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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Run::Profile 3pm"
.TH Bio::Tools::Run::Profile 3pm "2023-01-22" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Bio::Tools::Run::Profile \- wrapper for the pfscan program
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\& Build a Profile factory
\& # $paramfile is the full path to the seg binary file
\&
\& my @params = (\*(AqDB\*(Aq,$dbfile,\*(AqPROGRAM\*(Aq,$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);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
.Vb 1
\& Wrapper module for the pfscan program
.Ve
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Balamurugan Kumarasamy"
.IX Header "AUTHOR - Balamurugan Kumarasamy"
.Vb 1
\& Email: fugui@worf.fugu\-sg.org
.Ve
.SH "APPENDIX"
.IX Header "APPENDIX"
.Vb 2
\& The rest of the documentation details each of the object
\& methods. Internal methods are usually preceded with a _
.Ve
.SS "program_name"
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory>program_name()
\& Function: holds the program name
\& Returns:  string
\& Args    : None
.Ve
.SS "program_dir"
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable.
\& Returns:  string
\& Args    :
.Ve
.SS "new"
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Usage   : my $factory= Bio::Tools::Run::Profile\->new($param);
\& Function: creates a new Profile factory
\& Returns:  Bio::Tools::Run::Profile
\& Args    :
.Ve
.SS "predict_protein_features"
.IX Subsection "predict_protein_features"
.Vb 5
\& 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
.Ve
.SS "run"
.IX Subsection "run"
.Vb 5
\& Title   :   run
\& Usage   :   my @feats = $factory\->run($seq)
\& Function:   Runs Profile 
\& Returns :   An array of L<Bio::SeqFeature::FeaturePair> objects
\& Args    :   A Bio::PrimarySeqI
.Ve
.SS "_input"
.IX Subsection "_input"
.Vb 5
\& Title   :   _input
\& Usage   :   $factory\->_input($seqFile)
\& Function:   get/set for input file
\& Returns :
\& Args    :
.Ve
.SS "_run"
.IX Subsection "_run"
.Vb 5
\& Title   :   _run
\& Usage   :   $factory\->_run()
\& Function:   Makes a system call and runs pfscan
\& Returns :   An array of L<Bio::SeqFeature::FeaturePair> objects
\& Args    :
.Ve
.SS "_writeSeqFile"
.IX Subsection "_writeSeqFile"
.Vb 5
\& Title   :   _writeSeqFile
\& Usage   :   $factory\->_writeSeqFile($seq)
\& Function:   Creates a file from the given seq object
\& Returns :   A string(filename) 
\& Args    :   Bio::PrimarySeqI
.Ve