Search results for "dist:FAST Bio::Annotation::Reference"
FAST::Bio::Annotation::Reference - Specialised DBLink object for Literature References
Object which presents a literature reference. This is considered to be a specialised form of database link. The additional methods provided are all set/get methods to store strings commonly associated with references, in particular title, location (i...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AnnotationI - Annotation interface
Interface all annotations must support. There are two things that each annotation has to support. $annotation->as_text() Annotations have to support an "as_text" method. This should be a single text string, without newlines representing the annotatio...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqI - [Developers] Abstract Interface of Sequence (with features)
FAST::Bio::SeqI is the abstract interface of annotated Sequences. These methods are those which you can be guarenteed to get for any FAST::Bio::SeqI - for most users of the package the documentation (and methods) in this class are not at useful - thi...
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::MySeqI - Abstract Interface of Sequence (with features)
SeqI is the abstract interface of annotated Sequence. These methods are those which you can be guarenteed to get for any annseq. There aren't many here, because too many complicated functions here prevent implementations which are just wrappers aroun...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AnnotationCollectionI - Interface for annotation collections
Annotation Collections are a way of storing a series of "interesting facts" about something. We call an "interesting fact" in Bioperl an Annotation (this differs from a Sequence Feature, which is called a Sequence Feature and may or may not have an A...
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::AlignIO::arp - ARP MSA Sequence input/output stream
This object can create FAST::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 se...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::scf - .scf file input/output stream
This object can transform .scf files to and from FAST::Bio::Seq::SequenceTrace objects. Mechanisms are present to retrieve trace data from scf files....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::swiss - Swissprot sequence input/output stream
This object can transform FAST::Bio::Seq objects to and from Swiss-Pprot flat file databases. There is a lot of flexibility here about how to dump things which needs to be documented. GN (Gene name) line management details A Uniprot/Swiss-Prot entry ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::game - a class for parsing and writing game-XML
FAST::Bio::SeqIO::game will parse game XML (version 1.2) or write game XML from a FAST::Bio::SeqI implementing object. The XML is readable by the genome annotation editor 'Apollo' (www.gmod.org). It is not backwards compatible with the previous versi...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::bsml - BSML sequence input/output stream
This object can transform FAST::Bio::Seq objects to and from BSML (XML) flatfiles. NOTE: 2/1/02 - I have changed the API to more closely match argument passing used by other BioPerl methods ( -tag => value ). Internal methods are using the same API, ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SimpleAlign - Multiple alignments held as a set of sequences
SimpleAlign is an object that handles a multiple sequence alignment (MSA). It is very permissive of types (it does not insist on sequences being all same length, for example). Think of it as a set of sequences with a whole series of built-in manipula...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::table - sequence input/output stream from a delimited table
This class transforms records in a table-formatted text file into FAST::Bio::Seq objects. A table-formatted text file of sequence records for the purposes of this module is defined as a text file with each row corresponding to a sequence, and the att...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::agave - AGAVE sequence output stream.
This object can transform FAST::Bio::Seq objects to agave xml file and vice-versa. I (Simon) coded up this module because I needed a parser to extract data from AGAVE xml to be utitlized by the GenQuire genome annotation system (See http://www.bioinf...
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::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::seqxml - SeqXML sequence input/output stream
This object can transform FAST::Bio::Seq objects to and from SeqXML format. For more information on the SeqXML standard, visit <http://www.seqxml.org>. In short, SeqXML is a lightweight sequence format that takes advantage of the validation capabilit...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Ontology::Term - implementation of the interface for ontology terms
This is a simple implementation for ontology terms providing basic methods (it provides no functionality related to graphs). It implements the FAST::Bio::Ontology::TermI interface. This class also implements FAST::Bio::IdentifiableI and FAST::Bio::De...
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