| Bio::Seq::LargePrimarySeq(3pm) | User Contributed Perl Documentation | Bio::Seq::LargePrimarySeq(3pm) |
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
# 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.
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
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.
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
Email birney@ebi.ac.uk Email jason@bioperl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : length Usage : Function: Example : Returns : Args :
Title : seq Usage : Function: Example : Returns : Args :
Title : subseq Usage : Function: Example : Returns : Args :
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
Title : _filename Usage : $obj->_filename($newval) Function: Example : Returns : value of _filename Args : newvalue (optional)
Title : alphabet Usage : $obj->alphabet($newval) Function: Example : Returns : value of alphabet Args : newvalue (optional)
| 2021-08-15 | perl v5.32.1 |