NAME¶
Bio::Tools::Run::Profile
SYNOPSIS¶
Build a Profile factory
# $paramfile is the full path to the seg binary file
my @params = ('DB',$dbfile,'PROGRAM',$paramfile);
my $factory = Bio::Tools::Run::Profile->new($param);
# Pass the factory a Bio::PrimarySeqI object
# @feats is an array of Bio::SeqFeature::Generic objects
my @feats = $factory->run($seq);
DESCRIPTION¶
Wrapper module for the pfscan 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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Balamurugan Kumarasamy¶
Email: fugui@worf.fugu-sg.org
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 : my $factory= Bio::Tools::Run::Profile->new($param);
Function: creates a new Profile factory
Returns: Bio::Tools::Run::Profile
Args :
predict_protein_features¶
Title : predict_protein_features
Usage : DEPRECATED. Use $factory->run($seq) instead.
Function: Runs Profile and creates an array of featrues
Returns : An array of L<Bio::SeqFeature::FeaturePair> objects
Args : A Bio::PrimarySeqI
run¶
Title : run
Usage : my @feats = $factory->run($seq)
Function: Runs Profile
Returns : An array of L<Bio::SeqFeature::FeaturePair> objects
Args : A Bio::PrimarySeqI
Title : _input
Usage : $factory->_input($seqFile)
Function: get/set for input file
Returns :
Args :
_run¶
Title : _run
Usage : $factory->_run()
Function: Makes a system call and runs pfscan
Returns : An array of L<Bio::SeqFeature::FeaturePair> objects
Args :
_writeSeqFile¶
Title : _writeSeqFile
Usage : $factory->_writeSeqFile($seq)
Function: Creates a file from the given seq object
Returns : A string(filename)
Args : Bio::PrimarySeqI