Bio::Seq - Sequence object, with features River stage two • 74 direct dependents • 79 total dependents

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-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::SeqI - [Developers] Abstract Interface of Sequence (with features) River stage two • 74 direct dependents • 79 total dependents

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-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::DasI - DAS-style access to a feature database River stage two • 74 direct dependents • 79 total dependents

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-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::SeqIO - Handler for SeqIO Formats River stage two • 74 direct dependents • 79 total dependents

Bio::SeqIO is a handler module for the formats in the SeqIO set (eg, Bio::SeqIO::fasta). It is the officially sanctioned way of getting at the format objects, which most people should use. The Bio::SeqIO system can be thought of like biological file ...

CJFIELDS/BioPerl-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::Taxon - A node in a represented taxonomy River stage two • 74 direct dependents • 79 total dependents

This is the next generation (for Bioperl) of representing Taxonomy information. Previously all information was managed by a single object called Bio::Species. This new implementation allows representation of the intermediate nodes not just the specie...

CJFIELDS/BioPerl-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::Range - Pure perl RangeI implementation River stage two • 74 direct dependents • 79 total dependents

This provides a pure perl implementation of the BioPerl range interface. Ranges are modeled as having (start, end, length, strand). They use Bio-coordinates - all points >= start and <= end are within the range. End is always greater-than or equal-to...

CJFIELDS/BioPerl-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::RangeI - Range interface River stage two • 74 direct dependents • 79 total dependents

This provides a standard BioPerl range interface that should be implemented by any object that wants to be treated as a range. This serves purely as an abstract base class for implementers and can not be instantiated. Ranges are modeled as having (st...

CJFIELDS/BioPerl-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::TreeIO - Parser for Tree files River stage two • 74 direct dependents • 79 total dependents

This is the driver module for Tree reading from data streams and flatfiles. This is intended to be able to create Bio::Tree::TreeI objects....

CJFIELDS/BioPerl-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::AlignIO - Handler for AlignIO Formats River stage two • 74 direct dependents • 79 total dependents

Bio::AlignIO is a handler module for the formats in the AlignIO set, for example, Bio::AlignIO::fasta. It is the officially sanctioned way of getting at the alignment objects. The resulting alignment is a Bio::Align::AlignI-compliant object. The idea...

CJFIELDS/BioPerl-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::Species - Generic species object. River stage two • 74 direct dependents • 79 total dependents

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-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::SeqUtils - Additional methods for PrimarySeq objects River stage two • 74 direct dependents • 79 total dependents

This class is a holder of methods that work on Bio::PrimarySeqI- compliant sequence objects, e.g. Bio::PrimarySeq and Bio::Seq. These methods are not part of the Bio::PrimarySeqI interface and should in general not be essential to the primary functio...

CJFIELDS/BioPerl-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::SearchIO - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...) River stage two • 74 direct dependents • 79 total dependents

This is a driver for instantiating a parser for report files from sequence database searches. This object serves as a wrapper for the format parsers in Bio::SearchIO::* - you should not need to ever use those format parsers directly. (For people used...

CJFIELDS/BioPerl-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::WebAgent - A base class for Web (any protocol) access River stage two • 74 direct dependents • 79 total dependents

This abstract superclass is a subclass of LWP::UserAgent which allows protocol independent access of remote locations over the Net. It takes care of error handling, proxies and various net protocols. BioPerl classes accessing the net should inherit f...

CJFIELDS/BioPerl-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::LocationI - Abstract interface of a Location on a Sequence River stage two • 74 direct dependents • 79 total dependents

This Interface defines the methods for a 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 Bio::SeqFeatu...

CJFIELDS/BioPerl-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::AnalysisI - An interface to any (local or remote) analysis tool River stage two • 74 direct dependents • 79 total dependents

This interface contains all public methods for accessing and controlling local and remote analysis tools. It is meant to be used on the client side....

CJFIELDS/BioPerl-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::OntologyIO - Parser factory for Ontology formats River stage two • 74 direct dependents • 79 total dependents

This is the parser factory for different ontology sources and formats. Conceptually, it is very similar to Bio::SeqIO, but the difference is that the chunk of data returned as an object is an entire ontology....

CJFIELDS/BioPerl-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::PrimarySeq - Bioperl lightweight sequence object River stage two • 74 direct dependents • 79 total dependents

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...

CJFIELDS/BioPerl-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::PrimarySeqI - Interface definition for a Bio::PrimarySeq River stage two • 74 direct dependents • 79 total dependents

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 implemented b...

CJFIELDS/BioPerl-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::SeqFeatureI - Abstract interface of a Sequence Feature River stage two • 74 direct dependents • 79 total dependents

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...

CJFIELDS/BioPerl-1.7.7 - 07 Dec 2019 19:47:42 UTC

Bio::AnnotationI - Annotation interface River stage two • 74 direct dependents • 79 total dependents

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-1.7.7 - 07 Dec 2019 19:47:42 UTC

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