Wrapper for Primate, Guy Slater's near exact match finder for short sequence tags. 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"; } Primate is available under to ensembl-nci package at http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/ensembl-nci/?cvsroot=Ensembl

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://bio.perl.org/MailList.html - About the mailing lists

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://bugzilla.bioperl.org/ Email shawnh@fugu-sg.org 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, obtiained from ENV variable. Returns: string Args :

new
Title : new Usage : my $obj = new Bio::Tools::Run::Primate() 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