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Hp-ux11.11_openmotif
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Bio::Tools::Infernal(3pm) User Contributed Perl Documentation Bio::Tools::Infernal(3pm) NAME
Bio::Tools::Infernal - A parser for Infernal output SYNOPSIS
use Bio::Tools::Infernal; my $parser = Bio::Tools::Infernal->new(-file => $rna_output, -motiftag => 'misc_binding' -desctag => 'Lysine riboswitch', -cm => 'RF00168', -rfam => 'RF00168', -minscore => 20); #parse the results, get a Bio::SeqFeature::FeaturePair while( my $motif = $parser->next_prediction) { # do something here } DESCRIPTION
This is a highly experimental parser for Infernal output from the cmsearch program. At some point it is anticipated that this will morph into a proper SearchIO parser, along with the related RNAMotif and ERPIN tools. The Infernal suite of programs are used for generating RNA CM (covariance models) and searching sequences using CMs to locate potentially similar structures. The program is under active development; it is anticiapted that this will support the latest version available. This parser has been tested and is capable of parsing Infernal 0.7 and 0.71 output. However, future Infernal versions may break parsing as the output is constantly evolving, so keep an eye on this space for additional notes. Currently data is parsed into a Bio::SeqFeature::FeaturePair object, consisting of a query (the covariance model) and the hit (sequence searched). Model data is accessible via the following: Data SeqFeature::FeaturePair Note -------------------------------------------------------------------------- primary tag $sf->primary_tag Rfam ID (if passed to new()) start $sf->start Based on CM length end $sf->end Based on CM length score $sf->score Bit score strand $sf->strand 0 (CM does not have a strand) seqid $sf->seq_id Rfam ID (if passed to new()) display name $sf->feature1->display_name CM name (if passed to new()) source $sf->feature1->source tag 'Infernal' followed by version Hit data is accessible via the following: Data SeqFeature::FeaturePair Note ------------------------------------------------------------------ start $sf->hstart end $sf->hend score(bits) $sf->hscore strand $sf->hstrand seqid $sf->hseqid Primary Tag $sf->hprimary_tag Source Tag $sf->hsource_tag Added FeaturePair tags are : secstructure - entire description line (in case the regex used for sequence ID doesn't adequately catch the name model - name of the descriptor file (may include path to file) midline - contains structural information from the descriptor used as a query hit - sequence of motif, separated by spaces according to matches to the structure in the descriptor (in SecStructure). seqname - raw sequence name (for downstream parsing if needed) An additional parameter ('minscore') is added due to the huge number of spurious hits generated by cmsearch. This screens data, only building and returning objects when a minimal bitscore is present. See t/rnamotif.t for example usage. 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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Chris Fields Email 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 $obj = Bio::Tools::Infernal->new(); Function: Builds a new Bio::Tools::Infernal object Returns : an instance of Bio::Tools::Infernal Args : -fh/-file - for input filehandle/filename -motiftag - primary tag used in gene features (default 'misc_binding') -desctag - tag used for display_name name (default 'infernal') -srctag - source tag used in all features (default 'Infernal') -rfam - Rfam id number -cm - covariance model used in analysis (may be same as rfam #) -minscore - minimum score (simple screener, since Infernal generates a ton of spurious hits) -version - Infernal program version motif_tag Title : motif_tag Usage : $obj->motif_tag($newval) Function: Get/Set the value used for 'motif_tag', which is used for setting the primary_tag. Default is 'misc_binding' as set by the global $MotifTag. 'misc_binding' is used here because a conserved RNA motif is capable of binding proteins (regulatory proteins), antisense RNA (siRNA), small molecules (riboswitches), or nothing at all (tRNA, terminators, etc.). It is recommended that this be changed to other tags ('misc_RNA', 'protein_binding', 'tRNA', etc.) where appropriate. For more information, see: http://www.ncbi.nlm.nih.gov/collab/FT/index.html Returns : value of motif_tag (a scalar) Args : on set, new value (a scalar or undef, optional) source_tag Title : source_tag Usage : $obj->source_tag($newval) Function: Get/Set the value used for the 'source_tag'. Default is 'Infernal' as set by the global $SrcTag Returns : value of source_tag (a scalar) Args : on set, new value (a scalar or undef, optional) desc_tag Title : desc_tag Usage : $obj->desc_tag($newval) Function: Get/Set the value used for the query motif. This will be placed in the tag '-display_name'. Default is 'infernal' as set by the global $DescTag. Use this to manually set the descriptor (motif searched for). Since there is no way for this module to tell what the motif is from the name of the descriptor file or the Infernal output, this should be set every time an Infernal object is instantiated for clarity Returns : value of exon_tag (a scalar) Args : on set, new value (a scalar or undef, optional) covariance_model Title : covariance_model Usage : $obj->covariance_model($newval) Function: Get/Set the value used for the covariance model used in the analysis. Returns : value of exon_tag (a scalar) Args : on set, new value (a scalar or undef, optional) rfam Title : rfam Usage : $obj->rfam($newval) Function: Get/Set the Rfam accession number Returns : value of exon_tag (a scalar) Args : on set, new value (a scalar or undef, optional) minscore Title : minscore Usage : $obj->minscore($newval) Function: Get/Set the minimum score threshold for generating SeqFeatures Returns : value of exon_tag (a scalar) Args : on set, new value (a scalar or undef, optional) program_version Title : program_version Usage : $obj->program_version($newval) Function: Get/Set the Infernal program version Returns : value of exon_tag (a scalar) Args : on set, new value (a scalar or undef, optional) Note: this is set to $DEFAULT_VERSION by, um, default analysis_method Usage : $obj->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /Infernal/i. Returns : String Argument : n/a next_feature Title : next_feature Usage : while($gene = $obj->next_feature()) { # do something } Function: Returns the next gene structure prediction of the RNAMotif result file. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Returns : A Bio::Tools::Prediction::Gene object. Args : None (at present) next_prediction Title : next_prediction Usage : while($gene = $obj->next_prediction()) { # do something } Function: Returns the next gene structure prediction of the RNAMotif result file. Call this method repeatedly until FALSE is returned. Returns : A Bio::SeqFeature::Generic object Args : None (at present) perl v5.14.2 2012-03-02 Bio::Tools::Infernal(3pm)
Hp-ux11.11_openmotif