Search results for "dist:BioPerl Bio::Annotation::Reference"
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...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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...
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::SeqI - [Developers] Abstract Interface of Sequence (with features)
Bio::SeqI is the abstract interface of annotated Sequences. These methods are those which you can be guaranteed to get for any Bio::SeqI. For most users of the package the documentation (and methods) in this class are not at useful - this is a develo...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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 Bio::Prim...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DasI - DAS-style access to a feature database
Bio::DasI is a simplified alternative interface to sequence annotation databases used by the distributed annotation system (see Bio::Das). In this scheme, the genome is represented as a series of features, a subset of which are named. Named features ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::scf - .scf file input/output stream
This object can transform .scf files to and from Bio::Seq::SequenceTrace objects. Mechanisms are present to retrieve trace data from scf files....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::embl - EMBL sequence input/output stream
This object can transform 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 (probably ...
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::SeqIO::game - a class for parsing and writing game-XML
Bio::SeqIO::game will parse game XML (version 1.2) or write game XML from a 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 version of game X...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::swiss - Swissprot sequence input/output stream
This object can transform 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 holds ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::bsml - BSML sequence input/output stream
This object can transform Bio::Seq objects to and from BSML (XML) flatfiles....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::table - sequence input/output stream from a delimited table
This class transforms records in a table-formatted text file into 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 attribute...
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::Das::SegmentI - DAS-style access to a feature database
Bio::Das::SegmentI is a simplified alternative interface to sequence annotation databases used by the distributed annotation system. In this scheme, the genome is represented as a series of landmarks. Each Bio::Das::SegmentI object ("segment") corres...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::seqxml - SeqXML sequence input/output stream
This object can transform 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 capabilities of...
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
bp_genbank2gff3.pl - Genbank-gtgbrowse-friendly GFF3
This script uses Bio::SeqFeature::Tools::Unflattener and Bio::Tools::GFF to convert GenBank flatfiles to GFF3 with gene containment hierarchies mapped for optimal display in gbrowse. The input files are assumed to be gzipped GenBank flatfiles for ref...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC