go::model::seq(3pm) [debian man page]

GO::Model::Seq(3pm)					User Contributed Perl Documentation				       GO::Model::Seq(3pm)

NAME

	 GO::Model::Seq - biological sequence

SYNOPSIS

	   print $gene_product->seq->seq;

DESCRIPTION

       represents a biological sequence; uses the bioperl Bio::PrimarySeq class

       any call that you can do on a bioperl sequence object, you can do here, with the addition of the calls below

       to get bioperl, see http://www.bioperl.org

   pseq
	 Usage	 -
	 Returns - Bio::PrimarySeq
	 Args	 -

   md5checksum
	 Usage	 - my $md5 = $seq->md5checksum() OR $seq->md5checksum($md5)
	 Returns - 32 char hex string
	 Args	 - 32 char hex string [optional]

       checksum for seq - easy way to check if it has been changed etc

       (requires Digest::MD5 module from CPAN)

   to_fasta
	 Usage	 -
	 Returns -
	 Args	 -

   add_xref
	 - Usage : $term->add_xref($xref);
	 - Args  : GO::Term::Xref

perl v5.14.2							    2013-02-07						       GO::Model::Seq(3pm)

Bio::Seq::LargePrimarySeq(3pm)				User Contributed Perl Documentation			    Bio::Seq::LargePrimarySeq(3pm)

NAME

       Bio::Seq::LargePrimarySeq - PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method
       in Bio::Root::Root

SYNOPSIS

	 # normal primary seq usage

DESCRIPTION

       This object stores a sequence as a series of files in a temporary directory. The aim is to allow someone the ability to store very large
       sequences (eg, > 100MBases) in a file system without running out of memory (eg, on a 64 MB real memory machine!).

       Of course, to actually make use of this functionality, the programs which use this object must not call $primary_seq->seq otherwise the
       entire sequence will come out into memory and probably paste your machine. However, calls $primary_seq->subseq(10,100) will cause only 90
       characters to be brought into real memory.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Ewan Birney, Jason Stajich
       Email birney@ebi.ac.uk Email jason@bioperl.org

APPENDIX

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

   length
	Title	: length
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   seq
	Title	: seq
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   subseq
	Title	: subseq
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   add_sequence_as_string
	Title	: add_sequence_as_string
	Usage	: $seq->add_sequence_as_string("CATGAT");
	Function: Appends additional residues to an existing LargePrimarySeq object.
		  This allows one to build up a large sequence without storing
		  entire object in memory.
	Returns : Current length of sequence
	Args	: string to append

   _filename
	Title	: _filename
	Usage	: $obj->_filename($newval)
	Function:
	Example :
	Returns : value of _filename
	Args	: newvalue (optional)

   alphabet
	Title	: alphabet
	Usage	: $obj->alphabet($newval)
	Function:
	Example :
	Returns : value of alphabet
	Args	: newvalue (optional)

perl v5.14.2							    2012-03-02					    Bio::Seq::LargePrimarySeq(3pm)