bio 1.3.1 → 1.4.0

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Files changed (303) hide show
  1. data/ChangeLog +2105 -3728
  2. data/KNOWN_ISSUES.rdoc +35 -3
  3. data/README.rdoc +8 -2
  4. data/RELEASE_NOTES.rdoc +166 -0
  5. data/bin/bioruby +4 -1
  6. data/bioruby.gemspec +146 -1
  7. data/bioruby.gemspec.erb +3 -1
  8. data/doc/ChangeLog-before-1.3.1 +3961 -0
  9. data/doc/Tutorial.rd +154 -22
  10. data/doc/Tutorial.rd.html +125 -68
  11. data/lib/bio.rb +21 -6
  12. data/lib/bio/appl/bl2seq/report.rb +11 -202
  13. data/lib/bio/appl/blast/format0.rb +0 -193
  14. data/lib/bio/appl/blast/report.rb +2 -147
  15. data/lib/bio/appl/blast/wublast.rb +0 -208
  16. data/lib/bio/appl/fasta.rb +4 -19
  17. data/lib/bio/appl/fasta/format10.rb +0 -14
  18. data/lib/bio/appl/genscan/report.rb +0 -176
  19. data/lib/bio/appl/hmmer.rb +1 -15
  20. data/lib/bio/appl/hmmer/report.rb +0 -100
  21. data/lib/bio/appl/meme/mast.rb +156 -0
  22. data/lib/bio/appl/meme/mast/report.rb +91 -0
  23. data/lib/bio/appl/meme/motif.rb +48 -0
  24. data/lib/bio/appl/psort.rb +0 -111
  25. data/lib/bio/appl/psort/report.rb +1 -45
  26. data/lib/bio/appl/pts1.rb +2 -4
  27. data/lib/bio/appl/sosui/report.rb +5 -54
  28. data/lib/bio/appl/targetp/report.rb +1 -104
  29. data/lib/bio/appl/tmhmm/report.rb +0 -36
  30. data/lib/bio/command.rb +94 -10
  31. data/lib/bio/data/aa.rb +1 -77
  32. data/lib/bio/data/codontable.rb +1 -95
  33. data/lib/bio/data/na.rb +1 -26
  34. data/lib/bio/db/aaindex.rb +1 -38
  35. data/lib/bio/db/fasta.rb +1 -134
  36. data/lib/bio/db/fasta/format_qual.rb +204 -0
  37. data/lib/bio/db/fasta/qual.rb +102 -0
  38. data/lib/bio/db/fastq.rb +645 -0
  39. data/lib/bio/db/fastq/fastq_to_biosequence.rb +40 -0
  40. data/lib/bio/db/fastq/format_fastq.rb +175 -0
  41. data/lib/bio/db/genbank/genbank.rb +1 -86
  42. data/lib/bio/db/gff.rb +0 -17
  43. data/lib/bio/db/go.rb +4 -72
  44. data/lib/bio/db/kegg/common.rb +112 -0
  45. data/lib/bio/db/kegg/compound.rb +29 -20
  46. data/lib/bio/db/kegg/drug.rb +74 -34
  47. data/lib/bio/db/kegg/enzyme.rb +26 -5
  48. data/lib/bio/db/kegg/genes.rb +128 -15
  49. data/lib/bio/db/kegg/genome.rb +3 -41
  50. data/lib/bio/db/kegg/glycan.rb +19 -24
  51. data/lib/bio/db/kegg/orthology.rb +16 -56
  52. data/lib/bio/db/kegg/reaction.rb +81 -28
  53. data/lib/bio/db/kegg/taxonomy.rb +1 -52
  54. data/lib/bio/db/litdb.rb +1 -16
  55. data/lib/bio/db/phyloxml/phyloxml.xsd +582 -0
  56. data/lib/bio/db/phyloxml/phyloxml_elements.rb +1174 -0
  57. data/lib/bio/db/phyloxml/phyloxml_parser.rb +954 -0
  58. data/lib/bio/db/phyloxml/phyloxml_writer.rb +228 -0
  59. data/lib/bio/db/prosite.rb +2 -95
  60. data/lib/bio/db/rebase.rb +5 -6
  61. data/lib/bio/db/sanger_chromatogram/abif.rb +120 -0
  62. data/lib/bio/db/sanger_chromatogram/chromatogram.rb +133 -0
  63. data/lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb +32 -0
  64. data/lib/bio/db/sanger_chromatogram/scf.rb +210 -0
  65. data/lib/bio/io/das.rb +0 -44
  66. data/lib/bio/io/ddbjxml.rb +1 -181
  67. data/lib/bio/io/flatfile.rb +1 -7
  68. data/lib/bio/io/flatfile/autodetection.rb +6 -0
  69. data/lib/bio/io/keggapi.rb +0 -442
  70. data/lib/bio/io/ncbirest.rb +130 -132
  71. data/lib/bio/io/ncbisoap.rb +2 -1
  72. data/lib/bio/io/pubmed.rb +0 -88
  73. data/lib/bio/location.rb +0 -73
  74. data/lib/bio/pathway.rb +0 -171
  75. data/lib/bio/sequence.rb +18 -1
  76. data/lib/bio/sequence/adapter.rb +3 -0
  77. data/lib/bio/sequence/format.rb +16 -0
  78. data/lib/bio/sequence/quality_score.rb +205 -0
  79. data/lib/bio/tree.rb +70 -5
  80. data/lib/bio/util/restriction_enzyme/single_strand.rb +3 -2
  81. data/lib/bio/util/sirna.rb +1 -23
  82. data/lib/bio/version.rb +1 -1
  83. data/sample/demo_aaindex.rb +67 -0
  84. data/sample/demo_aminoacid.rb +101 -0
  85. data/sample/demo_bl2seq_report.rb +220 -0
  86. data/sample/demo_blast_report.rb +285 -0
  87. data/sample/demo_codontable.rb +119 -0
  88. data/sample/demo_das.rb +105 -0
  89. data/sample/demo_ddbjxml.rb +212 -0
  90. data/sample/demo_fasta_remote.rb +51 -0
  91. data/sample/demo_fastaformat.rb +105 -0
  92. data/sample/demo_genbank.rb +132 -0
  93. data/sample/demo_genscan_report.rb +202 -0
  94. data/sample/demo_gff1.rb +49 -0
  95. data/sample/demo_go.rb +98 -0
  96. data/sample/demo_hmmer_report.rb +149 -0
  97. data/sample/demo_kegg_compound.rb +57 -0
  98. data/sample/demo_kegg_drug.rb +65 -0
  99. data/sample/demo_kegg_genome.rb +74 -0
  100. data/sample/demo_kegg_glycan.rb +72 -0
  101. data/sample/demo_kegg_orthology.rb +62 -0
  102. data/sample/demo_kegg_reaction.rb +66 -0
  103. data/sample/demo_kegg_taxonomy.rb +92 -0
  104. data/sample/demo_keggapi.rb +502 -0
  105. data/sample/demo_litdb.rb +42 -0
  106. data/sample/demo_locations.rb +99 -0
  107. data/sample/demo_ncbi_rest.rb +130 -0
  108. data/sample/demo_nucleicacid.rb +49 -0
  109. data/sample/demo_pathway.rb +196 -0
  110. data/sample/demo_prosite.rb +120 -0
  111. data/sample/demo_psort.rb +138 -0
  112. data/sample/demo_psort_report.rb +70 -0
  113. data/sample/demo_pubmed.rb +118 -0
  114. data/sample/demo_sirna.rb +63 -0
  115. data/sample/demo_sosui_report.rb +89 -0
  116. data/sample/demo_targetp_report.rb +135 -0
  117. data/sample/demo_tmhmm_report.rb +68 -0
  118. data/sample/pmfetch.rb +13 -4
  119. data/sample/pmsearch.rb +15 -4
  120. data/sample/test_phyloxml_big.rb +205 -0
  121. data/test/bioruby_test_helper.rb +61 -0
  122. data/test/data/KEGG/1.1.1.1.enzyme +935 -0
  123. data/test/data/KEGG/C00025.compound +102 -0
  124. data/test/data/KEGG/D00063.drug +104 -0
  125. data/test/data/KEGG/G00024.glycan +47 -0
  126. data/test/data/KEGG/G01366.glycan +18 -0
  127. data/test/data/KEGG/K02338.orthology +902 -0
  128. data/test/data/KEGG/R00006.reaction +14 -0
  129. data/test/data/fastq/README.txt +109 -0
  130. data/test/data/fastq/error_diff_ids.fastq +20 -0
  131. data/test/data/fastq/error_double_qual.fastq +22 -0
  132. data/test/data/fastq/error_double_seq.fastq +22 -0
  133. data/test/data/fastq/error_long_qual.fastq +20 -0
  134. data/test/data/fastq/error_no_qual.fastq +20 -0
  135. data/test/data/fastq/error_qual_del.fastq +20 -0
  136. data/test/data/fastq/error_qual_escape.fastq +20 -0
  137. data/test/data/fastq/error_qual_null.fastq +0 -0
  138. data/test/data/fastq/error_qual_space.fastq +21 -0
  139. data/test/data/fastq/error_qual_tab.fastq +21 -0
  140. data/test/data/fastq/error_qual_unit_sep.fastq +20 -0
  141. data/test/data/fastq/error_qual_vtab.fastq +20 -0
  142. data/test/data/fastq/error_short_qual.fastq +20 -0
  143. data/test/data/fastq/error_spaces.fastq +20 -0
  144. data/test/data/fastq/error_tabs.fastq +21 -0
  145. data/test/data/fastq/error_trunc_at_plus.fastq +19 -0
  146. data/test/data/fastq/error_trunc_at_qual.fastq +19 -0
  147. data/test/data/fastq/error_trunc_at_seq.fastq +18 -0
  148. data/test/data/fastq/error_trunc_in_plus.fastq +19 -0
  149. data/test/data/fastq/error_trunc_in_qual.fastq +20 -0
  150. data/test/data/fastq/error_trunc_in_seq.fastq +18 -0
  151. data/test/data/fastq/error_trunc_in_title.fastq +17 -0
  152. data/test/data/fastq/illumina_full_range_as_illumina.fastq +8 -0
  153. data/test/data/fastq/illumina_full_range_as_sanger.fastq +8 -0
  154. data/test/data/fastq/illumina_full_range_as_solexa.fastq +8 -0
  155. data/test/data/fastq/illumina_full_range_original_illumina.fastq +8 -0
  156. data/test/data/fastq/longreads_as_illumina.fastq +40 -0
  157. data/test/data/fastq/longreads_as_sanger.fastq +40 -0
  158. data/test/data/fastq/longreads_as_solexa.fastq +40 -0
  159. data/test/data/fastq/longreads_original_sanger.fastq +120 -0
  160. data/test/data/fastq/misc_dna_as_illumina.fastq +16 -0
  161. data/test/data/fastq/misc_dna_as_sanger.fastq +16 -0
  162. data/test/data/fastq/misc_dna_as_solexa.fastq +16 -0
  163. data/test/data/fastq/misc_dna_original_sanger.fastq +16 -0
  164. data/test/data/fastq/misc_rna_as_illumina.fastq +16 -0
  165. data/test/data/fastq/misc_rna_as_sanger.fastq +16 -0
  166. data/test/data/fastq/misc_rna_as_solexa.fastq +16 -0
  167. data/test/data/fastq/misc_rna_original_sanger.fastq +16 -0
  168. data/test/data/fastq/sanger_full_range_as_illumina.fastq +8 -0
  169. data/test/data/fastq/sanger_full_range_as_sanger.fastq +8 -0
  170. data/test/data/fastq/sanger_full_range_as_solexa.fastq +8 -0
  171. data/test/data/fastq/sanger_full_range_original_sanger.fastq +8 -0
  172. data/test/data/fastq/solexa_full_range_as_illumina.fastq +8 -0
  173. data/test/data/fastq/solexa_full_range_as_sanger.fastq +8 -0
  174. data/test/data/fastq/solexa_full_range_as_solexa.fastq +8 -0
  175. data/test/data/fastq/solexa_full_range_original_solexa.fastq +8 -0
  176. data/test/data/fastq/wrapping_as_illumina.fastq +12 -0
  177. data/test/data/fastq/wrapping_as_sanger.fastq +12 -0
  178. data/test/data/fastq/wrapping_as_solexa.fastq +12 -0
  179. data/test/data/fastq/wrapping_original_sanger.fastq +24 -0
  180. data/test/data/meme/db +0 -0
  181. data/test/data/meme/mast +0 -0
  182. data/test/data/meme/mast.out +13 -0
  183. data/test/data/meme/meme.out +3 -0
  184. data/test/data/phyloxml/apaf.xml +666 -0
  185. data/test/data/phyloxml/bcl_2.xml +2097 -0
  186. data/test/data/phyloxml/made_up.xml +144 -0
  187. data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +65 -0
  188. data/test/data/phyloxml/phyloxml_examples.xml +415 -0
  189. data/test/data/sanger_chromatogram/test_chromatogram_abif.ab1 +0 -0
  190. data/test/data/sanger_chromatogram/test_chromatogram_scf_v2.scf +0 -0
  191. data/test/data/sanger_chromatogram/test_chromatogram_scf_v3.scf +0 -0
  192. data/test/functional/bio/appl/test_pts1.rb +7 -5
  193. data/test/functional/bio/io/test_ensembl.rb +4 -3
  194. data/test/functional/bio/io/test_pubmed.rb +9 -3
  195. data/test/functional/bio/io/test_soapwsdl.rb +5 -4
  196. data/test/functional/bio/io/test_togows.rb +5 -4
  197. data/test/functional/bio/sequence/test_output_embl.rb +6 -4
  198. data/test/functional/bio/test_command.rb +54 -5
  199. data/test/runner.rb +5 -3
  200. data/test/unit/bio/appl/bl2seq/test_report.rb +5 -4
  201. data/test/unit/bio/appl/blast/test_ncbioptions.rb +4 -2
  202. data/test/unit/bio/appl/blast/test_report.rb +5 -4
  203. data/test/unit/bio/appl/blast/test_rpsblast.rb +5 -4
  204. data/test/unit/bio/appl/gcg/test_msf.rb +5 -5
  205. data/test/unit/bio/appl/genscan/test_report.rb +8 -9
  206. data/test/unit/bio/appl/hmmer/test_report.rb +5 -4
  207. data/test/unit/bio/appl/iprscan/test_report.rb +6 -5
  208. data/test/unit/bio/appl/mafft/test_report.rb +6 -5
  209. data/test/unit/bio/appl/meme/mast/test_report.rb +46 -0
  210. data/test/unit/bio/appl/meme/test_mast.rb +103 -0
  211. data/test/unit/bio/appl/meme/test_motif.rb +38 -0
  212. data/test/unit/bio/appl/paml/codeml/test_rates.rb +5 -4
  213. data/test/unit/bio/appl/paml/codeml/test_report.rb +5 -4
  214. data/test/unit/bio/appl/paml/test_codeml.rb +5 -4
  215. data/test/unit/bio/appl/sim4/test_report.rb +5 -4
  216. data/test/unit/bio/appl/sosui/test_report.rb +6 -5
  217. data/test/unit/bio/appl/targetp/test_report.rb +5 -3
  218. data/test/unit/bio/appl/test_blast.rb +5 -4
  219. data/test/unit/bio/appl/test_fasta.rb +4 -2
  220. data/test/unit/bio/appl/test_pts1.rb +4 -2
  221. data/test/unit/bio/appl/tmhmm/test_report.rb +6 -5
  222. data/test/unit/bio/data/test_aa.rb +5 -3
  223. data/test/unit/bio/data/test_codontable.rb +5 -4
  224. data/test/unit/bio/data/test_na.rb +5 -3
  225. data/test/unit/bio/db/biosql/tc_biosql.rb +5 -1
  226. data/test/unit/bio/db/embl/test_common.rb +4 -2
  227. data/test/unit/bio/db/embl/test_embl.rb +6 -6
  228. data/test/unit/bio/db/embl/test_embl_rel89.rb +6 -6
  229. data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +7 -8
  230. data/test/unit/bio/db/embl/test_sptr.rb +6 -8
  231. data/test/unit/bio/db/embl/test_uniprot.rb +6 -5
  232. data/test/unit/bio/db/fasta/test_format_qual.rb +346 -0
  233. data/test/unit/bio/db/kegg/test_compound.rb +146 -0
  234. data/test/unit/bio/db/kegg/test_drug.rb +194 -0
  235. data/test/unit/bio/db/kegg/test_enzyme.rb +241 -0
  236. data/test/unit/bio/db/kegg/test_genes.rb +32 -4
  237. data/test/unit/bio/db/kegg/test_glycan.rb +260 -0
  238. data/test/unit/bio/db/kegg/test_orthology.rb +50 -0
  239. data/test/unit/bio/db/kegg/test_reaction.rb +96 -0
  240. data/test/unit/bio/db/pdb/test_pdb.rb +4 -2
  241. data/test/unit/bio/db/sanger_chromatogram/test_abif.rb +76 -0
  242. data/test/unit/bio/db/sanger_chromatogram/test_scf.rb +98 -0
  243. data/test/unit/bio/db/test_aaindex.rb +6 -6
  244. data/test/unit/bio/db/test_fasta.rb +5 -46
  245. data/test/unit/bio/db/test_fastq.rb +829 -0
  246. data/test/unit/bio/db/test_gff.rb +4 -2
  247. data/test/unit/bio/db/test_lasergene.rb +7 -5
  248. data/test/unit/bio/db/test_medline.rb +4 -2
  249. data/test/unit/bio/db/test_newick.rb +6 -6
  250. data/test/unit/bio/db/test_nexus.rb +4 -2
  251. data/test/unit/bio/db/test_phyloxml.rb +769 -0
  252. data/test/unit/bio/db/test_phyloxml_writer.rb +328 -0
  253. data/test/unit/bio/db/test_prosite.rb +6 -5
  254. data/test/unit/bio/db/test_qual.rb +63 -0
  255. data/test/unit/bio/db/test_rebase.rb +5 -3
  256. data/test/unit/bio/db/test_soft.rb +7 -6
  257. data/test/unit/bio/io/flatfile/test_autodetection.rb +6 -7
  258. data/test/unit/bio/io/flatfile/test_buffer.rb +6 -5
  259. data/test/unit/bio/io/flatfile/test_splitter.rb +4 -4
  260. data/test/unit/bio/io/test_ddbjxml.rb +4 -3
  261. data/test/unit/bio/io/test_ensembl.rb +5 -3
  262. data/test/unit/bio/io/test_fastacmd.rb +4 -3
  263. data/test/unit/bio/io/test_flatfile.rb +6 -5
  264. data/test/unit/bio/io/test_soapwsdl.rb +4 -3
  265. data/test/unit/bio/io/test_togows.rb +4 -2
  266. data/test/unit/bio/sequence/test_aa.rb +5 -3
  267. data/test/unit/bio/sequence/test_common.rb +4 -2
  268. data/test/unit/bio/sequence/test_compat.rb +4 -2
  269. data/test/unit/bio/sequence/test_dblink.rb +5 -3
  270. data/test/unit/bio/sequence/test_na.rb +4 -2
  271. data/test/unit/bio/sequence/test_quality_score.rb +330 -0
  272. data/test/unit/bio/shell/plugin/test_seq.rb +5 -3
  273. data/test/unit/bio/test_alignment.rb +5 -3
  274. data/test/unit/bio/test_command.rb +4 -3
  275. data/test/unit/bio/test_db.rb +5 -3
  276. data/test/unit/bio/test_feature.rb +4 -2
  277. data/test/unit/bio/test_location.rb +4 -2
  278. data/test/unit/bio/test_map.rb +5 -3
  279. data/test/unit/bio/test_pathway.rb +4 -2
  280. data/test/unit/bio/test_reference.rb +4 -2
  281. data/test/unit/bio/test_sequence.rb +5 -3
  282. data/test/unit/bio/test_shell.rb +5 -3
  283. data/test/unit/bio/test_tree.rb +6 -6
  284. data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +4 -2
  285. data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +4 -2
  286. data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +4 -2
  287. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +4 -2
  288. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +4 -2
  289. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +4 -2
  290. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +4 -2
  291. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +4 -2
  292. data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +4 -2
  293. data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +4 -2
  294. data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +4 -2
  295. data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +4 -2
  296. data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +17 -13
  297. data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +17 -13
  298. data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +4 -2
  299. data/test/unit/bio/util/test_color_scheme.rb +5 -3
  300. data/test/unit/bio/util/test_contingency_table.rb +5 -3
  301. data/test/unit/bio/util/test_restriction_enzyme.rb +4 -2
  302. data/test/unit/bio/util/test_sirna.rb +6 -4
  303. metadata +147 -2
data/test/data/phyloxml/made_up.xml ADDED
@@ -0,0 +1,144 @@
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+ <?xml version="1.0" encoding="UTF-8"?>
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+ <phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.00/phyloxml.xsd" xmlns="http://www.phyloxml.org">
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+ <phylogeny rooted="true" rerootable="false" branch_length_unit="1">
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+ <name>testing confidence</name>
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+ <confidence type="bootstrap">89</confidence>
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+ <confidence type="probability">0.71</confidence>
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+ <clade>
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+ <name>b</name>
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+ <width>0.2</width>
10
+ <clade>
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+ <name>c</name>
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+ <confidence type="probability">0.9</confidence>
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+ <confidence type="probability">0.71</confidence>
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+ </clade>
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+ </clade>
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+ </phylogeny>
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+ <phylogeny rooted="true">
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+ <name>testing polygon</name>
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+ <clade>
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+ <clade>
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+ <name>A</name>
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+ <distribution>
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+ <desc>Polygon from random points</desc>
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+ <polygon>
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+ <point geodetic_datum="WGS84" alt_unit="m">
26
+ <lat>47.481277</lat>
27
+ <long>8.769303</long>
28
+ <alt>472</alt>
29
+ </point>
30
+ <point geodetic_datum="WGS84">
31
+ <lat>35.155904</lat>
32
+ <long>136.915863</long>
33
+ <alt>10</alt>
34
+ </point>
35
+ <point geodetic_datum="WGS84">
36
+ <lat>47.376334</lat>
37
+ <long>8.548108</long>
38
+ <alt>452</alt>
39
+ </point>
40
+ </polygon>
41
+ <polygon>
42
+ <point geodetic_datum="WGS84">
43
+ <lat>40.481277</lat>
44
+ <long>8.769303</long>
45
+ <alt>42</alt>
46
+ </point>
47
+ <point geodetic_datum="WGS84">
48
+ <lat>25.155904</lat>
49
+ <long>136.915863</long>
50
+ <alt>10</alt>
51
+ </point>
52
+ <point geodetic_datum="WGS84">
53
+ <lat>47.376334</lat>
54
+ <long>7.548108</long>
55
+ <alt>452</alt>
56
+ </point>
57
+ </polygon>
58
+ </distribution>
59
+ </clade>
60
+ <clade>
61
+ <name>B</name>
62
+ </clade>
63
+ </clade>
64
+ </phylogeny>
65
+ <phylogeny rooted="true">
66
+ <name>testing references</name>
67
+ <clade>
68
+ <clade>
69
+ <name>A</name>
70
+ <reference doi="10.1093/bioinformatics/btm619">
71
+ <desc>Phyutility: a phyloinformatics tool for trees, alignments and molecular data</desc>
72
+ </reference>
73
+ <reference doi="10.1186/1471-2105-9-S1-S23"></reference>
74
+ </clade>
75
+ </clade>
76
+ </phylogeny>
77
+ <phylogeny rooted="true">
78
+ <clade>
79
+ <name>A</name>
80
+ </clade>
81
+ </phylogeny>
82
+ <phylogeny rooted="true">
83
+ <name>Example of domain. Taken from apaf.mxl</name>
84
+ <clade>
85
+ <clade>
86
+ <name>22_MOUSE</name>
87
+ <branch_length>0.05998</branch_length>
88
+ <taxonomy>
89
+ <code>MOUSE</code>
90
+ <synonym>murine</synonym>
91
+ <synonym>vermin</synonym>
92
+ </taxonomy>
93
+ <sequence>
94
+ <annotation>
95
+ <desc>alcohol dehydrogenase</desc>
96
+ <confidence type="probability">0.99</confidence>
97
+ <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m">1200</property>
98
+ </annotation>
99
+ <domain_architecture length="1249">
100
+ <domain from="6" to="90" confidence="7.0E-26" id="x">CARD</domain>
101
+ <domain from="109" to="414" confidence="7.2E-117">NB-ARC</domain>
102
+ <domain from="605" to="643" confidence="2.4E-6">WD40</domain>
103
+ <domain from="647" to="685" confidence="1.1E-12">WD40</domain>
104
+ <domain from="689" to="729" confidence="2.4E-7">WD40</domain>
105
+ <domain from="733" to="771" confidence="4.7E-14">WD40</domain>
106
+ <domain from="872" to="910" confidence="2.5E-8">WD40</domain>
107
+ <domain from="993" to="1031" confidence="4.6E-6">WD40</domain>
108
+ <domain from="1075" to="1113" confidence="6.3E-7">WD40</domain>
109
+ <domain from="1117" to="1155" confidence="1.4E-7">WD40</domain>
110
+ <domain from="1168" to="1204" confidence="0.3">WD40</domain>
111
+ </domain_architecture>
112
+ </sequence>
113
+ </clade>
114
+ </clade>
115
+ </phylogeny>
116
+ <phylogeny rooted="true" rerootable="false">
117
+ <name>dollo_on_domains__cofilin_e1/o_tol_332</name>
118
+ <description>[Method: Dollo parsimony on domain presence/absence] [Date: 2008/08/20 18:23:46] [Cost: 4] [Gains: 2] [Losses: 2] [Unchanged: 1314] [Parameters: E-value: 0.1, Cutoff-scores-file: not-set, Max-overlap: 0, Engulfing-overlaps: not-allowed, Ignore-dufs: false]</description>
119
+ <confidence type="parsimony">4.0</confidence>
120
+ <clade>
121
+ <name>cellular_organisms</name>
122
+ <binary_characters type="parsimony inferred" gained_count="0" lost_count="0" present_count="0">
123
+ </binary_characters>
124
+ <clade>
125
+ <name>Neomura</name>
126
+ <binary_characters type="parsimony inferred" gained_count="0" lost_count="0" present_count="0">
127
+ </binary_characters>
128
+ <clade>
129
+ <name>Eukaryota</name>
130
+ <binary_characters type="parsimony inferred" gained_count="2" lost_count="0" present_count="2">
131
+ <gained>
132
+ <bc>Cofilin_ADF</bc>
133
+ <bc>Gelsolin</bc>
134
+ </gained>
135
+ <present>
136
+ <bc>Cofilin_ADF</bc>
137
+ <bc>Gelsolin</bc>
138
+ </present>
139
+ </binary_characters>
140
+ </clade>
141
+ </clade>
142
+ </clade>
143
+ </phylogeny>
144
+ </phyloxml>
data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml ADDED
@@ -0,0 +1,65 @@
1
+ <?xml version="1.0" encoding="UTF-8"?>
2
+ <phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.00/phyloxml.xsd" xmlns="http://www.phyloxml.org">
3
+ <phylogeny rooted="true">
4
+ <clade>
5
+ <taxonomy>
6
+ <scientific_name>Mollusca</scientific_name>
7
+ </taxonomy>
8
+ <clade>
9
+ <taxonomy>
10
+ <scientific_name>Gastropoda</scientific_name>
11
+ </taxonomy>
12
+ <clade>
13
+ <taxonomy>
14
+ <scientific_name>Orthogastropoda</scientific_name>
15
+ </taxonomy>
16
+ <clade>
17
+ <taxonomy>
18
+ <scientific_name>Vetigastropoda</scientific_name>
19
+ </taxonomy>
20
+ <clade>
21
+ <taxonomy>
22
+ <scientific_name>Haliotoidea</scientific_name>
23
+ </taxonomy>
24
+ <clade>
25
+ <taxonomy>
26
+ <scientific_name>Haliotidae</scientific_name>
27
+ </taxonomy>
28
+ <clade>
29
+ <taxonomy>
30
+ <scientific_name>Sulculus</scientific_name>
31
+ </taxonomy>
32
+ <clade>
33
+ <taxonomy>
34
+ <scientific_name>Sulculus diversicolor</scientific_name>
35
+ </taxonomy>
36
+ </clade>
37
+ </clade>
38
+ </clade>
39
+ </clade>
40
+ </clade>
41
+ </clade>
42
+ <clade>
43
+ <taxonomy>
44
+ <scientific_name>Eogastropoda</scientific_name>
45
+ </taxonomy>
46
+ <clade>
47
+ <taxonomy>
48
+ <scientific_name>Docoglossa</scientific_name>
49
+ </taxonomy>
50
+ </clade>
51
+ </clade>
52
+ </clade>
53
+ <clade>
54
+ <taxonomy>
55
+ <scientific_name>Bivalvia</scientific_name>
56
+ </taxonomy>
57
+ <clade>
58
+ <taxonomy>
59
+ <scientific_name>Heteroconchia</scientific_name>
60
+ </taxonomy>
61
+ </clade>
62
+ </clade>
63
+ </clade>
64
+ </phylogeny>
65
+ </phyloxml>
data/test/data/phyloxml/phyloxml_examples.xml ADDED
@@ -0,0 +1,415 @@
1
+ <?xml version="1.0" encoding="UTF-8"?>
2
+ <phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.00/phyloxml.xsd" xmlns="http://www.phyloxml.org">
3
+ <phylogeny rooted="true">
4
+ <name>example from Prof. Joe Felsenstein's book "Inferring Phylogenies"</name>
5
+ <description>phyloXML allows to use either a "branch_length" attribute or element to indicate branch lengths.</description>
6
+ <clade>
7
+ <clade branch_length="0.06">
8
+ <clade branch_length="0.102">
9
+ <name>A</name>
10
+ </clade>
11
+ <clade branch_length="0.23">
12
+ <name>B</name>
13
+ </clade>
14
+ </clade>
15
+ <clade branch_length="0.4">
16
+ <name>C</name>
17
+ </clade>
18
+ </clade>
19
+ </phylogeny>
20
+ <phylogeny rooted="true">
21
+ <name>example from Prof. Joe Felsenstein's book "Inferring Phylogenies"</name>
22
+ <description>phyloXML allows to use either a "branch_length" attribute or element to indicate branch lengths.</description>
23
+ <clade>
24
+ <clade>
25
+ <branch_length>0.06</branch_length>
26
+ <clade>
27
+ <name>A</name>
28
+ <branch_length>0.102</branch_length>
29
+ </clade>
30
+ <clade>
31
+ <name>B</name>
32
+ <branch_length>0.23</branch_length>
33
+ </clade>
34
+ </clade>
35
+ <clade>
36
+ <name>C</name>
37
+ <branch_length>0.4</branch_length>
38
+ </clade>
39
+ </clade>
40
+ </phylogeny>
41
+ <phylogeny rooted="true">
42
+ <name>same example, with support of type "bootstrap"</name>
43
+ <clade>
44
+ <clade branch_length="0.06">
45
+ <name>AB</name>
46
+ <confidence type="bootstrap">89</confidence>
47
+ <clade branch_length="0.102">
48
+ <name>A</name>
49
+ </clade>
50
+ <clade branch_length="0.23">
51
+ <name>B</name>
52
+ </clade>
53
+ </clade>
54
+ <clade branch_length="0.4">
55
+ <name>C</name>
56
+ </clade>
57
+ </clade>
58
+ </phylogeny>
59
+ <phylogeny rooted="true">
60
+ <name>same example, with species and sequence</name>
61
+ <clade>
62
+ <clade>
63
+ <name>AB</name>
64
+ <clade>
65
+ <name>A</name>
66
+ <taxonomy>
67
+ <scientific_name>E. coli</scientific_name>
68
+ <authority>J. G. Cooper, 1863</authority>
69
+ </taxonomy>
70
+ <sequence>
71
+ <annotation>
72
+ <desc>alcohol dehydrogenase</desc>
73
+ <confidence type="probability">0.99</confidence>
74
+ </annotation>
75
+ </sequence>
76
+ </clade>
77
+ <clade>
78
+ <name>B</name>
79
+ <taxonomy>
80
+ <scientific_name>B. subtilis</scientific_name>
81
+ </taxonomy>
82
+ <sequence>
83
+ <annotation>
84
+ <desc>alcohol dehydrogenase</desc>
85
+ <confidence type="probability">0.91</confidence>
86
+ </annotation>
87
+ </sequence>
88
+ </clade>
89
+ </clade>
90
+ <clade>
91
+ <name>C</name>
92
+ <taxonomy>
93
+ <scientific_name>C. elegans</scientific_name>
94
+ </taxonomy>
95
+ <sequence>
96
+ <annotation>
97
+ <desc>alcohol dehydrogenase</desc>
98
+ <confidence type="probability">0.67</confidence>
99
+ </annotation>
100
+ </sequence>
101
+ </clade>
102
+ </clade>
103
+ </phylogeny>
104
+ <phylogeny rooted="true">
105
+ <name>same example, with gene duplication information and sequence relationships</name>
106
+ <clade>
107
+ <events>
108
+ <speciations>1</speciations>
109
+ </events>
110
+ <clade>
111
+ <events>
112
+ <duplications>1</duplications>
113
+ </events>
114
+ <clade>
115
+ <taxonomy>
116
+ <scientific_name>Bacillus subtilis</scientific_name>
117
+ </taxonomy>
118
+ <sequence id_source="x">
119
+ <symbol>adhB</symbol>
120
+ <accession source="ncbi">AAB80874</accession>
121
+ <name>alcohol dehydrogenase</name>
122
+ </sequence>
123
+ </clade>
124
+ <clade>
125
+ <taxonomy>
126
+ <scientific_name>Bacillus subtilis</scientific_name>
127
+ </taxonomy>
128
+ <sequence id_source="y">
129
+ <symbol>gbsB</symbol>
130
+ <accession source="ncbi">CAB15083</accession>
131
+ <name>alcohol dehydrogenase</name>
132
+ </sequence>
133
+ </clade>
134
+ </clade>
135
+ <clade>
136
+ <taxonomy>
137
+ <scientific_name>Caenorhabditis elegans</scientific_name>
138
+ </taxonomy>
139
+ <sequence id_source="z">
140
+ <symbol>ADHX</symbol>
141
+ <accession source="ncbi">Q17335</accession>
142
+ <name>alcohol dehydrogenase</name>
143
+ <annotation ref="InterPro:IPR002085"/>
144
+ </sequence>
145
+ </clade>
146
+ </clade>
147
+ <sequence_relation id_ref_0="x" id_ref_1="y" type="paralogy"/>
148
+ <sequence_relation id_ref_0="x" id_ref_1="z" type="orthology"/>
149
+ <sequence_relation id_ref_0="y" id_ref_1="z" type="orthology"/>
150
+ </phylogeny>
151
+ <phylogeny rooted="true">
152
+ <name>similar example, with more detailed sequence data</name>
153
+ <clade>
154
+ <clade>
155
+ <clade>
156
+ <taxonomy>
157
+ <id provider="NCBI">6645</id>
158
+ <code>OCTVU</code>
159
+ <scientific_name>Octopus vulgaris</scientific_name>
160
+ </taxonomy>
161
+ <sequence>
162
+ <symbol>ADHX</symbol>
163
+ <accession source="UniProtKB">P81431</accession>
164
+ <name>Alcohol dehydrogenase class-3</name>
165
+ <mol_seq is_aligned="true">TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD</mol_seq>
166
+ <annotation ref="EC:1.1.1.1"/>
167
+ <annotation ref="GO:0004022"/>
168
+ </sequence>
169
+ </clade>
170
+ <clade>
171
+ <taxonomy>
172
+ <id provider="NCBI">44689</id>
173
+ <code>DICDI</code>
174
+ <scientific_name>Dictyostelium discoideum</scientific_name>
175
+ </taxonomy>
176
+ <sequence>
177
+ <symbol>RT4I1</symbol>
178
+ <accession source="UniProtKB">Q54II4</accession>
179
+ <name>Reticulon-4-interacting protein 1 homolog, mitochondrial precursor</name>
180
+ <mol_seq is_aligned="true">MKGILLNGYGESLDLLEYKTDLPVPKPIKSQVLIKIHSTSINPLDNVMRK</mol_seq>
181
+ <annotation ref="GO:0008270"/>
182
+ <annotation ref="GO:0016491"/>
183
+ </sequence>
184
+ </clade>
185
+ </clade>
186
+ <clade>
187
+ <taxonomy>
188
+ <id provider="NCBI">1488</id>
189
+ <code>CLOAB</code>
190
+ <scientific_name>Clostridium acetobutylicum</scientific_name>
191
+ </taxonomy>
192
+ <sequence>
193
+ <symbol>ADHB</symbol>
194
+ <accession source="UniProtKB">Q04945</accession>
195
+ <name>NADH-dependent butanol dehydrogenase B</name>
196
+ <mol_seq is_aligned="true">MVDFEYSIPTRIFFGKDKINVLGRELKKYGSKVLIVYGGGSIKRNGIYDK</mol_seq>
197
+ <annotation ref="GO:0046872"/>
198
+ <annotation ref="KEGG:Tetrachloroethene degradation"/>
199
+ </sequence>
200
+ </clade>
201
+ </clade>
202
+ </phylogeny>
203
+ <phylogeny rooted="false">
204
+ <name>network, node B is connected to TWO nodes: AB and C</name>
205
+ <clade>
206
+ <clade id_source="ab" branch_length="0.06">
207
+ <name>AB</name>
208
+ <clade id_source="a" branch_length="0.102">
209
+ <name>A</name>
210
+ </clade>
211
+ <clade id_source="b" branch_length="0.23">
212
+ <name>B</name>
213
+ </clade>
214
+ </clade>
215
+ <clade id_source="c" branch_length="0.4">
216
+ <name>C</name>
217
+ </clade>
218
+ </clade>
219
+ <clade_relation id_ref_0="b" id_ref_1="c" type="network_connection"/>
220
+ </phylogeny>
221
+ <phylogeny rooted="true">
222
+ <name>same example, using property elements to indicate a "depth" value for marine organisms</name>
223
+ <clade>
224
+ <clade>
225
+ <name>AB</name>
226
+ <clade>
227
+ <name>A</name>
228
+ <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 1200 </property>
229
+ </clade>
230
+ <clade>
231
+ <name>B</name>
232
+ <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 2300 </property>
233
+ </clade>
234
+ </clade>
235
+ <clade>
236
+ <name>C</name>
237
+ <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 200 </property>
238
+ </clade>
239
+ </clade>
240
+ </phylogeny>
241
+ <phylogeny rooted="true">
242
+ <name>same example, using property elements to indicate a "depth" value for marine organisms by using id refs in
243
+ order to have property elements outside of the tree topology</name>
244
+ <clade>
245
+ <clade>
246
+ <name>AB</name>
247
+ <clade id_source="id_a">
248
+ <name>A</name>
249
+ </clade>
250
+ <clade id_source="id_b">
251
+ <name>B</name>
252
+ </clade>
253
+ </clade>
254
+ <clade id_source="id_c">
255
+ <name>C</name>
256
+ </clade>
257
+ </clade>
258
+ <property id_ref="id_a" datatype="xsd:integer" ref="NOAA:depth" applies_to="node" unit="METRIC:m"> 1200 </property>
259
+ <property id_ref="id_b" datatype="xsd:integer" ref="NOAA:depth" applies_to="node" unit="METRIC:m"> 2300 </property>
260
+ <property id_ref="id_c" datatype="xsd:integer" ref="NOAA:depth" applies_to="node" unit="METRIC:m"> 200 </property>
261
+ </phylogeny>
262
+ <phylogeny rooted="true">
263
+ <name>monitor lizards</name>
264
+ <description>a pylogeny of some monitor lizards</description>
265
+ <clade>
266
+ <taxonomy>
267
+ <id provider="NCBI">8556</id>
268
+ <scientific_name>Varanus</scientific_name>
269
+ <rank>genus</rank>
270
+ <uri desc="EMBL REPTILE DATABASE">http://www.embl-heidelberg.de/~uetz/families/Varanidae.html</uri>
271
+ </taxonomy>
272
+ <clade>
273
+ <taxonomy>
274
+ <id provider="NCBI">62046</id>
275
+ <scientific_name>Varanus niloticus</scientific_name>
276
+ <common_name>Nile monitor</common_name>
277
+ <rank>species</rank>
278
+ </taxonomy>
279
+ <distribution>
280
+ <desc>Africa</desc>
281
+ </distribution>
282
+ </clade>
283
+ <clade>
284
+ <taxonomy>
285
+ <scientific_name>Odatria</scientific_name>
286
+ <rank>subgenus</rank>
287
+ </taxonomy>
288
+ <clade>
289
+ <taxonomy>
290
+ <id provider="NCBI">169855</id>
291
+ <scientific_name>Varanus storri</scientific_name>
292
+ <common_name>Storr's monitor</common_name>
293
+ <rank>species</rank>
294
+ </taxonomy>
295
+ <distribution>
296
+ <desc>Australia</desc>
297
+ </distribution>
298
+ </clade>
299
+ <clade>
300
+ <taxonomy>
301
+ <id provider="NCBI">62053</id>
302
+ <scientific_name>Varanus timorensis</scientific_name>
303
+ <common_name>Timor monitor</common_name>
304
+ <rank>species</rank>
305
+ </taxonomy>
306
+ <distribution>
307
+ <desc>Asia</desc>
308
+ </distribution>
309
+ </clade>
310
+ </clade>
311
+ </clade>
312
+ </phylogeny>
313
+ <phylogeny rooted="true">
314
+ <name>A tree with phylogeographic information</name>
315
+ <clade>
316
+ <clade>
317
+ <clade>
318
+ <name>A</name>
319
+ <distribution>
320
+ <desc>Hirschweg, Winterthur, Switzerland</desc>
321
+ <point geodetic_datum="WGS84">
322
+ <lat>47.481277</lat>
323
+ <long>8.769303</long>
324
+ <alt>472</alt>
325
+ </point>
326
+ </distribution>
327
+ </clade>
328
+ <clade>
329
+ <name>B</name>
330
+ <distribution>
331
+ <desc>Nagoya, Aichi, Japan</desc>
332
+ <point geodetic_datum="WGS84">
333
+ <lat>35.155904</lat>
334
+ <long>136.915863</long>
335
+ <alt>10</alt>
336
+ </point>
337
+ </distribution>
338
+ </clade>
339
+ <clade>
340
+ <name>C</name>
341
+ <distribution>
342
+ <desc>ETH Zürich</desc>
343
+ <point geodetic_datum="WGS84">
344
+ <lat>47.376334</lat>
345
+ <long>8.548108</long>
346
+ <alt>452</alt>
347
+ </point>
348
+ </distribution>
349
+ </clade>
350
+ </clade>
351
+ <clade>
352
+ <name>D</name>
353
+ <distribution>
354
+ <desc>San Diego</desc>
355
+ <point geodetic_datum="WGS84">
356
+ <lat>32.880933</lat>
357
+ <long>-117.217543</long>
358
+ <alt>104</alt>
359
+ </point>
360
+ </distribution>
361
+ </clade>
362
+ </clade>
363
+ </phylogeny>
364
+ <phylogeny rooted="true">
365
+ <name>A tree with date information</name>
366
+ <clade>
367
+ <clade>
368
+ <clade>
369
+ <name>A</name>
370
+ <date unit="mya">
371
+ <desc>Silurian</desc>
372
+ <value>425</value>
373
+ </date>
374
+ </clade>
375
+ <clade>
376
+ <name>B</name>
377
+ <date unit="mya">
378
+ <desc>Devonian</desc>
379
+ <value>320</value>
380
+ </date>
381
+ </clade>
382
+ </clade>
383
+ <clade>
384
+ <name>C</name>
385
+ <date unit="mya">
386
+ <desc>Ediacaran</desc>
387
+ <value>600</value>
388
+ <minimum>570</minimum>
389
+ <maximum>630</maximum>
390
+ </date>
391
+ </clade>
392
+ </clade>
393
+ </phylogeny>
394
+ <phylogeny rooted="true">
395
+ <name>Using another XML language to store an alignment</name>
396
+ <clade>
397
+ <clade>
398
+ <clade>
399
+ <name>A</name>
400
+ </clade>
401
+ <clade>
402
+ <name>B</name>
403
+ </clade>
404
+ </clade>
405
+ <clade>
406
+ <name>C</name>
407
+ </clade>
408
+ </clade>
409
+ </phylogeny>
410
+ <align:alignment xmlns:align="http://example.org/align">
411
+ <seq name="A">acgtcgcggcccgtggaagtcctctcct</seq>
412
+ <seq name="B">aggtcgcggcctgtggaagtcctctcct</seq>
413
+ <seq name="C">taaatcgc--cccgtgg-agtccc-cct</seq>
414
+ </align:alignment>
415
+ </phyloxml>