Bio::SeqIO::gcg man page on Pidora

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

Bio::SeqIO::gcg(3)    User Contributed Perl Documentation   Bio::SeqIO::gcg(3)

NAME
       Bio::SeqIO::gcg - GCG sequence input/output stream

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

DESCRIPTION
       This object can transform Bio::Seq objects to and from GCG flat file
       databases.

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 - Ewan Birney & Lincoln Stein
       Email: <birney@ebi.ac.uk>
	      <lstein@cshl.org>

CONTRIBUTORS
       Jason Stajich, jason@bioperl.org

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

   next_seq
	Title	: next_seq
	Usage	: $seq = $stream->next_seq()
	Function: returns the next sequence in the stream
	Returns : Bio::Seq object
	Args	:

   write_seq
	Title	: write_seq
	Usage	: $stream->write_seq(@seq)
	Function: writes the formatted $seq object into the stream
	Returns : 1 for success and 0 for error
	Args	: array of Bio::PrimarySeqI object

   GCG_checksum
	Title	  : GCG_checksum
	Usage	  : $cksum = $gcgio->GCG_checksum($seq);
	Function  : returns a gcg checksum for the sequence specified

		    This method can also be called as a class method.
	Example	  :
	Returns	  : a GCG checksum string
	Argument  : a Bio::PrimarySeqI implementing object

   _validate_checksum
	Title	: _validate_checksum
	Usage	: n/a - internal method
	Function: if parsed gcg sequence contains a checksum field
		: we compare it to a value computed here on the parsed
		: sequence. A checksum mismatch would indicate some
		: type of parsing failure occured.
		:
	Returns : 1 for success, 0 for failure
	Args	: string containing parsed seq, value of parsed cheksum

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

List of man pages available for Pidora

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