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

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