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Bio::Tools::Run::PrimaUser)Contributed Perl DocumenBio::Tools::Run::Primate(3)

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

perl v5.24.1			  2017-07-08	   Bio::Tools::Run::Primate(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Shawn Hoon | APPENDIX

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