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: 0.974,1.00,1.006924,1.01,1.02

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 1.02 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

Other Files

Changes metacpan
MANIFEST metacpan
META.json metacpan
META.yml metacpan
Makefile.PL metacpan
README metacpan
README.md metacpan