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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 $feat->seqname."\t".$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://bugzilla.open-bio.org/
 
 

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