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Bio::Tools::Run::Infernal.3pm
Langue: en
Version: 2009-11-04 (ubuntu - 24/10/10)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::Infernal - Wrapper for local execution of cmalign, cmbuild, cmsearch, cmscoreSYNOPSIS
# parameters which are switches are set with any value that evals TRUE, # others are set to a specific value my @params = (hmmfb => 1, thresh => 20); 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 outfile()/tempfile # 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 # saves output to outfile()/tempfile $factory->cmscore(@seqs); # scores set cov. model against Bio::PrimarySeqI's, # saves output to outfile()/tempfile/STDERR. $factory->cmbuild($aln); # builds covariance model based on alignment # saves CM to model(), output to outfile()/tempfile/STDERR. $factory->cmemit($file); # emits sequence from specified cov. model; # set one if no file specified # 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, cmalign, cmemit, cmbuild, and cmscore. The only current BioPerl object returned is for cmsearch (as shown in the SYNOPSIS); all others are sent to either the designated outfile, a tempfile, or STDOUT.Since the Infernal suite is under constant development, consider this wrapper as highly experimental. It will only actively support the latest Infernal release (now at v. 0.81, used to build Rfam 8.0) until a 1.0 Infernal release is made.
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 - 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)
program_name
Title : program_name Usage : $factory>program_name() Function: holds the program name Returns: string Args : None
model
Title : model Usage : $obj->model() Function: Set the model 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 : [optional] File name containing covariance model (will use model() if not passed)
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
cmscore
Title : cmscore Usage : $obj->cmscore($seq) Function: Runs Infernal cmscore and saves output Returns : None Args : Bio::PrimarySeqI or file
_run
Title : _run Usage : $obj->_run() Function: Internal(not to be used directly) Returns : Args :
_setparams
Title : _setparams Usage : Internal function, not to be called directly Function: creates a string of params to be used in the command string Example : Returns : string of params Args :
_writeSeqFile
Title : _writeSeqFile Usage : obj->_writeSeqFile($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 :
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