bio-nexml 0.0.1 → 0.1.0

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Files changed (20) hide show
  1. data/LICENSE.txt +1 -1
  2. data/README.rdoc +6 -0
  3. data/lib/bio-nexml.rb +2 -0
  4. metadata +27 -142
  5. data/Gemfile +0 -15
  6. data/Gemfile.lock +0 -24
  7. data/Rakefile +0 -55
  8. data/TODO.txt +0 -6
  9. data/VERSION +0 -1
  10. data/bio-nexml.gemspec +0 -126
  11. data/extconf.rb +0 -2
  12. data/lib/bio.rb +0 -321
  13. data/test/data/nexml/test.xml +0 -69
  14. data/test/unit/bio/db/nexml/tc_factory.rb +0 -119
  15. data/test/unit/bio/db/nexml/tc_mapper.rb +0 -78
  16. data/test/unit/bio/db/nexml/tc_matrix.rb +0 -551
  17. data/test/unit/bio/db/nexml/tc_parser.rb +0 -21
  18. data/test/unit/bio/db/nexml/tc_taxa.rb +0 -118
  19. data/test/unit/bio/db/nexml/tc_trees.rb +0 -370
  20. data/test/unit/bio/db/nexml/tc_writer.rb +0 -633
data/extconf.rb DELETED
@@ -1,2 +0,0 @@
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- require 'mkmf'
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- create_makefile("bio-nexml")
data/lib/bio.rb DELETED
@@ -1,321 +0,0 @@
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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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-
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- module Bio
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-
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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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-
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- ### Basic data types
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-
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- ## Sequence
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-
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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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-
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- ## Locations/Location
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-
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- autoload :Location, 'bio/location'
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- autoload :Locations, 'bio/location'
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-
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- ## Features/Feature
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-
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- autoload :Feature, 'bio/feature'
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- autoload :Features, 'bio/compat/features'
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-
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- ## References/Reference
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-
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- autoload :Reference, 'bio/reference'
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- autoload :References, 'bio/compat/references'
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-
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- ## Pathway/Relation
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-
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- autoload :Pathway, 'bio/pathway'
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- autoload :Relation, 'bio/pathway'
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-
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- ## Alignment
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-
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- autoload :Alignment, 'bio/alignment'
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-
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- ## Tree
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- autoload :Tree, 'bio/tree'
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-
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- ## Map
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- autoload :Map, 'bio/map'
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-
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- ### Constants
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-
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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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-
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-
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- ### DB parsers
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-
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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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-
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- ## GenBank/RefSeq/DDBJ
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-
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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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-
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- ## EMBL/TrEMBL/Swiss-Prot/SPTR
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-
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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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-
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- ## KEGG
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-
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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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-
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- ## other formats
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-
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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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-
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- autoload :Newick, 'bio/db/newick'
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- autoload :Nexus, 'bio/db/nexus'
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-
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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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-
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- ### IO interface modules
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-
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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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-
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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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-
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- autoload :Ensembl, 'bio/io/ensembl'
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- autoload :Hinv, 'bio/io/hinv'
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-
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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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-
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- class KEGG
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- autoload :API, 'bio/io/keggapi'
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- end
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-
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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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-
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- class HGC
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- autoload :HiGet, 'bio/io/higet'
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- end
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-
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- class EBI
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- autoload :SOAP, 'bio/io/ebisoap'
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- end
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-
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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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-
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- autoload :TogoWS, 'bio/io/togows'
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-
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- ### Applications
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-
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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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-
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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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-
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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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-
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- autoload :EMBOSS, 'bio/appl/emboss' # use bio/command, improve
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-
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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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-
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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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-
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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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-
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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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-
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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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-
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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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-
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- autoload :Spidey, 'bio/appl/spidey/report'
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- autoload :Blat, 'bio/appl/blat/report'
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-
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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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-
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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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-
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- autoload :Iprscan, 'bio/appl/iprscan/report'
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-
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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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-
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- ### Utilities
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-
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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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-
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- ### Service libraries
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- autoload :Command, 'bio/command'
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-
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- ### NeXML lib
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- autoload :NeXML, 'bio/db/nexml'
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-
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- ### Provide BioRuby shell 'command' also as 'Bio.command' (like ChemRuby)
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-
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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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-
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- end
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-
data/test/data/nexml/test.xml DELETED
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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"
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- xmlns="http://www.nexml.org/2009"
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- xsi:schemaLocation="http://www.nexml.org/2009 http://www.nexml.org/2009/nexml.xsd">
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-
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- <otus id="taxa1" label="A taxa block">
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- <otu id="o1" label="A taxon"/>
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- <otu id="o2" label="A taxon"/>
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- </otus>
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- <trees otus="taxa1" id="trees1" label="A tree container">
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- <tree id="tree1" xsi:type="nex:FloatTree" label="A float tree">
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- <node id="n1" label="A node" root="true" otu="o1"/>
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- <node id="n2" label="A node"/>
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- <rootedge id="re1" label="A rootedge" target="n1" length="0.5"/>
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- <edge source="n1" target="n2" id="e1" length="0.4353" label="An edge"/>
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- </tree>
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- <network id="network1" xsi:type="nex:IntNetwork" label="An int network">
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- <node id="n1n1" label="A node" root="true" otu="o1"/>
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- <node id="n1n2" label="A node"/>
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- <edge source="n1n1" target="n1n2" id="n1e1" length="1" label="An edge"/>
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- <edge source="n1n2" target="n1n2" id="n1e2" length="0" label="An edge"/>
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- </network>
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- </trees>
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- <characters otus="taxa1" id="standardchars6" xsi:type="nex:StandardSeqs" label="Standard sequences">
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- <format>
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- <states id="sss1">
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- <state id="ss1" symbol="1"/>
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- <state id="ss2" symbol="2"/>
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- <polymorphic_state_set symbol="4" id="ss4">
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- <member state="ss1"/>
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- <member state="ss2"/>
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- </polymorphic_state_set>
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- <uncertain_state_set symbol="5" id="ss5">
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- <member state="ss2"/>
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- <member state="ss1"/>
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- </uncertain_state_set>
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- </states>
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- <char states="sss1" id="sc1"/>
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- <char states="sss1" id="sc2"/>
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- </format>
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- <matrix>
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- <row id="sr1" otu="o1">
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- <seq>1 2</seq>
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- </row>
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- <row id="sr2" otu="o2">
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- <seq>2 2</seq>
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- </row>
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- </matrix>
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- </characters>
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- <characters otus="taxa1" id="m2" xsi:type="nex:StandardCells" label="Categorical characters">
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- <format>
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- <states id="sss2">
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- <state id="ss6" symbol="1"/>
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- </states>
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- <char states="sss2" id="sc3"/>
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- </format>
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-
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- <matrix>
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- <row id="sr3" otu="o1">
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- <cell char="sc3" state="ss6"/>
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- </row>
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- </matrix>
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- </characters>
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- </nex:nexml>
data/test/unit/bio/db/nexml/tc_factory.rb DELETED
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- module Bio
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- module NeXML
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- class TestFactory < Test::Unit::TestCase
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- def setup
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- @nexml = Bio::NeXML::Nexml.new
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- @otus = @nexml.create_otus
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- end
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-
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- def test_otus
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- assert @otus.kind_of? Bio::NeXML::Otus
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- end
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-
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- def test_otu
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- otu = @otus.create_otu
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- assert otu.kind_of? Bio::NeXML::Otu
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- end
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-
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- def test_trees
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- trees = @nexml.create_trees( :otus => @otus )
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- otu = @otus.create_otu
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- assert_equal @otus, trees.otus
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- assert trees.instance_of? Bio::NeXML::Trees
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-
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- floattree = trees.create_tree
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- assert floattree.kind_of? Bio::NeXML::Tree
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- assert floattree.kind_of? Bio::Tree
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- assert floattree.kind_of? Bio::NeXML::FloatTree
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- floatnode = floattree.create_node( :otu => otu )
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- assert floatnode.kind_of? Bio::NeXML::Node
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- assert floatnode.kind_of? Bio::Tree::Node
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- assert_equal otu, floatnode.otu
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-
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- floatedge = floattree.create_edge( :source => floatnode, :target => floatnode )
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- assert floatedge.kind_of? Bio::NeXML::Edge
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- assert floatedge.kind_of? Bio::Tree::Edge
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- assert floatedge.kind_of? Bio::NeXML::FloatEdge
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- floatrootedge = floattree.create_rootedge( :target => floatnode )
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- assert floatrootedge.kind_of? Bio::NeXML::Edge
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- assert floatrootedge.kind_of? Bio::Tree::Edge
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- assert floatrootedge.kind_of? Bio::NeXML::RootEdge
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- assert floatrootedge.kind_of? Bio::NeXML::FloatRootEdge
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-
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- inttree = trees.create_tree( true )
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- assert inttree.kind_of? Bio::NeXML::Tree
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- assert inttree.kind_of? Bio::Tree
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- assert inttree.kind_of? Bio::NeXML::IntTree
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- intedge = inttree.create_edge
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- assert intedge.kind_of? Bio::NeXML::Edge
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- assert intedge.kind_of? Bio::Tree::Edge
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- assert intedge.kind_of? Bio::NeXML::IntEdge
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- introotedge = inttree.create_rootedge
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- assert introotedge.kind_of? Bio::NeXML::Edge
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- assert introotedge.kind_of? Bio::Tree::Edge
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- assert introotedge.kind_of? Bio::NeXML::RootEdge
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- assert introotedge.kind_of? Bio::NeXML::IntRootEdge
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-
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- floatnetwork = trees.create_network
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- assert floatnetwork.kind_of? Bio::NeXML::Tree
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- assert floatnetwork.kind_of? Bio::Tree
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- assert floatnetwork.kind_of? Bio::NeXML::FloatNetwork
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- floatnedge = floatnetwork.create_edge
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- assert floatnedge.kind_of? Bio::NeXML::Edge
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- assert floatnedge.kind_of? Bio::Tree::Edge
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- assert floatnedge.kind_of? Bio::NeXML::FloatEdge
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-
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- intnetwork = trees.create_network( true )
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- assert intnetwork.kind_of? Bio::NeXML::Tree
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- assert intnetwork.kind_of? Bio::Tree
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- assert intnetwork.kind_of? Bio::NeXML::IntNetwork
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- intnedge = intnetwork.create_edge
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- assert intnedge.kind_of? Bio::NeXML::Edge
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- assert intnedge.kind_of? Bio::Tree::Edge
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- 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