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Bio::AlignIO::proda.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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)