Search results for "distribution:BioPerl CJFIELDS"
Bio::Species - Generic species object.
NOTE: This class is planned for deprecation in favor of the simpler Bio::Taxon. Please use that class instead. Provides a very simple object for storing phylogenetic information. The classification is stored in an array, which is a list of nodes in a...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AlignIO::arp - ARP MSA Sequence input/output stream
This object can create Bio::SimpleAlign objects from ARP flat files. These are typically configuration-like data files for the program Arlequin. For more information, see: http://lgb.unige.ch/arlequin/ For the moment, this retains the allele sequence...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::HandlerBaseI - Interface class for handler methods which interact with any event-driven parsers (drivers).
This interface describes simple class methods used for processing data from an event-based parser (a driver). This is similar in theme to an XML SAX-based driver but differs in that one can optionally pass related data semi-intelligently as chunks (d...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::fastq - fastq sequence input/output stream
This object can transform Bio::Seq and Bio::Seq::Quality objects to and from FASTQ flat file databases. FASTQ is a file format used frequently at the Sanger Centre and in next-gen sequencing to bundle a FASTA sequence and its quality data. A typical ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::LocationI - A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects
This is a pure interface class - in other words, all this does is define methods which other (concrete) classes will actually implement. The Bio::DB::LocationI class defines methods used to retrieve location data from a sequence. This is returned in ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::ReferenceI - A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects
This is a pure interface class - in other words, all this does is define methods which other (concrete) classes will actually implement. The Bio::DB::ReferenceI class defines methods used to retrieve reference data from a sequence. This is returned i...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::ParameterBaseI - Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends.
This is a class interface which focuses on common parameter-related tasks such as building simple database queries, URI-related requests, program arguments, etc. Implementing classes use the following ways to set parameters: 1) Create a new instance ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::genbank - GenBank sequence input/output stream
This object can transform Bio::Seq objects to and from GenBank flat file databases. There is some flexibility here about how to write GenBank output that is not fully documented. Optional functions _show_dna() (output only) shows the dna or not _post...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::erpin - SearchIO-based ERPIN parser
This is an experimental SearchIO-based parser for output from the erpin program. It currently parses erpin output for ERPIN versions 4.2.5 and above; older versions may work but will not be supported....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::infernal - SearchIO-based Infernal parser
This is a SearchIO-based parser for Infernal output from the cmsearch program. It currently parses cmsearch output for Infernal versions 0.7-1.1; older versions may work but will not be supported. The latest version of Infernal is 1.1. The output has...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::rnamotif - SearchIO-based RNAMotif parser
This is a highly experimental SearchIO-based parser for output from the rnamotif program (one of the programs in the RNAMotif suite). It currently parses only raw rnamotif output for RNAMotif versions 3.0 and above; older versions may work but will n...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::GenericWebAgent - helper base class for parameter-based remote server access and response retrieval.
WARNING: Please do NOT spam the web servers with multiple requests. Bio::DB::GenericWebAgent is a generic wrapper around a web agent (LWP::UserAgent), an object which can retain, format, and build parameters for the user agent (Bio::ParameterBaseI), ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::HSP::ModelHSP - A HSP object for model-based searches
This object is a specialization of Bio::Search::HSP::ModelHSP and is used for searches which involve a query model, such as a Hidden Markov Model (HMM), covariance model (CM), descriptor, or anything else besides a sequence. Note that results from an...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Hit::ModelHit - A model-based implementation of the Bio::Search::Hit::HitI interface
This object handles the hit data from a database search using models or descriptors instead of sequences, such as Infernal, HMMER, RNAMotif, etc. Unless you're writing a parser, you won't ever need to create a ModelHit or any other HitI-implementing ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Factory::FTLocationFactory - A FeatureTable Location Parser
Implementation of string-encoded location parsing for the Genbank feature table encoding of locations....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AlignIO::Handler::GenericAlignHandler - Bio::HandlerI-based generic data handler class for alignment-based data
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 ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::Handler::GenericRichSeqHandler - Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data
This is an experimental implementation of a sequence-based HandlerBaseI parser and may change over time. It is possible (nay, likely) that the way handler methods are set up will change over development to allow more flexibility. Release pumpkins, pl...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC