--- name: "Bio::Tools::Run::Hmmer" section: "3pm" platform: "linux" package: "libbio-perl-run-perl" version: "1.7.3-13" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Tools::Run::Hmmer" --- # Bio::Tools::Run::Hmmer(3pm) Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch ## NAME Bio::Tools::Run::Hmmer - Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch ## SYNOPSIS ``` # run hmmsearch (similar for hmmpfam) my $factory = Bio::Tools::Run::Hmmer->new(-hmm => 'model.hmm'); # Pass the factory a Bio::Seq object or a file name, returns a Bio::SearchIO my $searchio = $factory->hmmsearch($seq); while (my $result = $searchio->next_result){ while(my $hit = $result->next_hit){ while (my $hsp = $hit->next_hsp){ print join("\t", ( $result->query_name, $hsp->query->start, $hsp->query->end, $hit->name, $hsp->hit->start, $hsp->hit->end, $hsp->score, $hsp->evalue, $hsp->seq_str, )), "\n"; } } } # build a hmm using hmmbuild my $aio = Bio::AlignIO->new(-file => "protein.msf", -format => 'msf'); my $aln = $aio->next_aln; my $factory = Bio::Tools::Run::Hmmer->new(-hmm => 'model.hmm'); $factory->hmmbuild($aln); # calibrate the hmm $factory->calibrate(); # emit a sequence stream from the hmm my $seqio = $factory->hmmemit(); # align sequences to the hmm my $alnio = $factory->hmmalign(@seqs); ``` ## DESCRIPTION Wrapper module for Sean Eddy's HMMER suite of program to allow running of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam and hmmsearch. Binaries are available at http://hmmer.janelia.org/ You can pass most options understood by the command-line programs to **new()**, or set the options by calling methods with the same name as the argument. In both instances, case sensitivity matters. Additional methods are **hmm()** to specifiy the hmm file (needed for all HMMER programs) which you would normally set in the call to **new()**. The HMMER programs must either be in your path, or you must set the environment variable HMMERDIR to point to their location. ## 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-at-gmx.net ``` ## CONTRIBUTORS ``` Shawn Hoon shawnh-at-gmx.net Jason Stajich jason -at- bioperl -dot- org Scott Markel scott -at- scitegic -dot com Sendu Bala bix@sendu.me.uk ``` ## APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_ ### new ``` Title : new Usage : $HMMER->new(@params) Function: Creates a new HMMER factory Returns : Bio::Tools::Run::HMMER Args : -hmm => filename # the hmm, used by all program types; if not set # here, must be set with hmm() method prior to # running anything -_READMETHOD => 'hmmer' (default) || 'hmmer_pull' # the parsing # module to use for # hmmpfam/hmmsearch Any option supported by a Hmmer program, where switches are given a true value, eg. -q => 1, EXCEPT for the following which are handled internally/ incompatible: h verbose a compat pvm WARNING: the default sequence format passed to hmmpfam is msf. If you are using a different format, you need to pass it with informat. e.g. my $factory = Bio::Tools::Run::Hmmer->new(-hmm => 'model.hmm', -informat => 'fasta'); -q is synonymous with -quiet -o is synonymous with -outfile # may be specified here, allowing run() to be used, or # it can be omitted and the corresponding method (eg. # hmmalign()) used later. -program => hmmalign|hmmbuild|hmmcalibrate|hmmemit|hmmpfam|hmmsearch ``` ### run ``` Title : run Usage : $obj->run($seqFile) Function: Runs one of the Hmmer programs, according to the current setting of program() (as typically set during new(-program => 'name')). Returns : A Bio::SearchIO, Bio::AlignIO, Bio::SeqIO or boolean depending on the program being run (see method corresponding to program name for details). Args : A Bio::PrimarySeqI, Bio::Align::AlignI or filename ``` ### hmmalign ``` Title : hmmalign Usage : $obj->hmmalign() Function: Runs hmmalign Returns : A Bio::AlignIO Args : list of Bio::SeqI OR Bio::Align::AlignI OR filename of file with sequences or an alignment ``` ### hmmbuild ``` Title : hmmbuild Usage : $obj->hmmbuild() Function: Runs hmmbuild, outputting an hmm to the file currently set by method hmm() or db(), or failing that, o() or outfile(), or failing that, to a temp location. Returns : true on success Args : Bio::Align::AlignI OR filename of file with an alignment ``` ### hmmcalibrate ``` Title : hmmcalibrate Usage : $obj->hmmcalibrate() Function: Runs hmmcalibrate Returns : true on success Args : none (hmm() must be set, most likely by the -hmm option of new()), OR optionally supply an hmm filename to set hmm() and run ``` ### hmmemit ``` Title : hmmemit Usage : $obj->hmmemit() Function: Runs hmmemit Returns : A Bio::SeqIO Args : none (hmm() must be set, most likely by the -hmm option of new()), OR optionally supply an hmm filename to set hmm() and run ``` ### hmmpfam ``` Title : hmmpfam Usage : $obj->hmmpfam() Function: Runs hmmpfam Returns : A Bio::SearchIO Args : A Bio::PrimarySeqI, Bio::Align::AlignI or filename ``` ### hmmsearch ``` Title : hmmsearch Usage : $obj->hmmsearch() Function: Runs hmmsearch Returns : A Bio::SearchIO Args : A Bio::PrimarySeqI, Bio::Align::AlignI or filename ``` ### \_setinput ``` Title : _setinput Usage : $obj->_setinput() Function: Internal(not to be used directly) Returns : filename Args : A Bio::PrimarySeqI, Bio::Align::AlignI or filename ``` ### \_run ``` Title : _run Usage : $obj->_run() Function: Internal(not to be used directly) Returns : Bio::SearchIO Args : file name ``` ### \_setparams ``` Title : _setparams Usage : Internal function, not to be called directly Function: creates a string of params to be used in the command string Returns : string of params Args : none ``` ### program\_name ``` Title : program_name Usage : $factory>program_name() Function: holds the program name Returns : string Args : none ``` ### program\_dir ``` Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns : string Args : none ``` ### \_writeSeqFile ``` Title : _writeSeqFile Usage : obj->_writeSeqFile($seq) Function: Internal(not to be used directly) Returns : filename Args : list of Bio::SeqI ``` ### \_writeAlignFile ``` Title : _writeAlignFile Usage : obj->_writeAlignFile($seq) Function: Internal(not to be used directly) Returns : filename Args : list of Bio::Align::AlignI ```