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bio::alignio::handler::genericalignhandler(3pm) [debian man page]

Bio::AlignIO::Handler::GenericAlignHandler(3pm) 	User Contributed Perl Documentation	   Bio::AlignIO::Handler::GenericAlignHandler(3pm)

NAME
Bio::AlignIO::Handler::GenericAlignHandler - Bio::HandlerI-based generic data handler class for alignment-based data SYNOPSIS
# MyHandler is a GenericAlignHandler object. # inside a parser (driver) constructor.... $self->alignhandler($handler || MyHandler->new(-format => 'stockholm')); # in next_aln() in driver... $hobj = $self->alignhandler(); # roll data up into hashref chunks, pass off into Handler for processing... $hobj->data_handler($data); # or retrieve Handler methods and pass data directly to Handler methods... my $hmeth = $hobj->handler_methods; if ($hmeth->{ $data->{NAME} }) { my $mth = $hmeth->{ $data->{NAME} }; $hobj->$mth($data); } DESCRIPTION
This is an experimental implementation of a alignment-based HandlerBaseI parser and may change over time. It is possible that the way handler methods are set up will change over development to allow more flexibility. Standard Developer caveats: Here thar be dragoons... Consider yourself warned! NOTES As in the SeqIO Handler object (still in development), data is passed in as chunks. The Annotation and SeqFeatures are essentially the same as the SeqIO parser; the significant difference is that data hash being passed could pertain to either the alignment or to a specific sequence, so an extra tag may be needed to disambiguate between the two in some cases. Here I use the ALIGNMENT tag as a boolean flag: it must be present and set to 0 for the data to be tagged for Bio::LocatableSeq or similar (in all other cases it is assumed to be for the alignment). In some cases this will not matter (the actual sequence data, for instance) but it is highly recommmended adding this tag in to prevent possible ambiguities. This is the current Annotation data chunk (via Data::Dumper): $VAR1 = { 'NAME' => 'REFERENCE', 'DATA' => '1 (bases 1 to 10001)' 'AUTHORS' => 'International Human Genome Sequencing Consortium.' 'TITLE' => 'The DNA sequence of Homo sapiens' 'JOURNAL' => 'Unpublished(2003)' 'ALIGNMENT' => 1, }; In the case of LocatableSeqs, one can pass them in as follows for simplicity (note the block line): $VAR1 = { 'NAME' => 'SEQUENCE', 'BLOCK_LINE' => 0, 'NSE' => 'Q7WNI7_BORBR/113-292', 'ALPHABET' => 'protein', 'DATA' => 'VALILGVYRRL...CYVNREM..RAG....QW', 'ALIGNMENT' => 0 }; This can be done as the parser parses each block instead of parsing all the blocks and then passing them in one at a time; the handler will store the sequence data by the block line in an internal hash, concatenating them along the way. This behaviour is b/c the alignment building step requires that the sequence be checked for start/end/strand, possible meta sequence, optional accession, etc. Similarly, a Meta sequence line can be passed in as follows: $VAR1 = { 'NAME' => 'NAMED_META', 'BLOCK_LINE' => 0, 'NSE' => 'Q7WNI7_BORBR/113-292', 'META_KEY' => 'pAS', 'DATA' => '................................', 'ALIGNMENT' => 0 }; The meta sequence will be checked against the NSE for the block position and stored based on the meta tag. A meta sequence does not have to correspond to a real sequence. At this time, unique meta sequence tags must be used for each sequence or they will be overwritten (this may change). An alignment consensus string: $VAR1 = { 'NAME' => 'CONSENSUS', 'DATA' => 'VALILGVYRRL...CYVNREM..RAG....QW', 'ALIGNMENT' => 1 }; A consensus meta sequence: $VAR1 = { 'NAME' => 'CONSENSUS_META', 'META_KEY' => 'pAS', 'DATA' => '................................', 'ALIGNMENT' => 1 }; 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: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Chris Fields Email cjfields at bioperl dot org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : Function: Returns : Args : -format Sequence format to be mapped for handler methods -builder Bio::Seq::SeqBuilder object (normally defined in SequenceStreamI object implementation constructor) Throws : On undefined '-format' sequence format parameter Note : Still under heavy development Bio::HandlerBaseI implementing methods handler_methods Title : handler_methods Usage : $handler->handler_methods('GenBank') %handlers = $handler->handler_methods(); Function: Retrieve the handler methods used for the current format() in the handler. This assumes the handler methods are already described in the HandlerI-implementing class. Returns : a hash reference with the data type handled and the code ref associated with it. Args : [optional] String representing the sequence format. If set here this will also set sequence_format() Throws : On unimplemented sequence format in %HANDLERS data_handler Title : data_handler Usage : $handler->data_handler($data) Function: Centralized method which accepts all data chunks, then distributes to the appropriate methods for processing based on the chunk name from within the HandlerBaseI object. One can also use Returns : None Args : an hash ref containing a data chunk. reset_parameters Title : reset_parameters Usage : $handler->reset_parameters() Function: Resets the internal cache of data (normally object parameters for a builder or factory) Returns : None Args : None format Title : format Usage : $handler->format('GenBank') Function: Get/Set the format for the report/record being parsed. This can be used to set handlers in classes which are capable of processing similar data chunks from multiple driver modules. Returns : String with the sequence format Args : [optional] String with the sequence format Note : The format may be used to set the handlers (as in the current GenericRichSeqHandler implementation) get_params Title : get_params Usage : $handler->get_params('-species') Function: Convenience method used to retrieve the specified parameters from the internal parameter cache Returns : Hash ref containing parameters requested and data as key-value pairs. Note that some parameter values may be objects, arrays, etc. Args : List (array) representing the parameters requested set_params Title : set_params Usage : $handler->set_param({'-seqs' => $seqs}) Function: Convenience method used to set specific parameters Returns : None Args : Hash ref containing the data to be passed as key-value pairs Methods unique to this implementation build_alignment Title : build_alignment Usage : Function: Returns : a Bio::SimpleAlign Args : Throws : Note : This may be replaced by a Builder object at some point annotation_collection Title : annotation_collection Usage : Function: Returns : Args : Throws : Note : seq_annotation_collection Title : seq_annotation_collection Usage : Function: Returns : Args : Throws : Note : process_seqs Title : process_seqs Usage : $handler->process_seqs; Function: checks internal sequences to ensure they are converted over to the proper Bio::AlignI-compatible sequence class Returns : 1 if successful Args : none perl v5.14.2 2012-03-02 Bio::AlignIO::Handler::GenericAlignHandler(3pm)
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