bio::seqio::abi(3pm) [debian man page]
Bio::SeqIO::abi(3pm) User Contributed Perl Documentation Bio::SeqIO::abi(3pm) NAME
Bio::SeqIO::abi - abi trace sequence input/output stream SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class. DESCRIPTION
This object can transform Bio::Seq objects to and from abi trace files. To optionally read the trace graph data (which can be used to draw chromatographs, for instance), set the optional '-get_trace_data' flag or the get_trace_data method to a value evaluating to TRUE. 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/ AUTHORS - Aaron Mackey Email: amackey@virginia.edu APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq::Quality object Args : NONE write_seq Title : write_seq Usage : $stream->write_seq(@seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object get_trace_data Title : get_trace_data Usage : $stream->get_trace_data(1) Function: set boolean flag to retrieve the trace data (possibly for output) Returns : bool value, TRUE = retrieve trace data (default FALSE) Args : bool value perl v5.14.2 2012-03-02 Bio::SeqIO::abi(3pm)
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Bio::SeqIO::swissdriver(3pm) User Contributed Perl Documentation Bio::SeqIO::swissdriver(3pm) NAME
Bio::SeqIO::swissdriver - SwissProt/UniProt handler-based push parser SYNOPSIS
#It is probably best not to use this object directly, but #rather go through the SeqIO handler: $stream = Bio::SeqIO->new(-file => $filename, -format => 'swissdriver'); while ( my $seq = $stream->next_seq() ) { # do something with $seq } DESCRIPTION
This object can transform Bio::Seq objects to and from UniProt flat file databases. The key difference between this parser and the tried- and-true Bio::SeqIO::swiss parser is this version separates the parsing and data manipulation into a 'driver' method (next_seq) and separate object handlers which deal with the data passed to it. The Driver The main purpose of the driver routine, in this case next_seq(), is to carve out the data into meaningful chunks which are passed along to relevant handlers (see below). Each chunk of data in the has a NAME tag attached to it, similar to that for XML parsing. This designates the type of data passed (annotation type or seqfeature) and the handler to be called for processing the 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 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 - Bioperl Project bioperl-l at bioperl.org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : none write_seq Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object (must be seq) to the stream Returns : 1 for success and 0 for error Args : array of 1 to n Bio::SeqI objects seqhandler Title : seqhandler Usage : $stream->seqhandler($handler) Function: Get/Set teh Bio::Seq::HandlerBaseI object Returns : Bio::Seq::HandlerBaseI Args : Bio::Seq::HandlerBaseI perl v5.14.2 2012-03-02 Bio::SeqIO::swissdriver(3pm)