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.\" ========================================================================
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.IX Title "Bio::Tools::Run::Primate 3pm"
.TH Bio::Tools::Run::Primate 3pm 2024-03-12 "perl v5.38.2" "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::Primate \- wrapper for Primate,  Guy Slater's near exact match
finder for short sequence tags.
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 2
\&  use Bio::Tools::Run::Primate;
\&  use Bio::SeqIO;
\&
\&  my $query = "primer.fa";
\&  my $target = "contig.fa";
\&
\&  my @params = ("query" => $query,"target" => $target,"m"=>0);
\&  my $fact = Bio::Tools::Run::Primate\->new(@params);
\&
\&  my @feat = $fact\->run;
\&  foreach my $feat(@feat) {
\&      print $feat\->seqname."\et".$feat\->primary_tag."\et".$feat\->start.
\&      "\et".$feat\->end."\et".$feat\->strand."\et".$feat\->seq\->seq."\en";
\&  }
.Ve
.SH DESCRIPTION
.IX Header "DESCRIPTION"
Primate is available under to ensembl-nci package at
http://cvsweb.sanger.ac.uk/cgi\-bin/cvsweb.cgi/ensembl\-nci/?cvsroot=Ensembl
.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 \- Shawn Hoon"
.IX Header "AUTHOR - Shawn Hoon"
Email shawnh@fugu\-sg.org
.SH APPENDIX
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.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 9
\& Title   : new
\& Usage   : my $obj = Bio::Tools::Run::Primate\->new()
\& Function: Builds a new Bio::Tools::Run::Primate objet
\& Returns : Bio::Tools::Run::Primate
\& Args    : query => the L<Bio::PrimarySeqI> object or a file path
\&           target => the L<Bio::PrimarySeqI> object or a file path
\&           m  => the number of mismatches allowed, default 1(integer)
\&           b  => [TRUE|FALSE] find best match, default FALSE
\&           executable=>where the program sits
.Ve
.SS version
.IX Subsection "version"
.Vb 5
\& Title   : version
\& Usage   : $primate\->version
\& Function: Determine the version number of the program
\& Returns : float or undef
\& Args    : none
.Ve
.SS search
.IX Subsection "search"
.Vb 5
\& Title   : search
\& Usage   : DEPRECATED. Use $factory\->run() instead
\& Function: Perform a primate search
\& Returns : Array of L<Bio::SeqFeature::Generic>
\& Args    :
.Ve
.SS run
.IX Subsection "run"
.Vb 5
\& Title   : run
\& Usage   : @feat = $factory\->run();
\& Function: Perform a primate search
\& Returns : Array of L<Bio::SeqFeature::Generic>
\& Args    :
.Ve
.SS _run
.IX Subsection "_run"
.Vb 5
\& Title   :  _run
\& Usage   : Internal function, not to be called directly
\& Function: makes actual system call to dba program
\& Returns : array of L<Bio::SeqFeature::Generic>
\& Args    : path to query and target file and parameter string
.Ve
.SS _parse_results
.IX Subsection "_parse_results"
.Vb 5
\& Title   :  _parse_results
\& Usage   :  Internal function, not to be called directly
\& Function:  Passes primate output
\& Returns : array of L<Bio::SeqFeature::Generic>
\& Args    : the name of the output file
.Ve
.SS \fB_setinput()\fP
.IX Subsection "_setinput()"
.Vb 5
\& Title   : _setinput
\& Usage   : Internal function, not to be called directly
\& Function: Create input files for primate
\& Returns : name of file containing query and target
\& Args    : query and target (either a filename or a L<Bio::PrimarySeqI>
.Ve
.SS \fB_setparams()\fP
.IX Subsection "_setparams()"
.Vb 5
\& Title   : _setparams
\& Usage   : Internal function, not to be called directly
\& Function: Create parameter inputs for primate program
\& Returns : parameter string to be passed to primate
\& Args    : the param array
.Ve
.SS \fB_query_seq()\fP
.IX Subsection "_query_seq()"
.Vb 5
\& Title   :  _query_seq
\& Usage   :  Internal function, not to be called directly
\& Function:  get/set for the query sequence
\& Returns :  a hash of seq with key the query tag
\& Args    :  optional
.Ve
.SS \fB_target_seq()\fP
.IX Subsection "_target_seq()"
.Vb 5
\& Title   : _target_seq
\& Usage   : Internal function, not to be called directly
\& Function: get/set for the target sequence
\& Returns : L<Bio::PrimarySeqI>
\& Args    : optional
.Ve