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Bio-DB-GFF-1.7.4
River stage one • 2 direct dependents • 2 total dependents
++

Changes for version 1.7.4 - 2020-01-08

  • Explicitly remove Bio::GMOD::CMap::Utils as a requirement, this is a non-CPAN module that is used in a loader script, so ignore.

Documentation

bp_bulk_load_gff.pl
Bulk-load a Bio::DB::GFF database from GFF files.
bp_fast_load_gff.pl
Fast-load a Bio::DB::GFF database from GFF files.
bp_genbank2gff.pl
Load a Bio::DB::GFF database from GENBANK files.
bp_generate_histogram.pl
Generate a histogram of Bio::DB::GFF features
bp_load_gff.pl
Load a Bio::DB::GFF database from GFF files.
bp_meta_gff.pl
Get/set Bio::DB::GFF meta-data

Modules

Bio::DB::GFF
Storage and retrieval of sequence annotation data
Bio::DB::GFF::Adaptor::berkeleydb
Bio::DB::GFF database adaptor for in-memory databases
Bio::DB::GFF::Adaptor::berkeleydb::iterator
iterator for Bio::DB::GFF::Adaptor::berkeleydb
Bio::DB::GFF::Adaptor::biofetch
Cache BioFetch objects in a Bio::DB::GFF database
Bio::DB::GFF::Adaptor::biofetch_oracle
Cache BioFetch objects in a Bio::DB::GFF database
Bio::DB::GFF::Adaptor::dbi
Database adaptor for DBI (SQL) databases
Bio::DB::GFF::Adaptor::dbi::caching_handle
Cache for database handles
Bio::DB::GFF::Adaptor::dbi::iterator
iterator for Bio::DB::GFF::Adaptor::dbi
Bio::DB::GFF::Adaptor::dbi::mysql
Database adaptor for a specific mysql schema
Bio::DB::GFF::Adaptor::dbi::mysqlcmap
Database adaptor for an integraded CMap/GBrowse mysql schema
Bio::DB::GFF::Adaptor::dbi::mysqlopt
Deprecated database adaptor
Bio::DB::GFF::Adaptor::dbi::oracle
Database adaptor for a specific oracle schema
Bio::DB::GFF::Adaptor::dbi::pg
Database adaptor for a specific postgres schema
Bio::DB::GFF::Adaptor::dbi::pg_fts
Database adaptor for a specific postgres schema with a TSearch2 implementation
Bio::DB::GFF::Adaptor::memory
Bio::DB::GFF database adaptor for in-memory databases
Bio::DB::GFF::Adaptor::memory::feature_serializer
utility methods for serializing and deserializing GFF features
Bio::DB::GFF::Adaptor::memory::iterator
iterator for Bio::DB::GFF::Adaptor::memory
Bio::DB::GFF::Aggregator
Aggregate GFF groups into composite features
Bio::DB::GFF::Aggregator::alignment
Alignment aggregator
Bio::DB::GFF::Aggregator::clone
Clone aggregator
Bio::DB::GFF::Aggregator::coding
The Coding Region Aggregator
Bio::DB::GFF::Aggregator::gene
Sequence Ontology Geene
Bio::DB::GFF::Aggregator::match
Match aggregator
Bio::DB::GFF::Aggregator::none
No aggregation
Bio::DB::GFF::Aggregator::orf
An aggregator for orf regions
Bio::DB::GFF::Aggregator::processed_transcript
Sequence Ontology Transcript
Bio::DB::GFF::Aggregator::so_transcript
Sequence Ontology Transcript
Bio::DB::GFF::Aggregator::transcript
Transcript aggregator
Bio::DB::GFF::Aggregator::ucsc_acembly
UCSC acembly aggregator
Bio::DB::GFF::Aggregator::ucsc_ensgene
UCSC ensGene aggregator
Bio::DB::GFF::Aggregator::ucsc_genscan
UCSC genscan aggregator
Bio::DB::GFF::Aggregator::ucsc_refgene
UCSC refGene aggregator
Bio::DB::GFF::Aggregator::ucsc_sanger22
UCSC sanger22 aggregator
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo
UCSC sanger22pseudo aggregator
Bio::DB::GFF::Aggregator::ucsc_softberry
UCSC softberry aggregator
Bio::DB::GFF::Aggregator::ucsc_twinscan
UCSC twinscan aggregator
Bio::DB::GFF::Aggregator::ucsc_unigene
UCSC UniGene aggregator
Bio::DB::GFF::Featname
The name of a feature
Bio::DB::GFF::Feature
A relative segment identified by a feature type
Bio::DB::GFF::Homol
A segment of DNA that is homologous to another
Bio::DB::GFF::RelSegment
Sequence segment with relative coordinate support
Bio::DB::GFF::Segment
Simple DNA segment object
Bio::DB::GFF::Typename
The name of a feature type

Provides

Bio::DB::GFF::Adaptor::dbi::faux_dbh
in lib/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
Bio::DB::GFF::FeatureIterator
in lib/Bio/DB/GFF.pm
Bio::DB::GFF::ID_Iterator
in lib/Bio/DB/GFF.pm
FeatureStore
in lib/Bio/DB/GFF/Adaptor/berkeleydb.pm

Other files