Bio::AlignIO::fasta man page on Fedora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Fedora logo
[printable version]

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

NAME
       Bio::AlignIO::fasta - fasta MSA Sequence input/output stream

SYNOPSIS
       Do not use this module directly.	 Use it via the Bio::AlignIO class.

DESCRIPTION
       This object can transform Bio::SimpleAlign objects to and from fasta
       flat file databases.  This is for the fasta alignment format, not for
       the FastA sequence analysis program.  To process the alignments from
       FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO module.

FEEDBACK
   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
       Peter Schattner

APPENDIX
       The rest of the documentation details each of the object methods.
       Internal methods are usually preceded with a _

   next_aln
	Title	: next_aln
	Usage	: $aln = $stream->next_aln
	Function: returns the next alignment in the stream.
	Returns : Bio::Align::AlignI object - returns 0 on end of file
		       or on error
	Args	: -width => optional argument to specify the width sequence
		  will be written (60 chars by default)

       See Bio::Align::AlignI

   write_aln
	Title	: write_aln
	Usage	: $stream->write_aln(@aln)
	Function: writes the $aln object into the stream in fasta format
	Returns : 1 for success and 0 for error
	Args	: L<Bio::Align::AlignI> object

       See Bio::Align::AlignI

   _get_len
	Title	: _get_len
	Usage	:
	Function: determine number of alphabetic chars
	Returns : integer
	Args	: sequence string

   width
	Title	: width
	Usage	: $obj->width($newwidth)
		  $width = $obj->width;
	Function: Get/set width of alignment
	Returns : integer value of width
	Args	: on set, new value (a scalar or undef, optional)

perl v5.14.1			  2011-07-22		Bio::AlignIO::fasta(3)
[top]

List of man pages available for Fedora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net