FAST 1.03
Kwalitee Issues
- use_strict
-
Add 'use strict' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules are strictly written.
Error: FAST::Bio::Location::Split, FAST::Bio::Search::BlastUtils, FAST::Bio::SearchIO::SearchWriterI, FAST::Bio::SearchIO::XML::BlastHandler, FAST::Bio::SearchIO::XML::PsiBlastHandler, FAST::Bio::SearchIO::cross_match, FAST::Bio::SeqIO::game, FAST::List::Generator
- use_warnings
-
Add 'use warnings' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.
Error: FAST::Bio::Align::AlignI, FAST::Bio::AlignIO, FAST::Bio::AlignIO::arp, FAST::Bio::AlignIO::bl2seq, FAST::Bio::AlignIO::clustalw, FAST::Bio::AlignIO::emboss, FAST::Bio::AlignIO::fasta, FAST::Bio::AlignIO::largemultifasta, FAST::Bio::AlignIO::maf, FAST::Bio::AlignIO::mase, FAST::Bio::AlignIO::mega, FAST::Bio::AlignIO::meme, FAST::Bio::AlignIO::metafasta, FAST::Bio::AlignIO::msf, FAST::Bio::AlignIO::nexml, FAST::Bio::AlignIO::nexus, FAST::Bio::AlignIO::pfam, FAST::Bio::AlignIO::phylip, FAST::Bio::AlignIO::po, FAST::Bio::AlignIO::proda, FAST::Bio::AlignIO::prodom, FAST::Bio::AlignIO::psi, FAST::Bio::AlignIO::selex, FAST::Bio::AlignIO::stockholm, FAST::Bio::AlignIO::xmfa, FAST::Bio::AnalysisParserI, FAST::Bio::AnalysisResultI, FAST::Bio::AnnotatableI, FAST::Bio::Annotation::AnnotationFactory, FAST::Bio::Annotation::Collection, FAST::Bio::Annotation::Comment, FAST::Bio::Annotation::DBLink, FAST::Bio::Annotation::OntologyTerm, FAST::Bio::Annotation::Reference, FAST::Bio::Annotation::SimpleValue, FAST::Bio::Annotation::TagTree, FAST::Bio::Annotation::Target, FAST::Bio::Annotation::TypeManager, FAST::Bio::AnnotationCollectionI, FAST::Bio::AnnotationI, FAST::Bio::Cluster::FamilyI, FAST::Bio::Cluster::SequenceFamily, FAST::Bio::ClusterI, FAST::Bio::DB::InMemoryCache, FAST::Bio::DB::RandomAccessI, FAST::Bio::DB::SeqI, FAST::Bio::DB::Taxonomy, FAST::Bio::DB::Taxonomy::entrez, FAST::Bio::DB::Taxonomy::flatfile, FAST::Bio::DB::Taxonomy::list, FAST::Bio::DescribableI, FAST::Bio::Event::EventGeneratorI, FAST::Bio::Event::EventHandlerI, FAST::Bio::Factory::FTLocationFactory, FAST::Bio::Factory::LocationFactoryI, FAST::Bio::Factory::ObjectBuilderI, FAST::Bio::Factory::ObjectFactory, FAST::Bio::Factory::ObjectFactoryI, FAST::Bio::Factory::SequenceFactoryI, FAST::Bio::Factory::SequenceStreamI, FAST::Bio::FeatureHolderI, FAST::Bio::GapSeq, FAST::Bio::GapSeqI, FAST::Bio::IdentifiableI, FAST::Bio::LocatableSeq, FAST::Bio::Location::Atomic, FAST::Bio::Location::CoordinatePolicyI, FAST::Bio::Location::Fuzzy, FAST::Bio::Location::FuzzyLocationI, FAST::Bio::Location::NarrowestCoordPolicy, FAST::Bio::Location::Simple, FAST::Bio::Location::Split, FAST::Bio::Location::SplitLocationI, FAST::Bio::Location::WidestCoordPolicy, FAST::Bio::LocationI, FAST::Bio::MyPrimarySeqI, FAST::Bio::MySeqI, FAST::Bio::MySeqUtils, FAST::Bio::Ontology::DocumentRegistry, FAST::Bio::Ontology::OBOEngine, FAST::Bio::Ontology::Ontology, FAST::Bio::Ontology::OntologyEngineI, FAST::Bio::Ontology::OntologyI, FAST::Bio::Ontology::OntologyStore, FAST::Bio::Ontology::Relationship, FAST::Bio::Ontology::RelationshipFactory, FAST::Bio::Ontology::RelationshipI, FAST::Bio::Ontology::RelationshipType, FAST::Bio::Ontology::SimpleGOEngine::GraphAdaptor, FAST::Bio::Ontology::SimpleGOEngine::GraphAdaptor02, FAST::Bio::Ontology::SimpleOntologyEngine, FAST::Bio::Ontology::Term, FAST::Bio::Ontology::TermFactory, FAST::Bio::Ontology::TermI, FAST::Bio::OntologyIO, FAST::Bio::OntologyIO::Handlers::BaseSAXHandler, FAST::Bio::OntologyIO::Handlers::InterProHandler, FAST::Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler, FAST::Bio::OntologyIO::InterProParser, FAST::Bio::OntologyIO::dagflat, FAST::Bio::OntologyIO::goflat, FAST::Bio::OntologyIO::obo, FAST::Bio::OntologyIO::simplehierarchy, FAST::Bio::OntologyIO::soflat, FAST::Bio::PrimarySeq, FAST::Bio::PrimarySeqI, FAST::Bio::PullParserI, FAST::Bio::Range, FAST::Bio::RangeI, FAST::Bio::Root::Exception, FAST::Bio::Root::IO, FAST::Bio::Root::Root, FAST::Bio::Root::RootI, FAST::Bio::Root::Version, FAST::Bio::Search::BlastUtils, FAST::Bio::Search::GenericStatistics, FAST::Bio::Search::HSP::BlastPullHSP, FAST::Bio::Search::HSP::GenericHSP, FAST::Bio::Search::HSP::HSPFactory, FAST::Bio::Search::HSP::HSPI, FAST::Bio::Search::HSP::HmmpfamHSP, FAST::Bio::Search::HSP::PullHSPI, FAST::Bio::Search::Hit::BlastPullHit, FAST::Bio::Search::Hit::GenericHit, FAST::Bio::Search::Hit::HitFactory, FAST::Bio::Search::Hit::HitI, FAST::Bio::Search::Hit::HmmpfamHit, FAST::Bio::Search::Hit::PullHitI, FAST::Bio::Search::Result::BlastPullResult, FAST::Bio::Search::Result::CrossMatchResult, FAST::Bio::Search::Result::GenericResult, FAST::Bio::Search::Result::HmmpfamResult, FAST::Bio::Search::Result::PullResultI, FAST::Bio::Search::Result::ResultFactory, FAST::Bio::Search::Result::ResultI, FAST::Bio::Search::SearchUtils, FAST::Bio::Search::StatisticsI, FAST::Bio::SearchIO::EventHandlerI, FAST::Bio::SearchIO::FastHitEventBuilder, FAST::Bio::SearchIO::IteratedSearchResultEventBuilder, FAST::Bio::SearchIO::SearchResultEventBuilder, FAST::Bio::SearchIO::SearchWriterI, FAST::Bio::SearchIO::Writer::BSMLResultWriter, FAST::Bio::SearchIO::Writer::GbrowseGFF, FAST::Bio::SearchIO::Writer::HSPTableWriter, FAST::Bio::SearchIO::Writer::HTMLResultWriter, FAST::Bio::SearchIO::Writer::HitTableWriter, FAST::Bio::SearchIO::Writer::ResultTableWriter, FAST::Bio::SearchIO::Writer::TextResultWriter, FAST::Bio::SearchIO::XML::BlastHandler, FAST::Bio::SearchIO::XML::PsiBlastHandler, FAST::Bio::SearchIO::axt, FAST::Bio::SearchIO::blast, FAST::Bio::SearchIO::blast_pull, FAST::Bio::SearchIO::blasttable, FAST::Bio::SearchIO::blastxml, FAST::Bio::SearchIO::cross_match, FAST::Bio::SearchIO::erpin, FAST::Bio::SearchIO::exonerate, FAST::Bio::SearchIO::fasta, FAST::Bio::SearchIO::hmmer, FAST::Bio::SearchIO::hmmer2, FAST::Bio::SearchIO::hmmer3, FAST::Bio::SearchIO::hmmer_pull, FAST::Bio::SearchIO::infernal, FAST::Bio::SearchIO::megablast, FAST::Bio::SearchIO::psl, FAST::Bio::SearchIO::rnamotif, FAST::Bio::SearchIO::sim4, FAST::Bio::SearchIO::waba, FAST::Bio::SearchIO::wise, FAST::Bio::Seq, FAST::Bio::Seq::LargeLocatableSeq, FAST::Bio::Seq::LargePrimarySeq, FAST::Bio::Seq::LargeSeqI, FAST::Bio::Seq::Meta, FAST::Bio::Seq::Meta::Array, FAST::Bio::Seq::MetaI, FAST::Bio::Seq::PrimaryQual, FAST::Bio::Seq::QualI, FAST::Bio::Seq::Quality, FAST::Bio::Seq::RichSeq, FAST::Bio::Seq::RichSeqI, FAST::Bio::Seq::SeqBuilder, FAST::Bio::Seq::SeqFactory, FAST::Bio::Seq::SeqFastaSpeedFactory, FAST::Bio::Seq::SequenceTrace, FAST::Bio::Seq::TraceI, FAST::Bio::SeqAnalysisParserI, FAST::Bio::SeqFeature::FeaturePair, FAST::Bio::SeqFeature::Gene::Exon, FAST::Bio::SeqFeature::Gene::ExonI, FAST::Bio::SeqFeature::Gene::GeneStructure, FAST::Bio::SeqFeature::Gene::GeneStructureI, FAST::Bio::SeqFeature::Gene::Intron, FAST::Bio::SeqFeature::Gene::NC_Feature, FAST::Bio::SeqFeature::Gene::Poly_A_site, FAST::Bio::SeqFeature::Gene::Promoter, FAST::Bio::SeqFeature::Gene::Transcript, FAST::Bio::SeqFeature::Gene::TranscriptI, FAST::Bio::SeqFeature::Gene::UTR, FAST::Bio::SeqFeature::Generic, FAST::Bio::SeqFeature::Similarity, FAST::Bio::SeqFeature::SimilarityPair, FAST::Bio::SeqFeature::Tools::FeatureNamer, FAST::Bio::SeqFeature::Tools::IDHandler, FAST::Bio::SeqFeature::Tools::TypeMapper, FAST::Bio::SeqFeature::Tools::Unflattener, FAST::Bio::SeqFeatureI, FAST::Bio::SeqI, FAST::Bio::SeqIO::FTHelper, FAST::Bio::SeqIO::MultiFile, FAST::Bio::SeqIO::abi, FAST::Bio::SeqIO::ace, FAST::Bio::SeqIO::agave, FAST::Bio::SeqIO::alf, FAST::Bio::SeqIO::asciitree, FAST::Bio::SeqIO::bsml, FAST::Bio::SeqIO::bsml_sax, FAST::Bio::SeqIO::chadoxml, FAST::Bio::SeqIO::chaos, FAST::Bio::SeqIO::chaosxml, FAST::Bio::SeqIO::ctf, FAST::Bio::SeqIO::embl, FAST::Bio::SeqIO::embldriver, FAST::Bio::SeqIO::entrezgene, FAST::Bio::SeqIO::excel, FAST::Bio::SeqIO::exp, FAST::Bio::SeqIO::fastq, FAST::Bio::SeqIO::flybase_chadoxml, FAST::Bio::SeqIO::game, FAST::Bio::SeqIO::game::featHandler, FAST::Bio::SeqIO::game::gameHandler, FAST::Bio::SeqIO::game::gameSubs, FAST::Bio::SeqIO::game::gameWriter, FAST::Bio::SeqIO::game::seqHandler, FAST::Bio::SeqIO::gbxml, FAST::Bio::SeqIO::gcg, FAST::Bio::SeqIO::genbank, FAST::Bio::SeqIO::interpro, FAST::Bio::SeqIO::kegg, FAST::Bio::SeqIO::largefasta, FAST::Bio::SeqIO::lasergene, FAST::Bio::SeqIO::locuslink, FAST::Bio::SeqIO::mbsout, FAST::Bio::SeqIO::metafasta, FAST::Bio::SeqIO::msout, FAST::Bio::SeqIO::nexml, FAST::Bio::SeqIO::phd, FAST::Bio::SeqIO::pir, FAST::Bio::SeqIO::pln, FAST::Bio::SeqIO::qual, FAST::Bio::SeqIO::raw, FAST::Bio::SeqIO::scf, FAST::Bio::SeqIO::seqxml, FAST::Bio::SeqIO::swiss, FAST::Bio::SeqIO::swissdriver, FAST::Bio::SeqIO::tab, FAST::Bio::SeqIO::table, FAST::Bio::SeqIO::tigr, FAST::Bio::SeqIO::tigrxml, FAST::Bio::SeqIO::tinyseq, FAST::Bio::SeqIO::ztr, FAST::Bio::SeqUtils, FAST::Bio::SimpleAlign, FAST::Bio::Taxon, FAST::Bio::Tools::AnalysisResult, FAST::Bio::Tools::CodonTable, FAST::Bio::Tools::GFF, FAST::Bio::Tools::Genewise, FAST::Bio::Tools::Genomewise, FAST::Bio::Tools::IUPAC, FAST::Bio::Tools::MySeqStats, FAST::Bio::Tools::Run::GenericParameters, FAST::Bio::Tools::Run::ParametersI, FAST::Bio::Tools::SeqPattern, FAST::Bio::Tools::SeqStats, FAST::Bio::Tree::Node, FAST::Bio::Tree::NodeI, FAST::Bio::Tree::Tree, FAST::Bio::Tree::TreeFunctionsI, FAST::Bio::Tree::TreeI, FAST::Bio::UnivAln, FAST::Bio::WebAgent, FAST::List::Generator
- consistent_version
-
Split the distribution, or fix the version numbers to make them consistent (use the highest version number to avoid version downgrade).
Error: 0.974,1.00,1.006924,1.01,1.03
- meta_yml_has_provides
-
Add all modules contained in this distribution to the META.yml field 'provides'. Module::Build or Dist::Zilla::Plugin::MetaProvides do this automatically for you.
- meta_yml_has_repository_resource
-
Add a 'repository' resource to the META.yml via 'meta_add' accessor (for Module::Build) or META_ADD parameter (for ExtUtils::MakeMaker).
- has_separate_license_file
-
This is not a critical issue. Currently mainly informative for the CPANTS authors. It might be removed later.
Modules
| Name | Abstract | Version | View |
|---|---|---|---|
| FAST | FAST Analysis of Sequences Toolbox | 1.03 | metacpan |
| FAST::Bio::Align::AlignI | An interface for describing sequence alignments. | metacpan | |
| FAST::Bio::AlignIO | Handler for AlignIO Formats | metacpan | |
| FAST::Bio::AlignIO::Handler::GenericAlignHandler | FAST::Bio::HandlerI-based generic data handler class for alignment-based data | metacpan | |
| FAST::Bio::AlignIO::arp | ARP MSA Sequence input/output stream | metacpan | |
| FAST::Bio::AlignIO::bl2seq | bl2seq sequence input/output stream | metacpan | |
| FAST::Bio::AlignIO::clustalw | clustalw sequence input/output stream | metacpan | |
| FAST::Bio::AlignIO::emboss | Parse EMBOSS alignment output (from applications water and needle) | metacpan | |
| FAST::Bio::AlignIO::fasta | fasta MSA Sequence input/output stream | metacpan | |
| FAST::Bio::AlignIO::largemultifasta | Largemultifasta MSA Sequence input/output stream | metacpan | |
| FAST::Bio::AlignIO::maf | Multiple Alignment Format sequence input stream | metacpan | |
| FAST::Bio::AlignIO::mase | mase sequence input/output stream | metacpan | |
| FAST::Bio::AlignIO::mega | Parse and Create MEGA format data files | metacpan | |
| FAST::Bio::AlignIO::meme | meme sequence input/output stream | metacpan | |
| FAST::Bio::AlignIO::metafasta | Metafasta MSA Sequence input/output stream | metacpan | |
| FAST::Bio::AlignIO::msf | msf sequence input/output stream | metacpan | |
| FAST::Bio::AlignIO::nexml | NeXML format sequence alignment input/output stream driver | metacpan | |
| FAST::Bio::AlignIO::nexus | NEXUS format sequence input/output stream | metacpan | |
| FAST::Bio::AlignIO::pfam | pfam sequence input/output stream | metacpan | |
| FAST::Bio::AlignIO::phylip | PHYLIP format sequence input/output stream | metacpan | |
| FAST::Bio::AlignIO::po | po MSA Sequence input/output stream | metacpan | |
| FAST::Bio::AlignIO::proda | proda sequence input/output stream | metacpan | |
| FAST::Bio::AlignIO::prodom | prodom sequence input/output stream | metacpan | |
| FAST::Bio::AlignIO::psi | Read/Write PSI-BLAST profile alignment files | metacpan | |
| FAST::Bio::AlignIO::selex | selex sequence input/output stream | metacpan | |
| FAST::Bio::AlignIO::stockholm | stockholm sequence input/output stream | metacpan | |
| FAST::Bio::AlignIO::xmfa | XMFA MSA Sequence input/output stream | metacpan | |
| FAST::Bio::AnalysisParserI | Generic analysis output parser interface | metacpan | |
| FAST::Bio::AnalysisResultI | Interface for analysis result objects | metacpan | |
| FAST::Bio::AnnotatableI | the base interface an annotatable object must implement | metacpan | |
| FAST::Bio::Annotation::AnnotationFactory | Instantiates a new FAST::Bio::AnnotationI (or derived class) through a factory | metacpan | |
| FAST::Bio::Annotation::Collection | Default Perl implementation of AnnotationCollectionI | metacpan | |
| FAST::Bio::Annotation::Comment | A comment object, holding text | metacpan | |
| FAST::Bio::Annotation::DBLink | untyped links between databases | metacpan | |
| FAST::Bio::Annotation::OntologyTerm | An ontology term adapted to AnnotationI | metacpan | |
| FAST::Bio::Annotation::Reference | Specialised DBLink object for Literature References | metacpan | |
| FAST::Bio::Annotation::SimpleValue | A simple scalar | metacpan | |
| FAST::Bio::Annotation::TagTree | AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text. | metacpan | |
| FAST::Bio::Annotation::Target | Provides an object which represents a target (ie, a similarity hit) from one object to something in another database | metacpan | |
| FAST::Bio::Annotation::TypeManager | Manages types for annotation collections | metacpan | |
| FAST::Bio::AnnotationCollectionI | Interface for annotation collections | metacpan | |
| FAST::Bio::AnnotationI | Annotation interface | metacpan | |
| FAST::Bio::Cluster::FamilyI | Family Interface | metacpan | |
| FAST::Bio::Cluster::SequenceFamily | Sequence Family object | metacpan | |
| FAST::Bio::ClusterI | Cluster Interface | metacpan | |
| FAST::Bio::DB::InMemoryCache | Abstract interface for a sequence database | metacpan | |
| FAST::Bio::DB::RandomAccessI | Abstract interface for a sequence database | metacpan | |
| FAST::Bio::DB::SeqI | Abstract Interface for Sequence databases | metacpan | |
| FAST::Bio::DB::Taxonomy | Access to a taxonomy database | metacpan | |
| FAST::Bio::DB::Taxonomy::entrez | Taxonomy Entrez driver | metacpan | |
| FAST::Bio::DB::Taxonomy::flatfile | An implementation of FAST::Bio::DB::Taxonomy which uses local flat files | metacpan | |
| FAST::Bio::DB::Taxonomy::list | An implementation of FAST::Bio::DB::Taxonomy that accepts lists of words to build a database | metacpan | |
| FAST::Bio::DescribableI | interface for objects with human readable names and descriptions | metacpan | |
| FAST::Bio::Event::EventGeneratorI | This interface describes the basic event generator class. | metacpan | |
| FAST::Bio::Event::EventHandlerI | An Event Handler Interface | metacpan | |
| FAST::Bio::Factory::FTLocationFactory | A FeatureTable Location Parser | metacpan | |
| FAST::Bio::Factory::LocationFactoryI | A factory interface for generating locations from a string | metacpan | |
| FAST::Bio::Factory::ObjectBuilderI | Interface for an object builder | metacpan | |
| FAST::Bio::Factory::ObjectFactory | Instantiates a new FAST::Bio::Root::RootI (or derived class) through a factory | metacpan | |
| FAST::Bio::Factory::ObjectFactoryI | A General object creator factory | metacpan | |
| FAST::Bio::Factory::SequenceFactoryI | This interface allows for generic building of sequences in factories which create sequences (like SeqIO) | metacpan | |
| FAST::Bio::Factory::SequenceStreamI | Interface describing the basics of a Sequence Stream. | metacpan | |
| FAST::Bio::FeatureHolderI | the base interface an object with features must implement | metacpan | |
| FAST::Bio::GapSeq | metacpan | ||
| FAST::Bio::GapSeqI | metacpan | ||
| FAST::Bio::HandlerBaseI | Interface class for handler methods which interact with any event-driven parsers (drivers). | metacpan | |
| FAST::Bio::IdentifiableI | interface for objects with identifiers | metacpan | |
| FAST::Bio::LocatableSeq | A FAST::Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. | metacpan | |
| FAST::Bio::Location::Atomic | Implementation of a Atomic Location on a Sequence | metacpan | |
| FAST::Bio::Location::CoordinatePolicyI | Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location | metacpan | |
| FAST::Bio::Location::Fuzzy | Implementation of a Location on a Sequence which has unclear start and/or end locations | metacpan | |
| FAST::Bio::Location::FuzzyLocationI | Abstract interface of a Location on a Sequence which has unclear start/end location | metacpan | |
| FAST::Bio::Location::NarrowestCoordPolicy | class implementing FAST::Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range | metacpan | |
| FAST::Bio::Location::Simple | Implementation of a Simple Location on a Sequence | metacpan | |
| FAST::Bio::Location::Split | Implementation of a Location on a Sequence which has multiple locations (start/end points) | metacpan | |
| FAST::Bio::Location::SplitLocationI | Abstract interface of a Location on a Sequence which has multiple locations (start/end points) | metacpan | |
| FAST::Bio::Location::WidestCoordPolicy | class implementing FAST::Bio::Location::CoordinatePolicy as the widest possible and reasonable range | metacpan | |
| FAST::Bio::LocationI | Abstract interface of a Location on a Sequence | metacpan | |
| FAST::Bio::MyPrimarySeqI | metacpan | ||
| FAST::Bio::MySeqI | metacpan | ||
| FAST::Bio::Ontology::DocumentRegistry | Keep track of where to find ontologies. Allows lookups by name. | metacpan | |
| FAST::Bio::Ontology::OBOEngine | An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium | metacpan | |
| FAST::Bio::Ontology::Ontology | standard implementation of an Ontology | metacpan | |
| FAST::Bio::Ontology::OntologyEngineI | Interface a minimal Ontology implementation should satisfy | metacpan | |
| FAST::Bio::Ontology::OntologyI | Interface for an ontology implementation | metacpan | |
| FAST::Bio::Ontology::OntologyStore | A repository of ontologies | metacpan | |
| FAST::Bio::Ontology::Relationship | a relationship for an ontology | metacpan | |
| FAST::Bio::Ontology::RelationshipFactory | Instantiates a new FAST::Bio::Ontology::RelationshipI (or derived class) through a factory | metacpan | |
| FAST::Bio::Ontology::RelationshipI | Interface for a relationship between ontology terms | metacpan | |
| FAST::Bio::Ontology::RelationshipType | a relationship type for an ontology | metacpan | |
| FAST::Bio::Ontology::SimpleGOEngine::GraphAdaptor | Graph adaptor for FAST::Bio::Ontology::SimpleGOEngine | 1.00 | metacpan |
| FAST::Bio::Ontology::SimpleGOEngine::GraphAdaptor02 | Graph adaptor (v02.x) for FAST::Bio::Ontology::SimpleGOEngine | metacpan | |
| FAST::Bio::Ontology::SimpleOntologyEngine | Implementation of OntologyEngineI interface | metacpan | |
| FAST::Bio::Ontology::Term | implementation of the interface for ontology terms | metacpan | |
| FAST::Bio::Ontology::TermFactory | Instantiates a new FAST::Bio::Ontology::TermI (or derived class) through a factory | metacpan | |
| FAST::Bio::Ontology::TermI | interface for ontology terms | metacpan | |
| FAST::Bio::OntologyIO | Parser factory for Ontology formats | metacpan | |
| FAST::Bio::OntologyIO::Handlers::BaseSAXHandler | metacpan | ||
| FAST::Bio::OntologyIO::Handlers::InterProHandler | XML handler class for InterProParser | metacpan | |
| FAST::Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler | parse an InterPro XML file and persist the resulting terms to a Biosql database | metacpan | |
| FAST::Bio::OntologyIO::InterProParser | Parser for InterPro xml files. | metacpan | |
| FAST::Bio::OntologyIO::dagflat | a base class parser for GO flat-file type formats | metacpan | |
| FAST::Bio::OntologyIO::goflat | a parser for the Gene Ontology flat-file format | metacpan | |
| FAST::Bio::OntologyIO::obo | a parser for OBO flat-file format from Gene Ontology Consortium | metacpan | |
| FAST::Bio::OntologyIO::simplehierarchy | a base class parser for simple hierarchy-by-indentation type formats | metacpan | |
| FAST::Bio::OntologyIO::soflat | a parser for the Sequence Ontology flat-file format | metacpan | |
| FAST::Bio::PrimarySeq | Bioperl lightweight Sequence Object | metacpan | |
| FAST::Bio::PrimarySeqI | Interface definition for a FAST::Bio::PrimarySeq | metacpan | |
| FAST::Bio::PullParserI | A base module for fast 'pull' parsing | metacpan | |
| FAST::Bio::Range | Pure perl RangeI implementation | metacpan | |
| FAST::Bio::RangeI | Range interface | metacpan | |
| FAST::Bio::Root::Exception | metacpan | ||
| FAST::Bio::Root::IO | metacpan | ||
| FAST::Bio::Root::Root | metacpan | ||
| FAST::Bio::Root::RootI | metacpan | ||
| FAST::Bio::Root::Version | 1.006924 | metacpan | |
| FAST::Bio::Search::BlastUtils | Utility functions for FAST::Bio::Search:: BLAST objects | metacpan | |
| FAST::Bio::Search::GenericStatistics | An object for statistics | metacpan | |
| FAST::Bio::Search::HSP::BlastPullHSP | A parser and HSP object for BlastN hsps | metacpan | |
| FAST::Bio::Search::HSP::GenericHSP | A "Generic" implementation of a High Scoring Pair | metacpan | |
| FAST::Bio::Search::HSP::HSPFactory | A factory to create FAST::Bio::Search::HSP::HSPI objects | metacpan | |
| FAST::Bio::Search::HSP::HSPI | Interface for a High Scoring Pair in a similarity search result | metacpan | |
| FAST::Bio::Search::HSP::HmmpfamHSP | A parser and HSP object for hmmpfam hsps | metacpan | |
| FAST::Bio::Search::HSP::PullHSPI | FAST::Bio::Search::HSP::HSPI interface for pull parsers. | metacpan | |
| FAST::Bio::Search::Hit::BlastPullHit | A parser and hit object for BLASTN hits | metacpan | |
| FAST::Bio::Search::Hit::GenericHit | A generic implementation of the FAST::Bio::Search::Hit::HitI interface | metacpan | |
| FAST::Bio::Search::Hit::HitFactory | A factory to create FAST::Bio::Search::Hit::HitI objects | metacpan | |
| FAST::Bio::Search::Hit::HitI | Interface for a hit in a similarity search result | metacpan | |
| FAST::Bio::Search::Hit::HmmpfamHit | A parser and hit object for hmmpfam hits | metacpan | |
| FAST::Bio::Search::Hit::PullHitI | FAST::Bio::Search::Hit::HitI interface for pull parsers. | metacpan | |
| FAST::Bio::Search::Result::BlastPullResult | A parser and result object for BLASTN results | metacpan | |
| FAST::Bio::Search::Result::CrossMatchResult | CrossMatch-specific subclass of FAST::Bio::Search::Result::GenericResult | metacpan | |
| FAST::Bio::Search::Result::GenericResult | Generic Implementation of FAST::Bio::Search::Result::ResultI interface applicable to most search results. | metacpan | |
| FAST::Bio::Search::Result::HmmpfamResult | A parser and result object for hmmpfam results | metacpan | |
| FAST::Bio::Search::Result::PullResultI | FAST::Bio::Search::Result::ResultI interface for 'pull' parsers | metacpan | |
| FAST::Bio::Search::Result::ResultFactory | A factory to create FAST::Bio::Search::Result::ResultI objects | metacpan | |
| FAST::Bio::Search::Result::ResultI | Abstract interface to Search Result objects | metacpan | |
| FAST::Bio::Search::SearchUtils | Utility functions for FAST::Bio::Search:: objects | metacpan | |
| FAST::Bio::Search::StatisticsI | A Base object for statistics | metacpan | |
| FAST::Bio::SearchIO | Driver for parsing Sequence Database Searches (BLAST, FASTA, ...) | metacpan | |
| FAST::Bio::SearchIO::EventHandlerI | An abstract Event Handler for Search Result parsing | metacpan | |
| FAST::Bio::SearchIO::FastHitEventBuilder | Event Handler for SearchIO events. | metacpan | |
| FAST::Bio::SearchIO::IteratedSearchResultEventBuilder | Event Handler for SearchIO events. | metacpan | |
| FAST::Bio::SearchIO::SearchResultEventBuilder | Event Handler for SearchIO events. | metacpan | |
| FAST::Bio::SearchIO::SearchWriterI | Interface for outputting parsed Search results | metacpan | |
| FAST::Bio::SearchIO::Writer::BSMLResultWriter | BSML output writer | metacpan | |
| FAST::Bio::SearchIO::Writer::GbrowseGFF | Interface for outputting parsed search results in Gbrowse GFF format | metacpan | |
| FAST::Bio::SearchIO::Writer::HSPTableWriter | Tab-delimited data for FAST::Bio::Search::HSP::HSPI objects | metacpan | |
| FAST::Bio::SearchIO::Writer::HTMLResultWriter | write a FAST::Bio::Search::ResultI in HTML | metacpan | |
| FAST::Bio::SearchIO::Writer::HitTableWriter | Tab-delimited data for FAST::Bio::Search::Hit::HitI objects | metacpan | |
| FAST::Bio::SearchIO::Writer::ResultTableWriter | Outputs tab-delimited data for each FAST::Bio::Search::Result::ResultI object. | metacpan | |
| FAST::Bio::SearchIO::Writer::TextResultWriter | Object to implement writing a FAST::Bio::Search::ResultI in Text. | metacpan | |
| FAST::Bio::SearchIO::XML::BlastHandler | XML Handler for NCBI Blast XML parsing. | metacpan | |
| FAST::Bio::SearchIO::XML::PsiBlastHandler | XML Handler for NCBI Blast PSIBLAST XML parsing. | metacpan | |
| FAST::Bio::SearchIO::axt | a parser for axt format reports | metacpan | |
| FAST::Bio::SearchIO::blast | Event generator for event based parsing of blast reports | metacpan | |
| FAST::Bio::SearchIO::blast_pull | A parser for BLAST output | metacpan | |
| FAST::Bio::SearchIO::blasttable | Driver module for SearchIO for parsing NCBI -m 8/9 format | metacpan | |
| FAST::Bio::SearchIO::blastxml | A SearchIO implementation of NCBI Blast XML parsing. | metacpan | |
| FAST::Bio::SearchIO::cross_match | CrossMatch-specific subclass of FAST::Bio::SearchIO | metacpan | |
| FAST::Bio::SearchIO::erpin | SearchIO-based ERPIN parser | metacpan | |
| FAST::Bio::SearchIO::exonerate | parser for Exonerate | metacpan | |
| FAST::Bio::SearchIO::fasta | A SearchIO parser for FASTA results | metacpan | |
| FAST::Bio::SearchIO::gmap_f9 | Event generator for parsing gmap reports (Z format) | metacpan | |
| FAST::Bio::SearchIO::hmmer | A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam) | metacpan | |
| FAST::Bio::SearchIO::hmmer2 | A parser for HMMER output (hmmpfam, hmmsearch) | metacpan | |
| FAST::Bio::SearchIO::hmmer3 | DESCRIPTION of Object | metacpan | |
| FAST::Bio::SearchIO::hmmer_pull | A parser for HMMER output | metacpan | |
| FAST::Bio::SearchIO::infernal | SearchIO-based Infernal parser | metacpan | |
| FAST::Bio::SearchIO::megablast | a driver module for FAST::Bio::SearchIO to parse megablast reports (format 0) | metacpan | |
| FAST::Bio::SearchIO::psl | A parser for PSL output (UCSC) | metacpan | |
| FAST::Bio::SearchIO::rnamotif | SearchIO-based RNAMotif parser | metacpan | |
| FAST::Bio::SearchIO::sim4 | parser for Sim4 alignments | metacpan | |
| FAST::Bio::SearchIO::waba | SearchIO parser for Jim Kent WABA program alignment output | metacpan | |
| FAST::Bio::SearchIO::wise | Parsing of wise output as alignments | metacpan | |
| FAST::Bio::Seq | Sequence object, with features | metacpan | |
| FAST::Bio::Seq::LargeLocatableSeq | LocatableSeq object that stores sequence as files in the tempdir | metacpan | |
| FAST::Bio::Seq::LargePrimarySeq | PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in FAST::Bio::Root::Root | metacpan | |
| FAST::Bio::Seq::LargeSeqI | Interface class for sequences that cache their residues in a temporary file | metacpan | |
| FAST::Bio::Seq::Meta | Generic superclass for sequence objects with residue-based meta information | metacpan | |
| FAST::Bio::Seq::Meta::Array | array-based generic implementation of a sequence class with residue-based meta information | metacpan | |
| FAST::Bio::Seq::MetaI | Interface for sequence objects with residue-based meta information | metacpan | |
| FAST::Bio::Seq::PrimaryQual | Bioperl lightweight Quality Object | metacpan | |
| FAST::Bio::Seq::QualI | Interface definition for a FAST::Bio::Seq::Qual | metacpan | |
| FAST::Bio::Seq::Quality | Implementation of sequence with residue quality and trace values | metacpan | |
| FAST::Bio::Seq::RichSeq | Module implementing a sequence created from a rich sequence database entry | metacpan | |
| FAST::Bio::Seq::RichSeqI | interface for sequences from rich data sources, mostly databases | metacpan | |
| FAST::Bio::Seq::SeqBuilder | Configurable object builder for sequence stream parsers | metacpan | |
| FAST::Bio::Seq::SeqFactory | Instantiates a new FAST::Bio::PrimarySeqI (or derived class) through a factory | metacpan | |
| FAST::Bio::Seq::SeqFastaSpeedFactory | Instantiates a new FAST::Bio::PrimarySeqI (or derived class) through a factory | metacpan | |
| FAST::Bio::Seq::SequenceTrace | Bioperl object packaging a sequence with its trace | metacpan | |
| FAST::Bio::Seq::TraceI | Interface definition for a FAST::Bio::Seq::Trace | metacpan | |
| FAST::Bio::SeqAnalysisParserI | Sequence analysis output parser interface | metacpan | |
| FAST::Bio::SeqFeature::FeaturePair | hold pair feature information e.g. blast hits | metacpan | |
| FAST::Bio::SeqFeature::Gene::Exon | a feature representing an exon | metacpan | |
| FAST::Bio::SeqFeature::Gene::ExonI | Interface for a feature representing an exon | metacpan | |
| FAST::Bio::SeqFeature::Gene::GeneStructure | A feature representing an arbitrarily complex structure of a gene | metacpan | |
| FAST::Bio::SeqFeature::Gene::GeneStructureI | A feature representing an arbitrarily complex structure of a gene | metacpan | |
| FAST::Bio::SeqFeature::Gene::Intron | An intron feature | metacpan | |
| FAST::Bio::SeqFeature::Gene::NC_Feature | metacpan | ||
| FAST::Bio::SeqFeature::Gene::Poly_A_site | poly A feature | metacpan | |
| FAST::Bio::SeqFeature::Gene::Promoter | Describes a promoter | metacpan | |
| FAST::Bio::SeqFeature::Gene::Transcript | A feature representing a transcript | metacpan | |
| FAST::Bio::SeqFeature::Gene::TranscriptI | Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site. | metacpan | |
| FAST::Bio::SeqFeature::Gene::UTR | A feature representing an untranslated region that is part of a transcriptional unit | metacpan | |
| FAST::Bio::SeqFeature::Generic | Generic SeqFeature | metacpan | |
| FAST::Bio::SeqFeature::Similarity | A sequence feature based on similarity | metacpan | |
| FAST::Bio::SeqFeature::SimilarityPair | Sequence feature based on the similarity of two sequences. | metacpan | |
| FAST::Bio::SeqFeature::Tools::FeatureNamer | generates unique persistent names for features | metacpan | |
| FAST::Bio::SeqFeature::Tools::IDHandler | maps $seq_feature->primary_tag | metacpan | |
| FAST::Bio::SeqFeature::Tools::TypeMapper | maps $seq_feature->primary_tag | metacpan | |
| FAST::Bio::SeqFeature::Tools::Unflattener | turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy | metacpan | |
| FAST::Bio::SeqFeatureI | Abstract interface of a Sequence Feature | metacpan | |
| FAST::Bio::SeqI | [Developers] Abstract Interface of Sequence (with features) | metacpan | |
| FAST::Bio::SeqIO | Handler for SeqIO Formats | metacpan | |
| FAST::Bio::SeqIO::FTHelper | Helper class for Embl/Genbank feature tables | metacpan | |
| FAST::Bio::SeqIO::Handler::GenericRichSeqHandler | FAST::Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data | metacpan | |
| FAST::Bio::SeqIO::MultiFile | Treating a set of files as a single input stream | metacpan | |
| FAST::Bio::SeqIO::abi | abi trace sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::ace | ace sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::agave | AGAVE sequence output stream. | metacpan | |
| FAST::Bio::SeqIO::alf | alf trace sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::asciitree | asciitree sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::bsml | BSML sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::bsml_sax | BSML sequence input/output stream using SAX | metacpan | |
| FAST::Bio::SeqIO::chadoxml | chadoxml sequence output stream | metacpan | |
| FAST::Bio::SeqIO::chaos | chaos sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::chaosxml | chaosxml sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::ctf | ctf trace sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::embl | EMBL sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::embldriver | EMBL sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::entrezgene | Entrez Gene ASN1 parser | metacpan | |
| FAST::Bio::SeqIO::excel | sequence input/output stream from a MSExcel-formatted table | metacpan | |
| FAST::Bio::SeqIO::exp | exp trace sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::fasta | fasta sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::fastq | fastq sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::flybase_chadoxml | FlyBase variant of chadoxml with sequence output stream | metacpan | |
| FAST::Bio::SeqIO::game | a class for parsing and writing game-XML | metacpan | |
| FAST::Bio::SeqIO::game::featHandler | a class for handling feature elements | metacpan | |
| FAST::Bio::SeqIO::game::gameHandler | PerlSAX handler for game-XML | metacpan | |
| FAST::Bio::SeqIO::game::gameSubs | a base class for game-XML parsing | metacpan | |
| FAST::Bio::SeqIO::game::gameWriter | a class for writing game-XML | metacpan | |
| FAST::Bio::SeqIO::game::seqHandler | a class for handling game-XML sequences | metacpan | |
| FAST::Bio::SeqIO::gbdriver | GenBank handler-based push parser | metacpan | |
| FAST::Bio::SeqIO::gbxml | GenBank sequence input/output stream using SAX | metacpan | |
| FAST::Bio::SeqIO::gcg | GCG sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::genbank | GenBank sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::interpro | InterProScan XML input/output stream | metacpan | |
| FAST::Bio::SeqIO::kegg | KEGG sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::largefasta | method i/o on very large fasta sequence files | metacpan | |
| FAST::Bio::SeqIO::lasergene | Lasergene sequence file input/output stream | metacpan | |
| FAST::Bio::SeqIO::locuslink | LocusLink input/output stream | metacpan | |
| FAST::Bio::SeqIO::mbsout | input stream for output by Teshima et al.'s mbs. | metacpan | |
| FAST::Bio::SeqIO::metafasta | metafasta sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::msout | input stream for output by Hudson's ms | metacpan | |
| FAST::Bio::SeqIO::nexml | NeXML sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::phd | phd file input/output stream | metacpan | |
| FAST::Bio::SeqIO::pir | PIR sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::pln | pln trace sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::qual | .qual file input/output stream | metacpan | |
| FAST::Bio::SeqIO::raw | raw sequence file input/output stream | metacpan | |
| FAST::Bio::SeqIO::scf | .scf file input/output stream | metacpan | |
| FAST::Bio::SeqIO::seqxml | SeqXML sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::strider | DNA strider sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::swiss | Swissprot sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::swissdriver | SwissProt/UniProt handler-based push parser | metacpan | |
| FAST::Bio::SeqIO::tab | nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n" | metacpan | |
| FAST::Bio::SeqIO::table | sequence input/output stream from a delimited table | metacpan | |
| FAST::Bio::SeqIO::tigr | TIGR XML sequence input/output stream | metacpan | |
| FAST::Bio::SeqIO::tigrxml | Parse TIGR (new) XML | metacpan | |
| FAST::Bio::SeqIO::tinyseq | reading/writing sequences in NCBI TinySeq format | metacpan | |
| FAST::Bio::SeqIO::tinyseq::tinyseqHandler | XML event handlers to support NCBI TinySeq XML parsing | metacpan | |
| FAST::Bio::SeqIO::ztr | ztr trace sequence input/output stream | metacpan | |
| FAST::Bio::SeqUtils | Additional methods for PrimarySeq objects | metacpan | |
| FAST::Bio::SimpleAlign | Multiple alignments held as a set of sequences | metacpan | |
| FAST::Bio::Species | Generic species object. | metacpan | |
| FAST::Bio::Taxon | A node in a represented taxonomy | metacpan | |
| FAST::Bio::Tools::AnalysisResult | Base class for analysis result objects and parsers | metacpan | |
| FAST::Bio::Tools::CodonTable | Codon table object | metacpan | |
| FAST::Bio::Tools::GFF | A FAST::Bio::SeqAnalysisParserI compliant GFF format parser | metacpan | |
| FAST::Bio::Tools::Genewise | Results of one Genewise run | metacpan | |
| FAST::Bio::Tools::Genomewise | Results of one Genomewise run | metacpan | |
| FAST::Bio::Tools::GuessSeqFormat | Module for determining the sequence format of the contents of a file, a string, or through a filehandle. | metacpan | |
| FAST::Bio::Tools::IUPAC | Generates unique Seq objects from an ambiguous Seq object | metacpan | |
| FAST::Bio::Tools::MySeqStats | metacpan | ||
| FAST::Bio::Tools::Run::GenericParameters | An object for the parameters used to run programs | metacpan | |
| FAST::Bio::Tools::Run::ParametersI | A Base object for the parameters used to run programs | metacpan | |
| FAST::Bio::Tools::SeqPattern | represent a sequence pattern or motif | metacpan | |
| FAST::Bio::Tools::SeqPattern::Backtranslate | metacpan | ||
| FAST::Bio::Tools::SeqStats | Object holding statistics for one particular sequence | metacpan | |
| FAST::Bio::Tree::Node | A Simple Tree Node | metacpan | |
| FAST::Bio::Tree::NodeI | Interface describing a Tree Node | metacpan | |
| FAST::Bio::Tree::Tree | An Implementation of TreeI interface. | metacpan | |
| FAST::Bio::Tree::TreeFunctionsI | Decorated Interface implementing basic Tree exploration methods | metacpan | |
| FAST::Bio::Tree::TreeI | A Tree object suitable for lots of things, designed originally for Phylogenetic Trees. | metacpan | |
| FAST::Bio::UnivAln | Bioperl alignment object | 1.01 | metacpan |
| FAST::Bio::WebAgent | A base class for Web (any protocol) access | metacpan | |
| FAST::List::Gen | provides functions for generating lists | 0.974 | metacpan |
| FAST::List::Gen::Benchmark | performance tips for using L<FAST::List::Gen> | metacpan | |
| FAST::List::Gen::Cookbook | how to get the most out of L<FAST::List::Gen> | metacpan | |
| FAST::List::Gen::Haskell | the haskell prelude in perl5 | metacpan | |
| FAST::List::Gen::Lazy | perl6 / haskell like laziness in perl5 | metacpan | |
| FAST::List::Gen::Lazy::Builtins | metacpan | ||
| FAST::List::Gen::Lazy::Ops | perl ops with partial + lazy application | metacpan | |
| FAST::List::Gen::Perl6 | perl6 meta operators in perl5 | metacpan | |
| FAST::List::Generator | provides functions for generating lists | metacpan |
Provides
| Name | File | View |
|---|---|---|
| FAST::FAST::Bio::Root::HTTPget | lib/FAST/Bio/Root/HTTPget.pm | metacpan |