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Bio::Tools::Run::InferUser3Contributed Perl DocumeBio::Tools::Run::Infernal(3)

NAME
       Bio::Tools::Run::Infernal - Wrapper for local execution of cmalign,
       cmbuild,	cmsearch, cmscore

SYNOPSIS
	 # parameters which are	switches are set with any value	that evals TRUE,
	 # others are set to a specific	value

	 my $factory = Bio::Tools::Run::Infernal->new(@params);

	 # run cmalign|cmbuild|cmsearch|cmscore|cmemit directly	as a wrapper method
	 # this	resets the program flag	if previously set

	 $factory->cmsearch(@seqs); # searches Bio::PrimarySeqI's based	on set cov. model
				    # saves output to optional outfile_name, returns
				    # Bio::SearchIO

	 # only	values which are allowed for a program are set,	so one can use the same
	 # wrapper for the following...

	 $factory->cmalign(@seqs); # aligns Bio::PrimarySeqI's to a set	cov. model,
				   # --merge option allows two alignments generated
				   #	 from the same CM to be	merged.
				   # output to outfile_name, returns Bio::AlignIO
	 $factory->cmscore();	   # scores set	cov. model against Bio::PrimarySeqI,
				   # output to outfile_name/STDOUT.
	 $factory->cmbuild($aln); # builds covariance model based on alignment
				  # CM to outfile_name or model_file (one is required
				  # here), output to STDOUT.
	 $factory->cmemit();	  # emits sequence from	specified cov. model;
				  # set	one if no file specified. output to
				  # outfile_name, returns Bio::SeqIO or	(if -a is set)
				  # Bio::AlignIO
	 $factory->cmcalibrate($file); # calibrates specified cov. model; output to
				       # STDOUT
	 $factory->cmstat($file); # summary stats for cov. model; set one if no	file
				  # specified; output to STDOUT

	 # run based on	the setting of the program parameter

	 my $factory = Bio::Tools::Run::Infernal->new(-program => 'cmsearch',
						       @params);
	 my $search = $factory->run($seq);

	 # using cmsearch returns a Bio::SearchIO object

	 while (my $result = $searchio->next_result){
	  while(my $hit	= $result->next_hit){
	   while (my $hsp = $hit->next_hsp){
		   print join("\t", ( $r->query_name,
				      $hit->name,
				      $hsp->hit->start,
				      $hsp->hit->end,
				      $hsp->meta,
				      $hsp->score,
				      )), "\n";
	   }
	  }
	 }

DESCRIPTION
       Wrapper module for Sean Eddy's Infernal suite of	programs. The current
       implementation runs cmsearch, cmcalibrate, cmalign, cmemit, cmbuild,
       cmscore,	and cmstat. cmsearch will return a Bio::SearchIO, cmemit a
       Bio::SeqIO/AlignIO, and cmalign a Bio::AlignIO.	All others send	output
       to STDOUT.  Optionally, any program's output can	be redirected to
       outfile_name.

       We HIGHLY suggest upgrading to Infernal 1.0.  In	that spirit, this
       wrapper now supports parameters for Infernal 1.0	only; for wrapping
       older versions of Infernal we suggest using the version of
       Bio::Tools::Run::Infernal that came with	previous versions of BioPerl-
       run.

       NOTE: Due to conflicts in the way Infernal parameters are now formatted
       vs.  subroutine naming in Perl (specifically the	inclusion of hyphens)
       and due to the very large number	of parameters available, setting and
       resetting parameters via	set_parameters() and reset_parameters()	is
       required. All valid parameters can be set, but only ones	valid for the
       executable set via program()/program_name() are used for	calling	the
       executables, the	others are silently ignored.

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 - Chris Fields
	Email: cjfields-at-uiuc-dot-edu

CONTRIBUTORS
	cjfields-at-uiuc-dot-edu

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   new
	Title	: new
	Usage	: my $wrapper =	Bio::Tools::Run::Infernal->new(@params)
	Function: creates a new	Infernal factory
	Returns:  Bio::Tools::Run::Infernal wrapper
	Args	: list of parameters

   program
	Title	:  program
	Usage	:  $obj->program()
	Function:  Set the program called when run() is	used.  Synonym of
		   program_name()
	Returns	:  String (program name)
	Args	:  String (program name)
	Status	:  Unstable (may delegate to program_name, which is the	interface method)

   program_name
	Title	: program_name
	Usage	: $factory>program_name()
	Function: holds	the program name
	Returns:  string
	Args	: None

   model_file
	Title	:  model_file
	Usage	:  $obj->model_file()
	Function:  Set the model file used when	run() is called.
	Returns	:  String (file	location of covariance model)
	Args	:  String (file	location of covariance model)

   program_dir
	Title	: program_dir
	Usage	: $factory->program_dir(@params)
	Function: returns the program directory, obtained from ENV variable.
	Returns:  string
	Args	:

   version
	Title	: version
	Usage	: $v = $prog->version();
	Function: Determine the	version	number of the program (uses cmsearch)
	Example	:
	Returns	: float	or undef
	Args	: none

   run
	Title	:   run
	Usage	:   $obj->run($seqFile)
	Function:   Runs Infernal and returns Bio::SearchIO
	Returns	:   A Bio::SearchIO
	Args	:   A Bio::PrimarySeqI or file name

Specific program interface methods
   cmsearch
	Title	:   cmsearch
	Usage	:   $obj->cmsearch($seqFile)
	Function:   Runs Infernal cmsearch and returns Bio::SearchIO
	Returns	:   A Bio::SearchIO
	Args	:   Bio::PrimarySeqI or	file name

   cmalign
	Title	:   cmalign
	Usage	:   $obj->cmalign($seqFile)
	Function:   Runs Infernal cmalign and returns Bio::AlignIO
	Returns	:   A Bio::AlignIO
	Args	:   Bio::PrimarySeqI or	file name

   cmemit
	Title	:   cmemit
	Usage	:   $obj->cmemit($modelfile)
	Function:   Runs Infernal cmemit and returns Bio::AlignIO
	Returns	:   A Bio::AlignIO
	Args	:   None; set model_file() to use a specific model

   cmbuild
	Title	:   cmbuild
	Usage	:   $obj->cmbuild($alignment)
	Function:   Runs Infernal cmbuild and saves covariance model
	Returns	:   1 on success (no object for	covariance models)
	Args	:   Bio::AlignIO with structural information (such as from Stockholm
		    format source) or alignment	file name

   cmscore
	Title	:   cmscore
	Usage	:   $obj->cmscore($seq)
	Function:   Runs Infernal cmscore and saves output
	Returns	:   None
	Args	:   None; set model_file() to use a specific model

   cmcalibrate
	Title	:   cmcalibrate
	Usage	:   $obj->cmcalibrate('file')
	Function:   Runs Infernal calibrate on specified CM
	Returns	:   None
	Args	:   None; set model_file() to use a specific model

   cmstat
	Title	:   cmstat
	Usage	:   $obj->cmstat($seq)
	Function:   Runs Infernal cmstat and saves output
	Returns	:   None
	Args	:   None; set model_file() to use a specific model

Bio::ParameterBaseI-specific methods
       These methods are part of the Bio::ParameterBaseI interface

   set_parameters
	Title	: set_parameters
	Usage	: $pobj->set_parameters(%params);
	Function: sets the parameters listed in	the hash or array
	Returns	: None
	Args	: [optional] hash or array of parameter/values.	 These can optionally
		  be hash or array references
	Note	: This only sets parameters; to	set methods use	the method name

   reset_parameters
	Title	: reset_parameters
	Usage	: resets values
	Function: resets parameters to either undef or value in	passed hash
	Returns	: none
	Args	: [optional] hash of parameter-value pairs

   validate_parameters
	Title	: validate_parameters
	Usage	: $pobj->validate_parameters(1);
	Function: sets a flag indicating whether to validate parameters	via
		  set_parameters() or reset_parameters()
	Returns	: Bool
	Args	: [optional] value evaluating to True/False
	Note	: Optionally implemented method; up to the implementation on whether
		  to automatically validate parameters or optionally do	so

   parameters_changed
	Title	: parameters_changed
	Usage	: if ($pobj->parameters_changed) {...}
	Function: Returns boolean true (1) if parameters have changed
	Returns	: Boolean (0 or	1)
	Args	: None
	Note	: This module does not run state checks, so this always	returns	True

   available_parameters
	Title	: available_parameters
	Usage	: @params = $pobj->available_parameters()
	Function: Returns a list of the	available parameters
	Returns	: Array	of parameters
	Args	: [optional] name of executable	being used; defaults to	returning all
		  available parameters

   get_parameters
	Title	: get_parameters
	Usage	: %params = $pobj->get_parameters;
	Function: Returns list of set key-value	pairs, parameter => value
	Returns	: List of key-value pairs
	Args	: [optional]
		  'full' - this	option returns everything associated with the parameter
			   as an array ref value; that is, not just the	value but also
			   the value, type, and	prefix.	Default	is value only.
		  'valid'- same	a 'full', but only returns the grouping	valid for the
			   currently set executable

to_* methods
       All to_*	methods	are implementation-specific

   to_exe_string
	Title	: to_exe_string
	Usage	: $string = $pobj->to_exe_string;
	Function: Returns string (command line string in this case)
	Returns	: String
	Args	:

   _writeSeqFile
	Title	:   _writeSeqFile
	Usage	:   obj->_writeSeqFile($seq)
	Function:   Internal(not to be used directly)
	Returns	:
	Args	:

   _writeAlignFile
	Title	:   _writeAlignFile
	Usage	:   obj->_writeAlignFile($seq)
	Function:   Internal(not to be used directly)
	Returns	:
	Args	:

perl v5.32.1			  2021-03-01	  Bio::Tools::Run::Infernal(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Chris Fields | CONTRIBUTORS | APPENDIX | Specific program interface methods | Bio::ParameterBaseI-specific methods | to_* methods

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