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21 Apr 2015 08:04:25 UTC
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Changes for version 1.06
- Fix in name of symbolic link to the popset data-file in t/data. Release corresponding to acceptance in Frontiers in Genetics
Documentation
filter sites in alignments based on variation and gap-contentcounts codon usageanalysis of monomer frequenciesConvert sequences or alignments to or from fasta format.select biosequence record data by character or field rangesSelect sequences by numerical values of name,value pairsprint sequence records matching a patternprint first sequence records on inputannotate sequence lengths to descriptionsconcatenate sequence record datareverse complement nucleotide sequences and alignmentssort sequences based on identifiersregex-based substitutions on sequence recordsprint last sequence records on inputselect sequence records by NCBI taxonomic names or IDssort sequence records based on NCBI taxonomycharacter-based transformations on sequence recordsRemove duplicate sequence records in a multifasta file or datastream.tally sequences and sequence characterstranslate sequences by a genetic code.cut sites from alignments by regex-matching on features in an annotated GenBank filesearch features from GenBank files and print corresponding sequencesModules
FAST Analysis of Sequences ToolboxAn interface for describing sequence alignments.Handler for AlignIO FormatsFAST::Bio::HandlerI-based generic data handler class for alignment-based dataARP MSA Sequence input/output streambl2seq sequence input/output streamclustalw sequence input/output streamParse EMBOSS alignment output (from applications water and needle)fasta MSA Sequence input/output streamLargemultifasta MSA Sequence input/output streamMultiple Alignment Format sequence input streammase sequence input/output streamParse and Create MEGA format data filesmeme sequence input/output streamMetafasta MSA Sequence input/output streammsf sequence input/output streamNeXML format sequence alignment input/output stream driverNEXUS format sequence input/output streampfam sequence input/output streamPHYLIP format sequence input/output streampo MSA Sequence input/output streamproda sequence input/output streamprodom sequence input/output streamRead/Write PSI-BLAST profile alignment filesselex sequence input/output streamstockholm sequence input/output streamXMFA MSA Sequence input/output streamGeneric analysis output parser interfaceInterface for analysis result objectsthe base interface an annotatable object must implementInstantiates a new FAST::Bio::AnnotationI (or derived class) through a factoryDefault Perl implementation of AnnotationCollectionIA comment object, holding textuntyped links between databasesAn ontology term adapted to AnnotationISpecialised DBLink object for Literature ReferencesA simple scalarAnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.Provides an object which represents a target (ie, a similarity hit) from one object to something in another databaseManages types for annotation collectionsInterface for annotation collectionsAnnotation interfaceFamily InterfaceSequence Family objectCluster InterfaceAbstract interface for a sequence databaseAbstract interface for a sequence databaseAbstract Interface for Sequence databasesAccess to a taxonomy databaseTaxonomy Entrez driverAn implementation of FAST::Bio::DB::Taxonomy which uses local flat filesAn implementation of FAST::Bio::DB::Taxonomy that accepts lists of words to build a databaseinterface for objects with human readable names and descriptionsThis interface describes the basic event generator class.An Event Handler InterfaceA FeatureTable Location ParserA factory interface for generating locations from a stringInterface for an object builderInstantiates a new FAST::Bio::Root::RootI (or derived class) through a factoryA General object creator factoryThis interface allows for generic building of sequences in factories which create sequences (like SeqIO)Interface describing the basics of a Sequence Stream.the base interface an object with features must implementGapSeq interface, for gapped sequencesInterface class for handler methods which interact with any event-driven parsers (drivers).interface for objects with identifiersA FAST::Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq.Implementation of a Atomic Location on a SequenceAbstract interface for objects implementing a certain policy of computing integer-valued coordinates of a LocationImplementation of a Location on a Sequence which has unclear start and/or end locationsAbstract interface of a Location on a Sequence which has unclear start/end locationclass implementing FAST::Bio::Location::CoordinatePolicy as the narrowest possible and reasonable rangeImplementation of a Simple Location on a SequenceImplementation of a Location on a Sequence which has multiple locations (start/end points)Abstract interface of a Location on a Sequence which has multiple locations (start/end points)class implementing FAST::Bio::Location::CoordinatePolicy as the widest possible and reasonable rangeAbstract interface of a Location on a SequenceInterface definition for a FAST::Bio::PrimarySeqAbstract Interface of Sequence (with features)Keep track of where to find ontologies. Allows lookups by name.An Ontology Engine for OBO style flat file format from the Gene Ontology Consortiumstandard implementation of an OntologyInterface a minimal Ontology implementation should satisfyInterface for an ontology implementationA repository of ontologiesa relationship for an ontologyInstantiates a new FAST::Bio::Ontology::RelationshipI (or derived class) through a factoryInterface for a relationship between ontology termsa relationship type for an ontologyGraph adaptor for FAST::Bio::Ontology::SimpleGOEngineGraph adaptor (v02.x) for FAST::Bio::Ontology::SimpleGOEngineImplementation of OntologyEngineI interfaceimplementation of the interface for ontology termsInstantiates a new FAST::Bio::Ontology::TermI (or derived class) through a factoryinterface for ontology termsParser factory for Ontology formatsXML handler class for InterProParserparse an InterPro XML file and persist the resulting terms to a Biosql databaseParser for InterPro xml files.a base class parser for GO flat-file type formatsa parser for the Gene Ontology flat-file formata parser for OBO flat-file format from Gene Ontology Consortiuma base class parser for simple hierarchy-by-indentation type formatsa parser for the Sequence Ontology flat-file formatBioperl lightweight Sequence ObjectInterface definition for a FAST::Bio::PrimarySeqA base module for fast 'pull' parsingPure perl RangeI implementationRange interfacemodule for fallback HTTP get operations when LWP:: is unavailableUtility functions for FAST::Bio::Search:: BLAST objectsAn object for statisticsA parser and HSP object for BlastN hspsA "Generic" implementation of a High Scoring PairA factory to create FAST::Bio::Search::HSP::HSPI objectsInterface for a High Scoring Pair in a similarity search resultA parser and HSP object for hmmpfam hspsFAST::Bio::Search::HSP::HSPI interface for pull parsers.A parser and hit object for BLASTN hitsA generic implementation of the FAST::Bio::Search::Hit::HitI interfaceA factory to create FAST::Bio::Search::Hit::HitI objectsInterface for a hit in a similarity search resultA parser and hit object for hmmpfam hitsFAST::Bio::Search::Hit::HitI interface for pull parsers.A parser and result object for BLASTN resultsCrossMatch-specific subclass of FAST::Bio::Search::Result::GenericResultGeneric Implementation of FAST::Bio::Search::Result::ResultI interface applicable to most search results.A parser and result object for hmmpfam resultsFAST::Bio::Search::Result::ResultI interface for 'pull' parsersA factory to create FAST::Bio::Search::Result::ResultI objectsAbstract interface to Search Result objectsUtility functions for FAST::Bio::Search:: objectsA Base object for statisticsDriver for parsing Sequence Database Searches (BLAST, FASTA, ...)An abstract Event Handler for Search Result parsingEvent Handler for SearchIO events.Event Handler for SearchIO events.Event Handler for SearchIO events.Interface for outputting parsed Search resultsBSML output writerInterface for outputting parsed search results in Gbrowse GFF formatTab-delimited data for FAST::Bio::Search::HSP::HSPI objectswrite a FAST::Bio::Search::ResultI in HTMLTab-delimited data for FAST::Bio::Search::Hit::HitI objectsOutputs tab-delimited data for each FAST::Bio::Search::Result::ResultI object.Object to implement writing a FAST::Bio::Search::ResultI in Text.XML Handler for NCBI Blast XML parsing.XML Handler for NCBI Blast PSIBLAST XML parsing.a parser for axt format reportsEvent generator for event based parsing of blast reportsA parser for BLAST outputDriver module for SearchIO for parsing NCBI -m 8/9 formatA SearchIO implementation of NCBI Blast XML parsing.CrossMatch-specific subclass of FAST::Bio::SearchIOSearchIO-based ERPIN parserparser for ExonerateA SearchIO parser for FASTA resultsEvent generator for parsing gmap reports (Z format)A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)A parser for HMMER output (hmmpfam, hmmsearch)DESCRIPTION of ObjectA parser for HMMER outputSearchIO-based Infernal parsera driver module for FAST::Bio::SearchIO to parse megablast reports (format 0)A parser for PSL output (UCSC)SearchIO-based RNAMotif parserparser for Sim4 alignmentsSearchIO parser for Jim Kent WABA program alignment outputParsing of wise output as alignmentsSequence object, with featuresLocatableSeq object that stores sequence as files in the tempdirPrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in FAST::Bio::Root::RootInterface class for sequences that cache their residues in a temporary fileGeneric superclass for sequence objects with residue-based meta informationarray-based generic implementation of a sequence class with residue-based meta informationInterface for sequence objects with residue-based meta informationBioperl lightweight Quality ObjectInterface definition for a FAST::Bio::Seq::QualImplementation of sequence with residue quality and trace valuesModule implementing a sequence created from a rich sequence database entryinterface for sequences from rich data sources, mostly databasesConfigurable object builder for sequence stream parsersInstantiates a new FAST::Bio::PrimarySeqI (or derived class) through a factoryInstantiates a new FAST::Bio::PrimarySeqI (or derived class) through a factoryBioperl object packaging a sequence with its traceInterface definition for a FAST::Bio::Seq::TraceSequence analysis output parser interfacehold pair feature information e.g. blast hitsa feature representing an exonInterface for a feature representing an exonA feature representing an arbitrarily complex structure of a geneA feature representing an arbitrarily complex structure of a geneAn intron featuresuperclass for non-coding featurespoly A featureDescribes a promoterA feature representing a transcriptInterface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.A feature representing an untranslated region that is part of a transcriptional unitGeneric SeqFeatureA sequence feature based on similaritySequence feature based on the similarity of two sequences.generates unique persistent names for featuresmaps $seq_feature-gtprimary_tagmaps $seq_feature-gtprimary_tagturns flat list of genbank-sourced features into a nested SeqFeatureI hierarchyAbstract interface of a Sequence Feature[Developers] Abstract Interface of Sequence (with features)Handler for SeqIO FormatsHelper class for Embl/Genbank feature tablesFAST::Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence dataTreating a set of files as a single input streamabi trace sequence input/output streamace sequence input/output streamAGAVE sequence output stream.alf trace sequence input/output streamasciitree sequence input/output streamBSML sequence input/output streamBSML sequence input/output stream using SAXchadoxml sequence output streamchaos sequence input/output streamchaosxml sequence input/output streamctf trace sequence input/output streamEMBL sequence input/output streamEMBL sequence input/output streamEntrez Gene ASN1 parsersequence input/output stream from a MSExcel-formatted tableexp trace sequence input/output streamfasta sequence input/output streamfastq sequence input/output streamFlyBase variant of chadoxml with sequence output streama class for parsing and writing game-XMLa class for handling feature elementsPerlSAX handler for game-XMLa base class for game-XML parsinga class for writing game-XMLa class for handling game-XML sequencesGenBank handler-based push parserGenBank sequence input/output stream using SAXGCG sequence input/output streamGenBank sequence input/output streamInterProScan XML input/output streamKEGG sequence input/output streammethod i/o on very large fasta sequence filesLasergene sequence file input/output streamLocusLink input/output streaminput stream for output by Teshima et al.'s mbs.metafasta sequence input/output streaminput stream for output by Hudson's msNeXML sequence input/output streamphd file input/output streamPIR sequence input/output streampln trace sequence input/output stream.qual file input/output streamraw sequence file input/output stream.scf file input/output streamSeqXML sequence input/output streamDNA strider sequence input/output streamSwissprot sequence input/output streamSwissProt/UniProt handler-based push parsernearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"sequence input/output stream from a delimited tableTIGR XML sequence input/output streamParse TIGR (new) XMLreading/writing sequences in NCBI TinySeq formatXML event handlers to support NCBI TinySeq XML parsingztr trace sequence input/output streamAdditional methods for PrimarySeq objectsMultiple alignments held as a set of sequencesGeneric species object.A node in a represented taxonomyBase class for analysis result objects and parsersCodon table objectA FAST::Bio::SeqAnalysisParserI compliant GFF format parserResults of one Genewise runResults of one Genomewise runModule for determining the sequence format of the contents of a file, a string, or through a filehandle.Generates unique Seq objects from an ambiguous Seq objectObject holding statistics for one particular sequenceAn object for the parameters used to run programsA Base object for the parameters used to run programsrepresent a sequence pattern or motifObject holding statistics for one particular sequenceA Simple Tree NodeInterface describing a Tree NodeAn Implementation of TreeI interface.Decorated Interface implementing basic Tree exploration methodsA Tree object suitable for lots of things, designed originally for Phylogenetic Trees.Bioperl alignment objectA base class for Web (any protocol) accessprovides functions for generating listsperformance tips for using FAST::List::Genhow to get the most out of FAST::List::Genthe haskell prelude in perl5perl6 / haskell like laziness in perl5perl builtin functions with partial + lazy applicationperl ops with partial + lazy applicationperl6 meta operators in perl5provides functions for generating listsProvides
in lib/FAST/Bio/GapSeq.pmin lib/FAST/Bio/Root/Exception.pmin lib/FAST/Bio/Root/IO.pmin lib/FAST/Bio/Root/Root.pmin lib/FAST/Bio/Root/RootI.pmin lib/FAST/Bio/Root/Version.pmin lib/FAST/Bio/MySeqUtils.pm
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