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#
# = bio.rb - Loading all BioRuby modules
#
# Copyright:: Copyright (C) 2001-2007
# Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
# $Id:$
#
module Bio
autoload :BIORUBY_VERSION, 'bio/version'
autoload :BIORUBY_EXTRA_VERSION, 'bio/version'
autoload :BIORUBY_VERSION_ID, 'bio/version'
### Basic data types
## Sequence
autoload :Sequence, 'bio/sequence'
## below are described in bio/sequence.rb
#class Sequence
# autoload :Common, 'bio/sequence/common'
# autoload :NA, 'bio/sequence/na'
# autoload :AA, 'bio/sequence/aa'
# autoload :Generic, 'bio/sequence/generic'
# autoload :Format, 'bio/sequence/format'
# autoload :Adapter, 'bio/sequence/adapter'
#end
## Locations/Location
autoload :Location, 'bio/location'
autoload :Locations, 'bio/location'
## Features/Feature
autoload :Feature, 'bio/feature'
autoload :Features, 'bio/compat/features'
## References/Reference
autoload :Reference, 'bio/reference'
autoload :References, 'bio/compat/references'
## Pathway/Relation
autoload :Pathway, 'bio/pathway'
autoload :Relation, 'bio/pathway'
## Alignment
autoload :Alignment, 'bio/alignment'
## Tree
autoload :Tree, 'bio/tree'
## Map
autoload :Map, 'bio/map'
### Constants
autoload :NucleicAcid, 'bio/data/na'
autoload :AminoAcid, 'bio/data/aa'
autoload :CodonTable, 'bio/data/codontable'
### DB parsers
autoload :DB, 'bio/db'
autoload :NCBIDB, 'bio/db'
autoload :KEGGDB, 'bio/db'
autoload :EMBLDB, 'bio/db'
## GenBank/RefSeq/DDBJ
autoload :GenBank, 'bio/db/genbank/genbank'
autoload :GenPept, 'bio/db/genbank/genpept'
autoload :RefSeq, 'bio/db/genbank/refseq'
autoload :DDBJ, 'bio/db/genbank/ddbj'
## below are described in bio/db/genbank/ddbj.rb
#class DDBJ
# autoload :XML, 'bio/io/ddbjxml'
# autoload :REST, 'bio/io/ddbjrest'
#end
## EMBL/TrEMBL/Swiss-Prot/SPTR
autoload :EMBL, 'bio/db/embl/embl'
autoload :SPTR, 'bio/db/embl/sptr'
autoload :TrEMBL, 'bio/db/embl/trembl'
autoload :UniProt, 'bio/db/embl/uniprot'
autoload :SwissProt, 'bio/db/embl/swissprot'
## KEGG
class KEGG
autoload :GENOME, 'bio/db/kegg/genome'
autoload :GENES, 'bio/db/kegg/genes'
autoload :ENZYME, 'bio/db/kegg/enzyme'
autoload :COMPOUND, 'bio/db/kegg/compound'
autoload :DRUG, 'bio/db/kegg/drug'
autoload :GLYCAN, 'bio/db/kegg/glycan'
autoload :REACTION, 'bio/db/kegg/reaction'
autoload :BRITE, 'bio/db/kegg/brite'
autoload :CELL, 'bio/db/kegg/cell'
autoload :EXPRESSION, 'bio/db/kegg/expression'
autoload :ORTHOLOGY, 'bio/db/kegg/orthology'
autoload :KGML, 'bio/db/kegg/kgml'
autoload :PATHWAY, 'bio/db/kegg/pathway'
autoload :MODULE, 'bio/db/kegg/module'
autoload :Taxonomy, 'bio/db/kegg/taxonomy'
end
## other formats
autoload :FastaFormat, 'bio/db/fasta'
autoload :FastaNumericFormat, 'bio/db/fasta/qual' # change to FastaFormat::Numeric ?
autoload :FastaDefline, 'bio/db/fasta/defline' # change to FastaFormat::Defline ?
autoload :Fastq, 'bio/db/fastq'
autoload :GFF, 'bio/db/gff'
autoload :AAindex, 'bio/db/aaindex'
autoload :AAindex1, 'bio/db/aaindex' # change to AAindex::AAindex1 ?
autoload :AAindex2, 'bio/db/aaindex' # change to AAindex::AAindex2 ?
autoload :TRANSFAC, 'bio/db/transfac'
autoload :PROSITE, 'bio/db/prosite'
autoload :LITDB, 'bio/db/litdb'
autoload :MEDLINE, 'bio/db/medline'
autoload :FANTOM, 'bio/db/fantom'
autoload :GO, 'bio/db/go'
autoload :PDB, 'bio/db/pdb'
autoload :NBRF, 'bio/db/nbrf'
autoload :REBASE, 'bio/db/rebase'
autoload :SOFT, 'bio/db/soft'
autoload :Lasergene, 'bio/db/lasergene'
autoload :SangerChromatogram, 'bio/db/sanger_chromatogram/chromatogram'
autoload :Scf, 'bio/db/sanger_chromatogram/scf'
autoload :Abif, 'bio/db/sanger_chromatogram/abif'
autoload :Newick, 'bio/db/newick'
autoload :Nexus, 'bio/db/nexus'
autoload :PhyloXML, 'bio/db/phyloxml/phyloxml_elements'
# Bio::Taxonomy will be moved to other file
autoload :Taxonomy, 'bio/db/phyloxml/phyloxml_elements'
## below are described in bio/db/phyloxml/phyloxml_elements.rb
#module PhyloXML
# autoload :Parser, 'bio/db/phyloxml/phyloxml_parser'
# autoload :Writer, 'bio/db/phyloxml/phyloxml_writer'
#end
### IO interface modules
autoload :Registry, 'bio/io/registry'
autoload :Fetch, 'bio/io/fetch'
autoload :SQL, 'bio/io/sql'
autoload :SOAPWSDL, 'bio/io/soapwsdl'
autoload :FlatFile, 'bio/io/flatfile'
autoload :FlatFileIndex, 'bio/io/flatfile/index' # chage to FlatFile::Index ?
## below are described in bio/io/flatfile/index.rb
#class FlatFileIndex
# autoload :Indexer, 'bio/io/flatfile/indexer'
# autoload :BDBdefault, 'bio/io/flatfile/bdb'
# autoload :BDBwrapper, 'bio/io/flatfile/bdb'
# autoload :BDB_1, 'bio/io/flatfile/bdb'
#end
autoload :PubMed, 'bio/io/pubmed'
autoload :DAS, 'bio/io/das'
autoload :DBGET, 'bio/io/dbget'
autoload :Ensembl, 'bio/io/ensembl'
autoload :Hinv, 'bio/io/hinv'
## below are described in bio/appl/blast.rb
#class Blast
# autoload :Fastacmd, 'bio/io/fastacmd'
#end
class KEGG
autoload :API, 'bio/io/keggapi'
end
## below are described in bio/db/genbank/ddbj.rb
#class DDBJ
# autoload :XML, 'bio/io/ddbjxml'
#end
class HGC
autoload :HiGet, 'bio/io/higet'
end
class EBI
autoload :SOAP, 'bio/io/ebisoap'
end
autoload :NCBI, 'bio/io/ncbirest'
## below are described in bio/io/ncbirest.rb
#class NCBI
# autoload :SOAP, 'bio/io/ncbisoap'
# autoload :REST, 'bio/io/ncbirest'
#end
autoload :TogoWS, 'bio/io/togows'
### Applications
autoload :Fasta, 'bio/appl/fasta'
## below are described in bio/appl/fasta.rb
#class Fasta
# autoload :Report, 'bio/appl/fasta/format10'
#end
autoload :Blast, 'bio/appl/blast'
## below are described in bio/appl/blast.rb
#class Blast
# autoload :Fastacmd, 'bio/io/fastacmd'
# autoload :Report, 'bio/appl/blast/report'
# autoload :Default, 'bio/appl/blast/format0'
# autoload :WU, 'bio/appl/blast/wublast'
# autoload :Bl2seq, 'bio/appl/bl2seq/report'
# autoload :RPSBlast, 'bio/appl/blast/rpsblast'
# autoload :NCBIOptions, 'bio/appl/blast/ncbioptions'
# autoload :Remote, 'bio/appl/blast/remote'
#end
autoload :HMMER, 'bio/appl/hmmer'
## below are described in bio/appl/hmmer.rb
#class HMMER
# autoload :Report, 'bio/appl/hmmer/report'
#end
autoload :EMBOSS, 'bio/appl/emboss' # use bio/command, improve
autoload :PSORT, 'bio/appl/psort'
## below are described in bio/appl/psort.rb
#class PSORT
# class PSORT1
# autoload :Report, 'bio/appl/psort/report'
# end
# class PSORT2
# autoload :Report, 'bio/appl/psort/report'
# end
#end
autoload :TMHMM, 'bio/appl/tmhmm/report'
autoload :TargetP, 'bio/appl/targetp/report'
autoload :SOSUI, 'bio/appl/sosui/report'
autoload :Genscan, 'bio/appl/genscan/report'
autoload :ClustalW, 'bio/appl/clustalw'
## below are described in bio/appl/clustalw.rb
#class ClustalW
# autoload :Report, 'bio/appl/clustalw/report'
#end
autoload :MAFFT, 'bio/appl/mafft'
## below are described in bio/appl/mafft.rb
#class MAFFT
# autoload :Report, 'bio/appl/mafft/report'
#end
autoload :Tcoffee, 'bio/appl/tcoffee'
autoload :Muscle, 'bio/appl/muscle'
autoload :Probcons, 'bio/appl/probcons'
autoload :Sim4, 'bio/appl/sim4'
## below are described in bio/appl/sim4.rb
#class Sim4
# autoload :Report, 'bio/appl/sim4/report'
#end
autoload :Spidey, 'bio/appl/spidey/report'
autoload :Blat, 'bio/appl/blat/report'
module GCG
autoload :Msf, 'bio/appl/gcg/msf'
autoload :Seq, 'bio/appl/gcg/seq'
end
module Phylip
autoload :PhylipFormat, 'bio/appl/phylip/alignment'
autoload :DistanceMatrix, 'bio/appl/phylip/distance_matrix'
end
autoload :Iprscan, 'bio/appl/iprscan/report'
autoload :PAML, 'bio/appl/paml/common'
## below are described in bio/appl/paml/common.rb
# module PAML
# autoload :Codeml, 'bio/appl/paml/codeml'
# autoload :Baseml, 'bio/appl/paml/baseml'
# autoload :Yn00, 'bio/appl/paml/yn00'
# end
### Utilities
autoload :SiRNA, 'bio/util/sirna'
autoload :ColorScheme, 'bio/util/color_scheme'
autoload :ContingencyTable, 'bio/util/contingency_table'
autoload :RestrictionEnzyme, 'bio/util/restriction_enzyme'
### Service libraries
autoload :Command, 'bio/command'
### Provide BioRuby shell 'command' also as 'Bio.command' (like ChemRuby)
def self.method_missing(*args)
require 'bio/shell'
extend Bio::Shell
public_class_method(*Bio::Shell.private_instance_methods)
if Bio.respond_to?(args.first)
Bio.send(*args)
else
raise NameError
end
end
end
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