bio-nexml 0.0.1 → 0.1.0
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- data/LICENSE.txt +1 -1
- data/README.rdoc +6 -0
- data/lib/bio-nexml.rb +2 -0
- metadata +27 -142
- data/Gemfile +0 -15
- data/Gemfile.lock +0 -24
- data/Rakefile +0 -55
- data/TODO.txt +0 -6
- data/VERSION +0 -1
- data/bio-nexml.gemspec +0 -126
- data/extconf.rb +0 -2
- data/lib/bio.rb +0 -321
- data/test/data/nexml/test.xml +0 -69
- data/test/unit/bio/db/nexml/tc_factory.rb +0 -119
- data/test/unit/bio/db/nexml/tc_mapper.rb +0 -78
- data/test/unit/bio/db/nexml/tc_matrix.rb +0 -551
- data/test/unit/bio/db/nexml/tc_parser.rb +0 -21
- data/test/unit/bio/db/nexml/tc_taxa.rb +0 -118
- data/test/unit/bio/db/nexml/tc_trees.rb +0 -370
- data/test/unit/bio/db/nexml/tc_writer.rb +0 -633
data/extconf.rb
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data/lib/bio.rb
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#
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# = bio.rb - Loading all BioRuby modules
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#
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# Copyright:: Copyright (C) 2001-2007
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# Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
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# $Id:$
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#
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module Bio
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autoload :BIORUBY_VERSION, 'bio/version'
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autoload :BIORUBY_EXTRA_VERSION, 'bio/version'
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autoload :BIORUBY_VERSION_ID, 'bio/version'
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### Basic data types
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## Sequence
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autoload :Sequence, 'bio/sequence'
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## below are described in bio/sequence.rb
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#class Sequence
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# autoload :Common, 'bio/sequence/common'
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# autoload :NA, 'bio/sequence/na'
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# autoload :AA, 'bio/sequence/aa'
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# autoload :Generic, 'bio/sequence/generic'
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# autoload :Format, 'bio/sequence/format'
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# autoload :Adapter, 'bio/sequence/adapter'
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#end
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## Locations/Location
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autoload :Location, 'bio/location'
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autoload :Locations, 'bio/location'
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## Features/Feature
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autoload :Feature, 'bio/feature'
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autoload :Features, 'bio/compat/features'
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## References/Reference
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autoload :Reference, 'bio/reference'
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autoload :References, 'bio/compat/references'
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## Pathway/Relation
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autoload :Pathway, 'bio/pathway'
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autoload :Relation, 'bio/pathway'
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## Alignment
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autoload :Alignment, 'bio/alignment'
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## Tree
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autoload :Tree, 'bio/tree'
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## Map
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autoload :Map, 'bio/map'
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### Constants
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autoload :NucleicAcid, 'bio/data/na'
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autoload :AminoAcid, 'bio/data/aa'
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autoload :CodonTable, 'bio/data/codontable'
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### DB parsers
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autoload :DB, 'bio/db'
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autoload :NCBIDB, 'bio/db'
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autoload :KEGGDB, 'bio/db'
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autoload :EMBLDB, 'bio/db'
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## GenBank/RefSeq/DDBJ
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autoload :GenBank, 'bio/db/genbank/genbank'
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autoload :GenPept, 'bio/db/genbank/genpept'
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autoload :RefSeq, 'bio/db/genbank/refseq'
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autoload :DDBJ, 'bio/db/genbank/ddbj'
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## below are described in bio/db/genbank/ddbj.rb
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#class DDBJ
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# autoload :XML, 'bio/io/ddbjxml'
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#end
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## EMBL/TrEMBL/Swiss-Prot/SPTR
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autoload :EMBL, 'bio/db/embl/embl'
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autoload :SPTR, 'bio/db/embl/sptr'
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autoload :TrEMBL, 'bio/db/embl/trembl'
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autoload :UniProt, 'bio/db/embl/uniprot'
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autoload :SwissProt, 'bio/db/embl/swissprot'
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## KEGG
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class KEGG
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autoload :GENOME, 'bio/db/kegg/genome'
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autoload :GENES, 'bio/db/kegg/genes'
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autoload :ENZYME, 'bio/db/kegg/enzyme'
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autoload :COMPOUND, 'bio/db/kegg/compound'
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autoload :DRUG, 'bio/db/kegg/drug'
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autoload :GLYCAN, 'bio/db/kegg/glycan'
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autoload :REACTION, 'bio/db/kegg/reaction'
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autoload :BRITE, 'bio/db/kegg/brite'
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autoload :CELL, 'bio/db/kegg/cell'
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autoload :EXPRESSION, 'bio/db/kegg/expression'
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autoload :ORTHOLOGY, 'bio/db/kegg/orthology'
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autoload :KGML, 'bio/db/kegg/kgml'
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autoload :Taxonomy, 'bio/db/kegg/taxonomy'
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end
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## other formats
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autoload :FastaFormat, 'bio/db/fasta'
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autoload :FastaNumericFormat, 'bio/db/fasta/qual' # change to FastaFormat::Numeric ?
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autoload :FastaDefline, 'bio/db/fasta/defline' # change to FastaFormat::Defline ?
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autoload :Fastq, 'bio/db/fastq'
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autoload :GFF, 'bio/db/gff'
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autoload :AAindex, 'bio/db/aaindex'
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autoload :AAindex1, 'bio/db/aaindex' # change to AAindex::AAindex1 ?
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autoload :AAindex2, 'bio/db/aaindex' # change to AAindex::AAindex2 ?
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autoload :TRANSFAC, 'bio/db/transfac'
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autoload :PROSITE, 'bio/db/prosite'
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autoload :LITDB, 'bio/db/litdb'
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autoload :MEDLINE, 'bio/db/medline'
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autoload :FANTOM, 'bio/db/fantom'
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autoload :GO, 'bio/db/go'
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autoload :PDB, 'bio/db/pdb'
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autoload :NBRF, 'bio/db/nbrf'
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autoload :REBASE, 'bio/db/rebase'
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autoload :SOFT, 'bio/db/soft'
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autoload :Lasergene, 'bio/db/lasergene'
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autoload :SangerChromatogram, 'bio/db/sanger_chromatogram/chromatogram'
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autoload :Scf, 'bio/db/sanger_chromatogram/scf'
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autoload :Abif, 'bio/db/sanger_chromatogram/abif'
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autoload :Newick, 'bio/db/newick'
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autoload :Nexus, 'bio/db/nexus'
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autoload :PhyloXML, 'bio/db/phyloxml/phyloxml_elements'
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# Bio::Taxonomy will be moved to other file
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autoload :Taxonomy, 'bio/db/phyloxml/phyloxml_elements'
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## below are described in bio/db/phyloxml/phyloxml_elements.rb
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#module PhyloXML
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# autoload :Parser, 'bio/db/phyloxml/phyloxml_parser'
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# autoload :Writer, 'bio/db/phyloxml/phyloxml_writer'
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#end
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### IO interface modules
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autoload :Registry, 'bio/io/registry'
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autoload :Fetch, 'bio/io/fetch'
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autoload :SQL, 'bio/io/sql'
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autoload :SOAPWSDL, 'bio/io/soapwsdl'
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autoload :FlatFile, 'bio/io/flatfile'
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autoload :FlatFileIndex, 'bio/io/flatfile/index' # chage to FlatFile::Index ?
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## below are described in bio/io/flatfile/index.rb
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#class FlatFileIndex
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# autoload :Indexer, 'bio/io/flatfile/indexer'
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# autoload :BDBdefault, 'bio/io/flatfile/bdb'
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# autoload :BDBwrapper, 'bio/io/flatfile/bdb'
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# autoload :BDB_1, 'bio/io/flatfile/bdb'
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#end
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autoload :PubMed, 'bio/io/pubmed'
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autoload :DAS, 'bio/io/das'
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autoload :DBGET, 'bio/io/dbget'
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autoload :Ensembl, 'bio/io/ensembl'
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autoload :Hinv, 'bio/io/hinv'
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## below are described in bio/appl/blast.rb
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#class Blast
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# autoload :Fastacmd, 'bio/io/fastacmd'
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#end
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class KEGG
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autoload :API, 'bio/io/keggapi'
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end
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## below are described in bio/db/genbank/ddbj.rb
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#class DDBJ
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# autoload :XML, 'bio/io/ddbjxml'
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#end
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class HGC
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autoload :HiGet, 'bio/io/higet'
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end
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class EBI
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autoload :SOAP, 'bio/io/ebisoap'
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end
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autoload :NCBI, 'bio/io/ncbirest'
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## below are described in bio/io/ncbirest.rb
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#class NCBI
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# autoload :SOAP, 'bio/io/ncbisoap'
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# autoload :REST, 'bio/io/ncbirest'
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#end
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autoload :TogoWS, 'bio/io/togows'
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### Applications
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autoload :Fasta, 'bio/appl/fasta'
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## below are described in bio/appl/fasta.rb
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#class Fasta
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# autoload :Report, 'bio/appl/fasta/format10'
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#end
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autoload :Blast, 'bio/appl/blast'
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## below are described in bio/appl/blast.rb
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#class Blast
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# autoload :Fastacmd, 'bio/io/fastacmd'
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# autoload :Report, 'bio/appl/blast/report'
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# autoload :Default, 'bio/appl/blast/format0'
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# autoload :WU, 'bio/appl/blast/wublast'
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# autoload :Bl2seq, 'bio/appl/bl2seq/report'
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# autoload :RPSBlast, 'bio/appl/blast/rpsblast'
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# autoload :NCBIOptions, 'bio/appl/blast/ncbioptions'
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# autoload :Remote, 'bio/appl/blast/remote'
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#end
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autoload :HMMER, 'bio/appl/hmmer'
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## below are described in bio/appl/hmmer.rb
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#class HMMER
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# autoload :Report, 'bio/appl/hmmer/report'
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#end
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autoload :EMBOSS, 'bio/appl/emboss' # use bio/command, improve
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autoload :PSORT, 'bio/appl/psort'
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## below are described in bio/appl/psort.rb
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#class PSORT
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# class PSORT1
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# autoload :Report, 'bio/appl/psort/report'
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# end
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# class PSORT2
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# autoload :Report, 'bio/appl/psort/report'
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# end
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#end
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autoload :TMHMM, 'bio/appl/tmhmm/report'
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autoload :TargetP, 'bio/appl/targetp/report'
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autoload :SOSUI, 'bio/appl/sosui/report'
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autoload :Genscan, 'bio/appl/genscan/report'
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autoload :ClustalW, 'bio/appl/clustalw'
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## below are described in bio/appl/clustalw.rb
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#class ClustalW
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# autoload :Report, 'bio/appl/clustalw/report'
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#end
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autoload :MAFFT, 'bio/appl/mafft'
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## below are described in bio/appl/mafft.rb
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#class MAFFT
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# autoload :Report, 'bio/appl/mafft/report'
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#end
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autoload :Tcoffee, 'bio/appl/tcoffee'
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autoload :Muscle, 'bio/appl/muscle'
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autoload :Probcons, 'bio/appl/probcons'
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autoload :Sim4, 'bio/appl/sim4'
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## below are described in bio/appl/sim4.rb
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#class Sim4
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# autoload :Report, 'bio/appl/sim4/report'
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#end
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autoload :Spidey, 'bio/appl/spidey/report'
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autoload :Blat, 'bio/appl/blat/report'
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module GCG
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autoload :Msf, 'bio/appl/gcg/msf'
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autoload :Seq, 'bio/appl/gcg/seq'
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end
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module Phylip
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autoload :PhylipFormat, 'bio/appl/phylip/alignment'
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autoload :DistanceMatrix, 'bio/appl/phylip/distance_matrix'
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end
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autoload :Iprscan, 'bio/appl/iprscan/report'
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autoload :PAML, 'bio/appl/paml/common'
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## below are described in bio/appl/paml/common.rb
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# module PAML
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# autoload :Codeml, 'bio/appl/paml/codeml'
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# autoload :Baseml, 'bio/appl/paml/baseml'
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# autoload :Yn00, 'bio/appl/paml/yn00'
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# end
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### Utilities
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autoload :SiRNA, 'bio/util/sirna'
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autoload :ColorScheme, 'bio/util/color_scheme'
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autoload :ContingencyTable, 'bio/util/contingency_table'
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autoload :RestrictionEnzyme, 'bio/util/restriction_enzyme'
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### Service libraries
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autoload :Command, 'bio/command'
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### NeXML lib
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autoload :NeXML, 'bio/db/nexml'
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### Provide BioRuby shell 'command' also as 'Bio.command' (like ChemRuby)
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def self.method_missing(*args)
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require 'bio/shell'
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extend Bio::Shell
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public_class_method(*Bio::Shell.private_instance_methods)
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if Bio.respond_to?(args.first)
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Bio.send(*args)
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else
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raise NameError
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end
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end
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end
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data/test/data/nexml/test.xml
DELETED
@@ -1,69 +0,0 @@
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<?xml version="1.0" encoding="ISO-8859-1"?>
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<nex:nexml
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version="0.9"
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generator="eclipse"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xmlns:xml="http://www.w3.org/XML/1998/namespace"
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-
xmlns:nex="http://www.nexml.org/2009"
|
8
|
-
xmlns="http://www.nexml.org/2009"
|
9
|
-
xsi:schemaLocation="http://www.nexml.org/2009 http://www.nexml.org/2009/nexml.xsd">
|
10
|
-
|
11
|
-
<otus id="taxa1" label="A taxa block">
|
12
|
-
<otu id="o1" label="A taxon"/>
|
13
|
-
<otu id="o2" label="A taxon"/>
|
14
|
-
</otus>
|
15
|
-
<trees otus="taxa1" id="trees1" label="A tree container">
|
16
|
-
<tree id="tree1" xsi:type="nex:FloatTree" label="A float tree">
|
17
|
-
<node id="n1" label="A node" root="true" otu="o1"/>
|
18
|
-
<node id="n2" label="A node"/>
|
19
|
-
<rootedge id="re1" label="A rootedge" target="n1" length="0.5"/>
|
20
|
-
<edge source="n1" target="n2" id="e1" length="0.4353" label="An edge"/>
|
21
|
-
</tree>
|
22
|
-
<network id="network1" xsi:type="nex:IntNetwork" label="An int network">
|
23
|
-
<node id="n1n1" label="A node" root="true" otu="o1"/>
|
24
|
-
<node id="n1n2" label="A node"/>
|
25
|
-
<edge source="n1n1" target="n1n2" id="n1e1" length="1" label="An edge"/>
|
26
|
-
<edge source="n1n2" target="n1n2" id="n1e2" length="0" label="An edge"/>
|
27
|
-
</network>
|
28
|
-
</trees>
|
29
|
-
<characters otus="taxa1" id="standardchars6" xsi:type="nex:StandardSeqs" label="Standard sequences">
|
30
|
-
<format>
|
31
|
-
<states id="sss1">
|
32
|
-
<state id="ss1" symbol="1"/>
|
33
|
-
<state id="ss2" symbol="2"/>
|
34
|
-
<polymorphic_state_set symbol="4" id="ss4">
|
35
|
-
<member state="ss1"/>
|
36
|
-
<member state="ss2"/>
|
37
|
-
</polymorphic_state_set>
|
38
|
-
<uncertain_state_set symbol="5" id="ss5">
|
39
|
-
<member state="ss2"/>
|
40
|
-
<member state="ss1"/>
|
41
|
-
</uncertain_state_set>
|
42
|
-
</states>
|
43
|
-
<char states="sss1" id="sc1"/>
|
44
|
-
<char states="sss1" id="sc2"/>
|
45
|
-
</format>
|
46
|
-
<matrix>
|
47
|
-
<row id="sr1" otu="o1">
|
48
|
-
<seq>1 2</seq>
|
49
|
-
</row>
|
50
|
-
<row id="sr2" otu="o2">
|
51
|
-
<seq>2 2</seq>
|
52
|
-
</row>
|
53
|
-
</matrix>
|
54
|
-
</characters>
|
55
|
-
<characters otus="taxa1" id="m2" xsi:type="nex:StandardCells" label="Categorical characters">
|
56
|
-
<format>
|
57
|
-
<states id="sss2">
|
58
|
-
<state id="ss6" symbol="1"/>
|
59
|
-
</states>
|
60
|
-
<char states="sss2" id="sc3"/>
|
61
|
-
</format>
|
62
|
-
|
63
|
-
<matrix>
|
64
|
-
<row id="sr3" otu="o1">
|
65
|
-
<cell char="sc3" state="ss6"/>
|
66
|
-
</row>
|
67
|
-
</matrix>
|
68
|
-
</characters>
|
69
|
-
</nex:nexml>
|
@@ -1,119 +0,0 @@
|
|
1
|
-
module Bio
|
2
|
-
module NeXML
|
3
|
-
class TestFactory < Test::Unit::TestCase
|
4
|
-
def setup
|
5
|
-
@nexml = Bio::NeXML::Nexml.new
|
6
|
-
@otus = @nexml.create_otus
|
7
|
-
end
|
8
|
-
|
9
|
-
def test_otus
|
10
|
-
assert @otus.kind_of? Bio::NeXML::Otus
|
11
|
-
end
|
12
|
-
|
13
|
-
def test_otu
|
14
|
-
otu = @otus.create_otu
|
15
|
-
assert otu.kind_of? Bio::NeXML::Otu
|
16
|
-
end
|
17
|
-
|
18
|
-
def test_trees
|
19
|
-
trees = @nexml.create_trees( :otus => @otus )
|
20
|
-
otu = @otus.create_otu
|
21
|
-
assert_equal @otus, trees.otus
|
22
|
-
assert trees.instance_of? Bio::NeXML::Trees
|
23
|
-
|
24
|
-
floattree = trees.create_tree
|
25
|
-
assert floattree.kind_of? Bio::NeXML::Tree
|
26
|
-
assert floattree.kind_of? Bio::Tree
|
27
|
-
assert floattree.kind_of? Bio::NeXML::FloatTree
|
28
|
-
floatnode = floattree.create_node( :otu => otu )
|
29
|
-
assert floatnode.kind_of? Bio::NeXML::Node
|
30
|
-
assert floatnode.kind_of? Bio::Tree::Node
|
31
|
-
assert_equal otu, floatnode.otu
|
32
|
-
|
33
|
-
floatedge = floattree.create_edge( :source => floatnode, :target => floatnode )
|
34
|
-
assert floatedge.kind_of? Bio::NeXML::Edge
|
35
|
-
assert floatedge.kind_of? Bio::Tree::Edge
|
36
|
-
assert floatedge.kind_of? Bio::NeXML::FloatEdge
|
37
|
-
floatrootedge = floattree.create_rootedge( :target => floatnode )
|
38
|
-
assert floatrootedge.kind_of? Bio::NeXML::Edge
|
39
|
-
assert floatrootedge.kind_of? Bio::Tree::Edge
|
40
|
-
assert floatrootedge.kind_of? Bio::NeXML::RootEdge
|
41
|
-
assert floatrootedge.kind_of? Bio::NeXML::FloatRootEdge
|
42
|
-
|
43
|
-
inttree = trees.create_tree( true )
|
44
|
-
assert inttree.kind_of? Bio::NeXML::Tree
|
45
|
-
assert inttree.kind_of? Bio::Tree
|
46
|
-
assert inttree.kind_of? Bio::NeXML::IntTree
|
47
|
-
intedge = inttree.create_edge
|
48
|
-
assert intedge.kind_of? Bio::NeXML::Edge
|
49
|
-
assert intedge.kind_of? Bio::Tree::Edge
|
50
|
-
assert intedge.kind_of? Bio::NeXML::IntEdge
|
51
|
-
introotedge = inttree.create_rootedge
|
52
|
-
assert introotedge.kind_of? Bio::NeXML::Edge
|
53
|
-
assert introotedge.kind_of? Bio::Tree::Edge
|
54
|
-
assert introotedge.kind_of? Bio::NeXML::RootEdge
|
55
|
-
assert introotedge.kind_of? Bio::NeXML::IntRootEdge
|
56
|
-
|
57
|
-
floatnetwork = trees.create_network
|
58
|
-
assert floatnetwork.kind_of? Bio::NeXML::Tree
|
59
|
-
assert floatnetwork.kind_of? Bio::Tree
|
60
|
-
assert floatnetwork.kind_of? Bio::NeXML::FloatNetwork
|
61
|
-
floatnedge = floatnetwork.create_edge
|
62
|
-
assert floatnedge.kind_of? Bio::NeXML::Edge
|
63
|
-
assert floatnedge.kind_of? Bio::Tree::Edge
|
64
|
-
assert floatnedge.kind_of? Bio::NeXML::FloatEdge
|
65
|
-
|
66
|
-
intnetwork = trees.create_network( true )
|
67
|
-
assert intnetwork.kind_of? Bio::NeXML::Tree
|
68
|
-
assert intnetwork.kind_of? Bio::Tree
|
69
|
-
assert intnetwork.kind_of? Bio::NeXML::IntNetwork
|
70
|
-
intnedge = intnetwork.create_edge
|
71
|
-
assert intnedge.kind_of? Bio::NeXML::Edge
|
72
|
-
assert intnedge.kind_of? Bio::Tree::Edge
|
73
|
-
assert intnedge.kind_of? Bio::NeXML::IntEdge
|
74
|
-
end
|
75
|
-
def test_characters_seqs
|
76
|
-
otu = @otus.create_otu
|
77
|
-
dnaseqs = @nexml.create_characters( "Dna", false, :otus => @otus )
|
78
|
-
assert dnaseqs.kind_of? Bio::NeXML::Characters
|
79
|
-
assert dnaseqs.kind_of? Bio::NeXML::Dna
|
80
|
-
assert dnaseqs.kind_of? Bio::NeXML::DnaSeqs
|
81
|
-
assert_equal @otus, dnaseqs.otus
|
82
|
-
|
83
|
-
format = dnaseqs.create_format
|
84
|
-
assert format.kind_of? Bio::NeXML::Format
|
85
|
-
assert_equal format, dnaseqs.format
|
86
|
-
|
87
|
-
matrix = dnaseqs.create_matrix
|
88
|
-
assert matrix.kind_of? Bio::NeXML::Matrix
|
89
|
-
assert matrix.kind_of? Bio::NeXML::SeqMatrix
|
90
|
-
assert_equal matrix, dnaseqs.matrix
|
91
|
-
|
92
|
-
row = matrix.create_row( :otu => otu )
|
93
|
-
assert row.kind_of? Bio::NeXML::Row
|
94
|
-
assert row.kind_of? Bio::NeXML::SeqRow
|
95
|
-
assert_equal otu, row.otu
|
96
|
-
|
97
|
-
seq = 'ACATGCAG'
|
98
|
-
newrow = dnaseqs.create_raw( seq )
|
99
|
-
assert_equal newrow.sequences.first.value, seq
|
100
|
-
end
|
101
|
-
def test_characters_cells
|
102
|
-
otu1 = @otus.create_otu
|
103
|
-
otu2 = @otus.create_otu
|
104
|
-
standardcells = @nexml.create_characters( "Standard", true, :otus => @otus )
|
105
|
-
newrow1 = standardcells.create_raw('1 2 3 4 5')
|
106
|
-
newrow1.otu = otu1
|
107
|
-
newrow2 = standardcells.create_raw('1 2 3 4 5')
|
108
|
-
newrow2.otu = otu2
|
109
|
-
assert_equal otu1, newrow1.otu
|
110
|
-
assert_equal otu2, newrow2.otu
|
111
|
-
assert newrow1.kind_of? Bio::NeXML::Row
|
112
|
-
assert newrow1.kind_of? Bio::NeXML::CellRow
|
113
|
-
assert standardcells.kind_of? Bio::NeXML::Characters
|
114
|
-
assert standardcells.kind_of? Bio::NeXML::Standard
|
115
|
-
assert standardcells.kind_of? Bio::NeXML::StandardCells
|
116
|
-
end
|
117
|
-
end
|
118
|
-
end
|
119
|
-
end
|