/ 
BioPerl-Run-1.007003
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Primate

NAME

Wrapper for Primate, Guy Slater's near exact match finder for short sequence tags.

SYNOPSIS

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 $feat->seqname."\t".$feat->primary_tag."\t".$feat->start.
    "\t".$feat->end."\t".$feat->strand."\t".$feat->seq->seq."\n";
}

DESCRIPTION

Primate is available under to ensembl-nci package at http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/ensembl-nci/?cvsroot=Ensembl

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 - Shawn Hoon

Email shawnh@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 $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

version

Title   : version
Usage   : $primate->version
Function: Determine the version number of the program
Returns : float or undef
Args    : none
Title   : search
Usage   : DEPRECATED. Use $factory->run() instead
Function: Perform a primate search
Returns : Array of L<Bio::SeqFeature::Generic>
Args    :

run

Title   : run
Usage   : @feat = $factory->run();
Function: Perform a primate search
Returns : Array of L<Bio::SeqFeature::Generic>
Args    :

_run

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

_parse_results

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

_setinput()

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>

_setparams()

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

_query_seq()

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

_target_seq()

Title   : _target_seq
Usage   : Internal function, not to be called directly
Function: get/set for the target sequence
Returns : L<Bio::PrimarySeqI>
Args    : optional