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

NAME

       Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as files in /tmp

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

       Email birney@ebi.ac.uk

APPENDIX

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

   trunc
        Title   : trunc
        Usage   : $subseq = $myseq->trunc(10,100);
        Function: Provides a truncation of a sequence,

        Example :
        Returns : a fresh Bio::SeqI object
        Args    :

   Bio::Seq::LargePrimarySeq methods
   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