Bio::Tools::Run::Primate(3pm) User Contributed Perl Documentation Bio::Tools::Run::Primate(3pm)
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 $feat->seqname." ".$feat->primary_tag." ".$feat->start.
" ".$feat->end." ".$feat->strand." ".$feat->seq->seq."
";
}
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
search
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
perl v5.12.3 2011-06-18 Bio::Tools::Run::Primate(3pm)