/ 
BioPerl-1.6.924
River stage two • 60 direct dependents • 65 total dependents
/ Bio::AlignIO::proda

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)