Search results for "dist:FAST genbank"
FAST::Bio::SeqIO::genbank - GenBank sequence input/output stream
This object can transform FAST::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...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::gbxml - GenBank sequence input/output stream using SAX
This object can transform FAST::Bio::Seq objects to and from GenBank XML flatfiles....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::gbdriver - GenBank handler-based push parser
This object can transform FAST::Bio::Seq objects to and from GenBank flat file databases. The key difference between this parser and the tried-and-true FAST::Bio::SeqIO::genbank parser is this version separates the parsing and data manipulation into ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::FTHelper - Helper class for Embl/Genbank feature tables
Represents one particular Feature with the following fields key - the key of the feature loc - the location string of the feature <other fields> - other fields...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Seq - Sequence object, with features
A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In Bioperl we have 3 main players that people are going to use frequently FAST::Bio...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO - Handler for SeqIO Formats
FAST::Bio::SeqIO is a handler module for the formats in the SeqIO set (eg, FAST::Bio::SeqIO::fasta). It is the officially sanctioned way of getting at the format objects, which most people should use. The FAST::Bio::SeqIO system can be thought of lik...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Taxon - A node in a represented taxonomy
This is the next generation (for Bioperl) of representing Taxonomy information. Previously all information was managed by a single object called FAST::Bio::Species. This new implementation allows representation of the intermediate nodes not just the ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Species - Generic species object.
NOTE: This class is planned for deprecation in favor of the simpler FAST::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 node...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::LocationI - Abstract interface of a Location on a Sequence
This Interface defines the methods for a FAST::Bio::LocationI, an object which encapsulates a location on a biological sequence. Locations need not be attached to actual sequences as they are stand alone objects. LocationI objects are used by FAST::B...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
gbfcut - search features from GenBank files and print corresponding sequences
gbfcut takes GenBank-sequence input and outputs subsequences that correspond to features annotated on all input sequences in Multi-Fasta format. Both simple and more complex split features are supported. Optionally, gbfcut may be directed to only out...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::PrimarySeq - Bioperl lightweight Sequence Object
PrimarySeq is a lightweight Sequence object, storing the sequence, its name, a computer-useful unique name, and other fundamental attributes. It does not contain sequence features or other information. To have a sequence with sequence features you sh...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Seq::QualI - Interface definition for a FAST::Bio::Seq::Qual
This object defines an abstract interface to basic quality information. PrimaryQual is an object just for the quality and its name(s), nothing more. There is a pure perl implementation of this in FAST::Bio::Seq::PrimaryQual. If you just want to use F...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::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...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::embl - EMBL sequence input/output stream
This object can transform FAST::Bio::Seq objects to and from EMBL flat file databases. There is a lot of flexibility here about how to dump things which should be documented more fully. There should be a common object that this and Genbank share (pro...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqFeatureI - Abstract interface of a Sequence Feature
This interface is the functions one can expect for any Sequence Feature, whatever its implementation or whether it is a more complex type (eg, a Gene). This object does not actually provide any implementation, it just provides the definitions of what...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::PrimarySeqI - Interface definition for a FAST::Bio::PrimarySeq
This object defines an abstract interface to basic sequence information - for most users of the package the documentation (and methods) in this class are not useful - this is a developers-only class which defines what methods have to be implmented by...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AnnotatableI - the base interface an annotatable object must implement
This is the base interface that all annotatable objects must implement. A good example is FAST::Bio::Seq which is an AnnotableI object....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Seq::RichSeq - Module implementing a sequence created from a rich sequence database entry
This module implements FAST::Bio::Seq::RichSeqI, an interface for sequences created from or created for entries from/of rich sequence databanks, like EMBL, GenBank, and SwissProt. Methods added to the FAST::Bio::SeqI interface therefore focus on data...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
gbfalncut - cut sites from alignments by regex-matching on features in an annotated GenBank file
gbfalncut extracts sites from alignments that correspond to one or more features annotated on a sequence in a GenBank file. The alignment must contain exactly one sequence with the same identifier as the sequence in the GenBank file. By default all f...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC