xmfa(3pm) [debian man page]
Bio::AlignIO::xmfa(3pm) User Contributed Perl Documentation Bio::AlignIO::xmfa(3pm) NAME
Bio::AlignIO::xmfa - XMFA 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 from XMFA flat file databases. For more information, see: http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-output-file-formats.html This module is based on the AlignIO::fasta parser written by Peter Schattner TODO
Finish write_aln(), clean up code, allow LargeLocatableSeq (ie for very large sequences a'la Mauve) 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
Chris Fields 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. Returns : Bio::Align::AlignI object - returns 0 on end of file or on error Args : -width => optional argument to specify the width sequence will be written (60 chars by default) See Bio::Align::AlignI write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in xmfa format Returns : 1 for success and 0 for error Args : L<Bio::Align::AlignI> object See Bio::Align::AlignI _get_len Title : _get_len Usage : Function: determine number of alphabetic chars Returns : integer Args : sequence string width Title : width Usage : $obj->width($newwidth) $width = $obj->width; Function: Get/set width of alignment Returns : integer value of width Args : on set, new value (a scalar or undef, optional) perl v5.14.2 2012-03-02 Bio::AlignIO::xmfa(3pm)
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Bio::AlignIO::metafasta(3pm) User Contributed Perl Documentation Bio::AlignIO::metafasta(3pm) NAME
Bio::AlignIO::metafasta - Metafasta 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 metafasta flat file databases. The format of a metafasta file is >test/1-25 ABCDEFHIJKLMNOPQRSTUVWXYZ &charge NBNAANCNJCNNNONNCNNUNNXNZ &chemical LBSAARCLJCLSMOIMCHHULRXRZ where the sequence block is followed by one or several meta blocks. Each meta block starts with the ampersand character '&' in the first column and is immediately followed by the name of the meta data which continues until the new line. The meta data follows it. All characters, except new line, are important in meta data. SEE ALSO
Bio::SeqIO::metafasta 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/ AUTHOR - Heikki Lehvaslaiho Email 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_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 fasta format Returns : 1 for success and 0 for error Args : L<Bio::Align::AlignI> object width Title : width Usage : $obj->width($newval) Function: Get/Set the line width for METAFASTA output Returns : value of width Args : newvalue (optional) perl v5.14.2 2012-03-02 Bio::AlignIO::metafasta(3pm)