.\" Automatically generated by Pod::Man 2.27 (Pod::Simple 3.28) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. 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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Bio::Tools::Infernal \- A parser for Infernal output .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 11 \& use Bio::Tools::Infernal; \& my $parser = Bio::Tools::Infernal\->new(\-file => $rna_output, \& \-motiftag => \*(Aqmisc_binding\*(Aq \& \-desctag => \*(AqLysine riboswitch\*(Aq, \& \-cm => \*(AqRF00168\*(Aq, \& \-rfam => \*(AqRF00168\*(Aq, \& \-minscore => 20); \& #parse the results, get a Bio::SeqFeature::FeaturePair \& while( my $motif = $parser\->next_prediction) { \& # do something here \& } .Ve .SH "DESCRIPTION" .IX Header "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 \s-1ERPIN\s0 tools. .PP The Infernal suite of programs are used for generating \s-1RNA CM \s0(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. .PP 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. .PP Currently data is parsed into a Bio::SeqFeature::FeaturePair object, consisting of a query (the covariance model) and the hit (sequence searched). .PP Model data is accessible via the following: .PP .Vb 10 \& 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 \*(AqInfernal\*(Aq followed by version .Ve .PP Hit data is accessible via the following: .PP .Vb 9 \& 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 .Ve .PP Added FeaturePair tags are : .PP .Vb 9 \& secstructure \- entire description line (in case the regex used for \& sequence ID doesn\*(Aqt 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) .Ve .PP 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. .PP See t/rnamotif.t for example usage. .SH "FEEDBACK" .IX Header "FEEDBACK" .SS "Mailing Lists" .IX Subsection "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. .PP .Vb 2 \& bioperl\-l@bioperl.org \- General discussion \& http://bioperl.org/wiki/Mailing_lists \- About the mailing lists .Ve .SS "Support" .IX Subsection "Support" Please direct usage questions or support issues to the mailing list: .PP \&\fIbioperl\-l@bioperl.org\fR .PP 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. .SS "Reporting Bugs" .IX Subsection "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: .PP .Vb 1 \& https://github.com/bioperl/bioperl\-live/issues .Ve .SH "AUTHOR \- Chris Fields" .IX Header "AUTHOR - Chris Fields" Email cjfields-at-uiuc-dot-edu .SH "APPENDIX" .IX Header "APPENDIX" The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ .SS "new" .IX Subsection "new" .Vb 10 \& 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 \*(Aqmisc_binding\*(Aq) \& \-desctag \- tag used for display_name name (default \*(Aqinfernal\*(Aq) \& \-srctag \- source tag used in all features (default \*(AqInfernal\*(Aq) \& \-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 .Ve .SS "motif_tag" .IX Subsection "motif_tag" .Vb 10 \& Title : motif_tag \& Usage : $obj\->motif_tag($newval) \& Function: Get/Set the value used for \*(Aqmotif_tag\*(Aq, which is used for setting the \& primary_tag. \& Default is \*(Aqmisc_binding\*(Aq as set by the global $MotifTag. \& \*(Aqmisc_binding\*(Aq 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 (\*(Aqmisc_RNA\*(Aq, \*(Aqprotein_binding\*(Aq, \*(AqtRNA\*(Aq, 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) .Ve .SS "source_tag" .IX Subsection "source_tag" .Vb 6 \& Title : source_tag \& Usage : $obj\->source_tag($newval) \& Function: Get/Set the value used for the \*(Aqsource_tag\*(Aq. \& Default is \*(AqInfernal\*(Aq as set by the global $SrcTag \& Returns : value of source_tag (a scalar) \& Args : on set, new value (a scalar or undef, optional) .Ve .SS "desc_tag" .IX Subsection "desc_tag" .Vb 10 \& 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 \*(Aq\-display_name\*(Aq. Default is \*(Aqinfernal\*(Aq 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) .Ve .SS "covariance_model" .IX Subsection "covariance_model" .Vb 5 \& 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) .Ve .SS "rfam" .IX Subsection "rfam" .Vb 5 \& 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) .Ve .SS "minscore" .IX Subsection "minscore" .Vb 5 \& 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) .Ve .SS "program_version" .IX Subsection "program_version" .Vb 6 \& 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 .Ve .SS "analysis_method" .IX Subsection "analysis_method" .Vb 5 \& Usage : $obj\->analysis_method(); \& Purpose : Inherited method. Overridden to ensure that the name matches \& /Infernal/i. \& Returns : String \& Argument : n/a .Ve .SS "next_feature" .IX Subsection "next_feature" .Vb 12 \& Title : next_feature \& Usage : while($gene = $obj\->next_feature()) { \& # do something \& } \& Function: Returns the next gene structure prediction of the RNAMotif result \& file. Call this method repeatedly until FALSE is returned. \& The returned object is actually a SeqFeatureI implementing object. \& This method is required for classes implementing the \& SeqAnalysisParserI interface, and is merely an alias for \& next_prediction() at present. \& Returns : A Bio::Tools::Prediction::Gene object. \& Args : None (at present) .Ve .SS "next_prediction" .IX Subsection "next_prediction" .Vb 8 \& Title : next_prediction \& Usage : while($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) .Ve