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Bio::AlignIO::proda(3)User Contributed Perl DocumentatioBio::AlignIO::proda(3)

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)

perl v5.32.1			  2019-12-07		Bio::AlignIO::proda(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHORS - Albert Vilella | APPENDIX

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