Bio::Tools::Run::AlignUser:Contributed PerlBio::Tools::Run::Alignment::Blat(3)NAMEBio::Tools::Run::Alignment::BlatSYNOPSIS
Build a Blat factory.
use Bio::Tools::Run::Alignment::Blat;
my $factory = Bio::Tools::Run::Alignment::Blat->new();
# Pass the factory a Bio::Seq object
# @feats is an array of Bio::SeqFeature::Generic objects
my @feats = $factory->run($seq,$DB);
DESCRIPTION
Wrapper module for Blat program
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 - Bala
Email bala@tll.org.sg
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
program_name
Title : program_name
Usage : $factory->program_name()
Function: holds the program name
Returns : string
Args : None
program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns : string
Args :
new
Title : new
Usage : $blat->new(@params)
Function: creates a new Blat factory
Returns : Bio::Tools::Run::Alignment::Blat
Args :
run
Title : run()
Usage : $obj->run($query)
Function: Runs Blat and creates an array of featrues
Returns : An array of Bio::SeqFeature::Generic objects
Args : A Bio::PrimarySeqI
align
Title : align
Usage : $obj->align($query)
Function: Alias to run()
_input
Title : _input
Usage : obj->_input($seqFile)
Function: Internal (not to be used directly)
Returns :
Args :
_database
Title : _database
Usage : obj->_database($seqFile)
Function: Internal (not to be used directly)
Returns :
Args :
_run
Title : _run
Usage : $obj->_run()
Function: Internal (not to be used directly)
Returns : An array of Bio::SeqFeature::Generic objects
Args :
_writeSeqFile
Title : _writeSeqFile
Usage : obj->_writeSeqFile($seq)
Function: Internal (not to be used directly)
Returns :
Args :
perl v5.14.12011-07-2Bio::Tools::Run::Alignment::Blat(3)
