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motif reqired for hp-ux 11.11
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Bio::Tools::ERPIN(3pm) User Contributed Perl Documentation Bio::Tools::ERPIN(3pm) NAME
Bio::Tools::ERPIN - a parser for ERPIN output SYNOPSIS
use Bio::Tools::ERPIN; my $parser = Bio::Tools::ERPIN->new( -file => $rna_output, -motiftag => 'protein_bind' -desctag => 'TRAP_binding'); #parse the results while( my $motif = $parser->next_prediction) { # do something here } DESCRIPTION
Parses raw ERPIN output. This module is not currently complete. As is, it will parse raw ERPIN long format output and pack information into Bio::SeqFeature::Generic objects. Several values have also been added in the 'tag' hash. These can be accessed using the following syntax: my ($entry) = $feature->get_Annotations('SecStructure'); Added tags are : tset - training set used for the sequence tsetdesc - training set description line cutoff - cutoff value used database - name of database dbdesc - description of database dbratios - nucleotide ratios of database (used to calculate evalue) descline - entire description line (in case the regex used for sequence ID doesn't adequately catch the name accession - accession number of sequence (if present) logodds - logodds score value sequence - sequence from hit, separated based on training set See t/ERPIN.t for example usage. At some point a more complicated feature object may be used to support this data rather than forcing most of the information into tag/value pairs in a SeqFeature::Generic. This will hopefully allow for more flexible analysis of data (specifically RNA secondary structural data). 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::ERPIN->new(); Function: Builds a new Bio::Tools::ERPIN object Returns : an instance of Bio::Tools::ERPIN Args : -fh/-file for input filename -motiftag => primary tag used in gene features (default 'misc_binding') -desctag => tag used for display_name name (default 'erpin') -srctag => source tag used in all features (default 'ERPIN') motif_tag Title : motiftag Usage : $obj->motiftag($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 'ERPIN' 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 'erpin' 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 ERPIN output, this should be set every time an ERPIN object is instantiated for clarity Returns : value of exon_tag (a scalar) Args : on set, new value (a scalar or undef, optional) analysis_method Usage : $obj->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /ERPIN/i. Returns : String Argument : n/a next_feature Title : next_feature Usage : while($gene = $obj->next_feature()) { # do something } Function: Returns the next gene structure prediction of the ERPIN result file. Call this method repeatedly until FALSE is returned. The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Returns : A Bio::Tools::Prediction::Gene object. Args : None (at present) next_prediction Title : next_prediction Usage : while($gene = $obj->next_prediction()) { # do something } Function: Returns the next gene structure prediction of the ERPIN result file. Call this method repeatedly until FALSE is returned. Returns : A Bio::Tools::Prediction::Gene object. Args : None (at present) perl v5.14.2 2012-03-02 Bio::Tools::ERPIN(3pm)
motif reqired for hp-ux 11.11