| Bio::AlignIO::proda(3pm) | User Contributed Perl Documentation | Bio::AlignIO::proda(3pm) |
Bio::AlignIO::proda - proda sequence input/output stream
This provides the basic capabilities to parse the output alignments from the ProDA multiple sequence alignment program (http://proda.stanford.edu)
Do not use this module directly. Use it via the Bio::AlignIO class.
This object can transform Bio::Align::AlignI objects to and from proda files.
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
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.
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://github.com/bioperl/bioperl-live/issues
Email: avilella-at-gmail-dot-com
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new
Usage : $alignio = Bio::AlignIO->new(-format => 'proda',
-file => 'filename');
Function: returns a new Bio::AlignIO object to handle proda files
Returns : Bio::AlignIO::proda 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 (proda only)
-linelength=> alignment output line length (default 60)
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
Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the proda-format object (.aln) into the stream Returns : 1 for success and 0 for error Args : Bio::Align::AlignI object
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)
Title : line_length Usage : $obj->line_length($newval) Function: Set the alignment output line length Returns : value of line_length Args : newvalue (optional)
Title : no_header Usage : $obj->no_header($newval) Function: Set if the alignment input has a CLUSTAL header or not Returns : value of no_header Args : newvalue (optional)
| 2018-10-27 | perl v5.26.2 |