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bio::tools::run::infernal(3pm) [debian man page]

Bio::Tools::Run::Infernal(3pm)				User Contributed Perl Documentation			    Bio::Tools::Run::Infernal(3pm)

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(" ", ( $r->query_name, $hit->name, $hsp->hit->start, $hsp->hit->end, $hsp->meta, $hsp->score, )), " "; } } } 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 v5.12.3 2011-06-18 Bio::Tools::Run::Infernal(3pm)
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