bionic (3) Bio::Seq::LargePrimarySeq.3pm.gz

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://github.com/bioperl/bioperl-live/issues

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)