NAME

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)

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 proda 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://github.com/bioperl/bioperl-live/issues

AUTHORS - Albert Vilella

Email: avilella-at-gmail-dot-com

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 => '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)

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 proda-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)

no_header

 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)