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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:

   http://bugzilla.open-bio.org/
 
 

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)