Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as files in /tmp # normal primary seq usage 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.

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://www.bioperl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email birney@ebi.ac.uk 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