bio-nexml 0.0.1 → 0.1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
data/extconf.rb DELETED
@@ -1,2 +0,0 @@
1
- require 'mkmf'
2
- create_makefile("bio-nexml")
data/lib/bio.rb DELETED
@@ -1,321 +0,0 @@
1
- #
2
- # = bio.rb - Loading all BioRuby modules
3
- #
4
- # Copyright:: Copyright (C) 2001-2007
5
- # Toshiaki Katayama <k@bioruby.org>
6
- # License:: The Ruby License
7
- #
8
- # $Id:$
9
- #
10
-
11
- module Bio
12
-
13
- autoload :BIORUBY_VERSION, 'bio/version'
14
- autoload :BIORUBY_EXTRA_VERSION, 'bio/version'
15
- autoload :BIORUBY_VERSION_ID, 'bio/version'
16
-
17
- ### Basic data types
18
-
19
- ## Sequence
20
-
21
- autoload :Sequence, 'bio/sequence'
22
- ## below are described in bio/sequence.rb
23
- #class Sequence
24
- # autoload :Common, 'bio/sequence/common'
25
- # autoload :NA, 'bio/sequence/na'
26
- # autoload :AA, 'bio/sequence/aa'
27
- # autoload :Generic, 'bio/sequence/generic'
28
- # autoload :Format, 'bio/sequence/format'
29
- # autoload :Adapter, 'bio/sequence/adapter'
30
- #end
31
-
32
- ## Locations/Location
33
-
34
- autoload :Location, 'bio/location'
35
- autoload :Locations, 'bio/location'
36
-
37
- ## Features/Feature
38
-
39
- autoload :Feature, 'bio/feature'
40
- autoload :Features, 'bio/compat/features'
41
-
42
- ## References/Reference
43
-
44
- autoload :Reference, 'bio/reference'
45
- autoload :References, 'bio/compat/references'
46
-
47
- ## Pathway/Relation
48
-
49
- autoload :Pathway, 'bio/pathway'
50
- autoload :Relation, 'bio/pathway'
51
-
52
- ## Alignment
53
-
54
- autoload :Alignment, 'bio/alignment'
55
-
56
- ## Tree
57
- autoload :Tree, 'bio/tree'
58
-
59
- ## Map
60
- autoload :Map, 'bio/map'
61
-
62
- ### Constants
63
-
64
- autoload :NucleicAcid, 'bio/data/na'
65
- autoload :AminoAcid, 'bio/data/aa'
66
- autoload :CodonTable, 'bio/data/codontable'
67
-
68
-
69
- ### DB parsers
70
-
71
- autoload :DB, 'bio/db'
72
- autoload :NCBIDB, 'bio/db'
73
- autoload :KEGGDB, 'bio/db'
74
- autoload :EMBLDB, 'bio/db'
75
-
76
- ## GenBank/RefSeq/DDBJ
77
-
78
- autoload :GenBank, 'bio/db/genbank/genbank'
79
- autoload :GenPept, 'bio/db/genbank/genpept'
80
- autoload :RefSeq, 'bio/db/genbank/refseq'
81
- autoload :DDBJ, 'bio/db/genbank/ddbj'
82
- ## below are described in bio/db/genbank/ddbj.rb
83
- #class DDBJ
84
- # autoload :XML, 'bio/io/ddbjxml'
85
- #end
86
-
87
- ## EMBL/TrEMBL/Swiss-Prot/SPTR
88
-
89
- autoload :EMBL, 'bio/db/embl/embl'
90
- autoload :SPTR, 'bio/db/embl/sptr'
91
- autoload :TrEMBL, 'bio/db/embl/trembl'
92
- autoload :UniProt, 'bio/db/embl/uniprot'
93
- autoload :SwissProt, 'bio/db/embl/swissprot'
94
-
95
- ## KEGG
96
-
97
- class KEGG
98
- autoload :GENOME, 'bio/db/kegg/genome'
99
- autoload :GENES, 'bio/db/kegg/genes'
100
- autoload :ENZYME, 'bio/db/kegg/enzyme'
101
- autoload :COMPOUND, 'bio/db/kegg/compound'
102
- autoload :DRUG, 'bio/db/kegg/drug'
103
- autoload :GLYCAN, 'bio/db/kegg/glycan'
104
- autoload :REACTION, 'bio/db/kegg/reaction'
105
- autoload :BRITE, 'bio/db/kegg/brite'
106
- autoload :CELL, 'bio/db/kegg/cell'
107
- autoload :EXPRESSION, 'bio/db/kegg/expression'
108
- autoload :ORTHOLOGY, 'bio/db/kegg/orthology'
109
- autoload :KGML, 'bio/db/kegg/kgml'
110
- autoload :Taxonomy, 'bio/db/kegg/taxonomy'
111
- end
112
-
113
- ## other formats
114
-
115
- autoload :FastaFormat, 'bio/db/fasta'
116
- autoload :FastaNumericFormat, 'bio/db/fasta/qual' # change to FastaFormat::Numeric ?
117
- autoload :FastaDefline, 'bio/db/fasta/defline' # change to FastaFormat::Defline ?
118
- autoload :Fastq, 'bio/db/fastq'
119
- autoload :GFF, 'bio/db/gff'
120
- autoload :AAindex, 'bio/db/aaindex'
121
- autoload :AAindex1, 'bio/db/aaindex' # change to AAindex::AAindex1 ?
122
- autoload :AAindex2, 'bio/db/aaindex' # change to AAindex::AAindex2 ?
123
- autoload :TRANSFAC, 'bio/db/transfac'
124
- autoload :PROSITE, 'bio/db/prosite'
125
- autoload :LITDB, 'bio/db/litdb'
126
- autoload :MEDLINE, 'bio/db/medline'
127
- autoload :FANTOM, 'bio/db/fantom'
128
- autoload :GO, 'bio/db/go'
129
- autoload :PDB, 'bio/db/pdb'
130
- autoload :NBRF, 'bio/db/nbrf'
131
- autoload :REBASE, 'bio/db/rebase'
132
- autoload :SOFT, 'bio/db/soft'
133
- autoload :Lasergene, 'bio/db/lasergene'
134
- autoload :SangerChromatogram, 'bio/db/sanger_chromatogram/chromatogram'
135
- autoload :Scf, 'bio/db/sanger_chromatogram/scf'
136
- autoload :Abif, 'bio/db/sanger_chromatogram/abif'
137
-
138
- autoload :Newick, 'bio/db/newick'
139
- autoload :Nexus, 'bio/db/nexus'
140
-
141
- autoload :PhyloXML, 'bio/db/phyloxml/phyloxml_elements'
142
- # Bio::Taxonomy will be moved to other file
143
- autoload :Taxonomy, 'bio/db/phyloxml/phyloxml_elements'
144
- ## below are described in bio/db/phyloxml/phyloxml_elements.rb
145
- #module PhyloXML
146
- # autoload :Parser, 'bio/db/phyloxml/phyloxml_parser'
147
- # autoload :Writer, 'bio/db/phyloxml/phyloxml_writer'
148
- #end
149
-
150
- ### IO interface modules
151
-
152
- autoload :Registry, 'bio/io/registry'
153
- autoload :Fetch, 'bio/io/fetch'
154
- autoload :SQL, 'bio/io/sql'
155
- autoload :SOAPWSDL, 'bio/io/soapwsdl'
156
- autoload :FlatFile, 'bio/io/flatfile'
157
- autoload :FlatFileIndex, 'bio/io/flatfile/index' # chage to FlatFile::Index ?
158
- ## below are described in bio/io/flatfile/index.rb
159
- #class FlatFileIndex
160
- # autoload :Indexer, 'bio/io/flatfile/indexer'
161
- # autoload :BDBdefault, 'bio/io/flatfile/bdb'
162
- # autoload :BDBwrapper, 'bio/io/flatfile/bdb'
163
- # autoload :BDB_1, 'bio/io/flatfile/bdb'
164
- #end
165
-
166
- autoload :PubMed, 'bio/io/pubmed'
167
- autoload :DAS, 'bio/io/das'
168
- autoload :DBGET, 'bio/io/dbget'
169
-
170
- autoload :Ensembl, 'bio/io/ensembl'
171
- autoload :Hinv, 'bio/io/hinv'
172
-
173
- ## below are described in bio/appl/blast.rb
174
- #class Blast
175
- # autoload :Fastacmd, 'bio/io/fastacmd'
176
- #end
177
-
178
- class KEGG
179
- autoload :API, 'bio/io/keggapi'
180
- end
181
-
182
- ## below are described in bio/db/genbank/ddbj.rb
183
- #class DDBJ
184
- # autoload :XML, 'bio/io/ddbjxml'
185
- #end
186
-
187
- class HGC
188
- autoload :HiGet, 'bio/io/higet'
189
- end
190
-
191
- class EBI
192
- autoload :SOAP, 'bio/io/ebisoap'
193
- end
194
-
195
- autoload :NCBI, 'bio/io/ncbirest'
196
- ## below are described in bio/io/ncbirest.rb
197
- #class NCBI
198
- # autoload :SOAP, 'bio/io/ncbisoap'
199
- # autoload :REST, 'bio/io/ncbirest'
200
- #end
201
-
202
- autoload :TogoWS, 'bio/io/togows'
203
-
204
- ### Applications
205
-
206
- autoload :Fasta, 'bio/appl/fasta'
207
- ## below are described in bio/appl/fasta.rb
208
- #class Fasta
209
- # autoload :Report, 'bio/appl/fasta/format10'
210
- #end
211
-
212
- autoload :Blast, 'bio/appl/blast'
213
- ## below are described in bio/appl/blast.rb
214
- #class Blast
215
- # autoload :Fastacmd, 'bio/io/fastacmd'
216
- # autoload :Report, 'bio/appl/blast/report'
217
- # autoload :Default, 'bio/appl/blast/format0'
218
- # autoload :WU, 'bio/appl/blast/wublast'
219
- # autoload :Bl2seq, 'bio/appl/bl2seq/report'
220
- # autoload :RPSBlast, 'bio/appl/blast/rpsblast'
221
- # autoload :NCBIOptions, 'bio/appl/blast/ncbioptions'
222
- # autoload :Remote, 'bio/appl/blast/remote'
223
- #end
224
-
225
- autoload :HMMER, 'bio/appl/hmmer'
226
- ## below are described in bio/appl/hmmer.rb
227
- #class HMMER
228
- # autoload :Report, 'bio/appl/hmmer/report'
229
- #end
230
-
231
- autoload :EMBOSS, 'bio/appl/emboss' # use bio/command, improve
232
-
233
- autoload :PSORT, 'bio/appl/psort'
234
- ## below are described in bio/appl/psort.rb
235
- #class PSORT
236
- # class PSORT1
237
- # autoload :Report, 'bio/appl/psort/report'
238
- # end
239
- # class PSORT2
240
- # autoload :Report, 'bio/appl/psort/report'
241
- # end
242
- #end
243
-
244
- autoload :TMHMM, 'bio/appl/tmhmm/report'
245
- autoload :TargetP, 'bio/appl/targetp/report'
246
- autoload :SOSUI, 'bio/appl/sosui/report'
247
- autoload :Genscan, 'bio/appl/genscan/report'
248
-
249
- autoload :ClustalW, 'bio/appl/clustalw'
250
- ## below are described in bio/appl/clustalw.rb
251
- #class ClustalW
252
- # autoload :Report, 'bio/appl/clustalw/report'
253
- #end
254
-
255
- autoload :MAFFT, 'bio/appl/mafft'
256
- ## below are described in bio/appl/mafft.rb
257
- #class MAFFT
258
- # autoload :Report, 'bio/appl/mafft/report'
259
- #end
260
-
261
- autoload :Tcoffee, 'bio/appl/tcoffee'
262
- autoload :Muscle, 'bio/appl/muscle'
263
- autoload :Probcons, 'bio/appl/probcons'
264
-
265
- autoload :Sim4, 'bio/appl/sim4'
266
- ## below are described in bio/appl/sim4.rb
267
- #class Sim4
268
- # autoload :Report, 'bio/appl/sim4/report'
269
- #end
270
-
271
- autoload :Spidey, 'bio/appl/spidey/report'
272
- autoload :Blat, 'bio/appl/blat/report'
273
-
274
- module GCG
275
- autoload :Msf, 'bio/appl/gcg/msf'
276
- autoload :Seq, 'bio/appl/gcg/seq'
277
- end
278
-
279
- module Phylip
280
- autoload :PhylipFormat, 'bio/appl/phylip/alignment'
281
- autoload :DistanceMatrix, 'bio/appl/phylip/distance_matrix'
282
- end
283
-
284
- autoload :Iprscan, 'bio/appl/iprscan/report'
285
-
286
- autoload :PAML, 'bio/appl/paml/common'
287
- ## below are described in bio/appl/paml/common.rb
288
- # module PAML
289
- # autoload :Codeml, 'bio/appl/paml/codeml'
290
- # autoload :Baseml, 'bio/appl/paml/baseml'
291
- # autoload :Yn00, 'bio/appl/paml/yn00'
292
- # end
293
-
294
- ### Utilities
295
-
296
- autoload :SiRNA, 'bio/util/sirna'
297
- autoload :ColorScheme, 'bio/util/color_scheme'
298
- autoload :ContingencyTable, 'bio/util/contingency_table'
299
- autoload :RestrictionEnzyme, 'bio/util/restriction_enzyme'
300
-
301
- ### Service libraries
302
- autoload :Command, 'bio/command'
303
-
304
- ### NeXML lib
305
- autoload :NeXML, 'bio/db/nexml'
306
-
307
- ### Provide BioRuby shell 'command' also as 'Bio.command' (like ChemRuby)
308
-
309
- def self.method_missing(*args)
310
- require 'bio/shell'
311
- extend Bio::Shell
312
- public_class_method(*Bio::Shell.private_instance_methods)
313
- if Bio.respond_to?(args.first)
314
- Bio.send(*args)
315
- else
316
- raise NameError
317
- end
318
- end
319
-
320
- end
321
-
@@ -1,69 +0,0 @@
1
- <?xml version="1.0" encoding="ISO-8859-1"?>
2
- <nex:nexml
3
- version="0.9"
4
- generator="eclipse"
5
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
6
- xmlns:xml="http://www.w3.org/XML/1998/namespace"
7
- 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