wwood-bioruby 1.2.11
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- data/README.rdoc +205 -0
- data/README_DEV.rdoc +285 -0
- data/VERSION.yml +4 -0
- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +293 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/lib/bio.rb +306 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +505 -0
- data/lib/bio/appl/blast/ddbj.rb +142 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/genomenet.rb +263 -0
- data/lib/bio/appl/blast/ncbioptions.rb +220 -0
- data/lib/bio/appl/blast/remote.rb +105 -0
- data/lib/bio/appl/blast/report.rb +767 -0
- data/lib/bio/appl/blast/rexml.rb +144 -0
- data/lib/bio/appl/blast/rpsblast.rb +277 -0
- data/lib/bio/appl/blast/wublast.rb +635 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blat/report.rb +530 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta.rb +235 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/gcg/msf.rb +212 -0
- data/lib/bio/appl/gcg/seq.rb +195 -0
- data/lib/bio/appl/genscan/report.rb +552 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/hmmer/report.rb +683 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/paml/baseml.rb +95 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/codeml.rb +242 -0
- data/lib/bio/appl/paml/codeml/rates.rb +67 -0
- data/lib/bio/appl/paml/codeml/report.rb +67 -0
- data/lib/bio/appl/paml/common.rb +348 -0
- data/lib/bio/appl/paml/common_report.rb +38 -0
- data/lib/bio/appl/paml/yn00.rb +103 -0
- data/lib/bio/appl/paml/yn00/report.rb +32 -0
- data/lib/bio/appl/phylip/alignment.rb +133 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/psort/report.rb +542 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +124 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sosui/report.rb +151 -0
- data/lib/bio/appl/spidey/report.rb +593 -0
- data/lib/bio/appl/targetp/report.rb +267 -0
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +231 -0
- data/lib/bio/command.rb +593 -0
- data/lib/bio/compat/features.rb +157 -0
- data/lib/bio/compat/references.rb +128 -0
- data/lib/bio/data/aa.rb +353 -0
- data/lib/bio/data/codontable.rb +722 -0
- data/lib/bio/data/na.rb +223 -0
- data/lib/bio/db.rb +329 -0
- data/lib/bio/db/aaindex.rb +357 -0
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +67 -0
- data/lib/bio/db/biosql/sequence.rb +508 -0
- data/lib/bio/db/embl/common.rb +352 -0
- data/lib/bio/db/embl/embl.rb +500 -0
- data/lib/bio/db/embl/embl_to_biosequence.rb +85 -0
- data/lib/bio/db/embl/format_embl.rb +190 -0
- data/lib/bio/db/embl/sptr.rb +1283 -0
- data/lib/bio/db/embl/swissprot.rb +42 -0
- data/lib/bio/db/embl/trembl.rb +41 -0
- data/lib/bio/db/embl/uniprot.rb +42 -0
- data/lib/bio/db/fantom.rb +597 -0
- data/lib/bio/db/fasta.rb +410 -0
- data/lib/bio/db/fasta/defline.rb +532 -0
- data/lib/bio/db/fasta/fasta_to_biosequence.rb +63 -0
- data/lib/bio/db/fasta/format_fasta.rb +97 -0
- data/lib/bio/db/genbank/common.rb +307 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/format_genbank.rb +187 -0
- data/lib/bio/db/genbank/genbank.rb +250 -0
- data/lib/bio/db/genbank/genbank_to_biosequence.rb +86 -0
- data/lib/bio/db/genbank/genpept.rb +60 -0
- data/lib/bio/db/genbank/refseq.rb +18 -0
- data/lib/bio/db/gff.rb +1846 -0
- data/lib/bio/db/go.rb +481 -0
- data/lib/bio/db/kegg/brite.rb +41 -0
- data/lib/bio/db/kegg/compound.rb +131 -0
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +148 -0
- data/lib/bio/db/kegg/expression.rb +155 -0
- data/lib/bio/db/kegg/genes.rb +263 -0
- data/lib/bio/db/kegg/genome.rb +241 -0
- data/lib/bio/db/kegg/glycan.rb +166 -0
- data/lib/bio/db/kegg/keggtab.rb +357 -0
- data/lib/bio/db/kegg/kgml.rb +256 -0
- data/lib/bio/db/kegg/orthology.rb +136 -0
- data/lib/bio/db/kegg/reaction.rb +82 -0
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +107 -0
- data/lib/bio/db/medline.rb +326 -0
- data/lib/bio/db/nbrf.rb +191 -0
- data/lib/bio/db/newick.rb +658 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +29 -0
- data/lib/bio/db/pdb/atom.rb +77 -0
- data/lib/bio/db/pdb/chain.rb +210 -0
- data/lib/bio/db/pdb/chemicalcomponent.rb +224 -0
- data/lib/bio/db/pdb/model.rb +148 -0
- data/lib/bio/db/pdb/pdb.rb +1911 -0
- data/lib/bio/db/pdb/residue.rb +176 -0
- data/lib/bio/db/pdb/utils.rb +399 -0
- data/lib/bio/db/prosite.rb +597 -0
- data/lib/bio/db/rebase.rb +456 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/db/url.rb +42 -0
- data/lib/bio/feature.rb +139 -0
- data/lib/bio/io/biosql/biodatabase.rb +64 -0
- data/lib/bio/io/biosql/bioentry.rb +29 -0
- data/lib/bio/io/biosql/bioentry_dbxref.rb +11 -0
- data/lib/bio/io/biosql/bioentry_path.rb +12 -0
- data/lib/bio/io/biosql/bioentry_qualifier_value.rb +10 -0
- data/lib/bio/io/biosql/bioentry_reference.rb +10 -0
- data/lib/bio/io/biosql/bioentry_relationship.rb +10 -0
- data/lib/bio/io/biosql/biosequence.rb +11 -0
- data/lib/bio/io/biosql/comment.rb +7 -0
- data/lib/bio/io/biosql/config/database.yml +20 -0
- data/lib/bio/io/biosql/dbxref.rb +13 -0
- data/lib/bio/io/biosql/dbxref_qualifier_value.rb +12 -0
- data/lib/bio/io/biosql/location.rb +32 -0
- data/lib/bio/io/biosql/location_qualifier_value.rb +11 -0
- data/lib/bio/io/biosql/ontology.rb +10 -0
- data/lib/bio/io/biosql/reference.rb +9 -0
- data/lib/bio/io/biosql/seqfeature.rb +32 -0
- data/lib/bio/io/biosql/seqfeature_dbxref.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_path.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_qualifier_value.rb +20 -0
- data/lib/bio/io/biosql/seqfeature_relationship.rb +11 -0
- data/lib/bio/io/biosql/taxon.rb +12 -0
- data/lib/bio/io/biosql/taxon_name.rb +9 -0
- data/lib/bio/io/biosql/term.rb +27 -0
- data/lib/bio/io/biosql/term_dbxref.rb +11 -0
- data/lib/bio/io/biosql/term_path.rb +12 -0
- data/lib/bio/io/biosql/term_relationship.rb +13 -0
- data/lib/bio/io/biosql/term_relationship_term.rb +11 -0
- data/lib/bio/io/biosql/term_synonym.rb +10 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +638 -0
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +163 -0
- data/lib/bio/io/fetch.rb +195 -0
- data/lib/bio/io/flatfile.rb +482 -0
- data/lib/bio/io/flatfile/autodetection.rb +545 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/buffer.rb +237 -0
- data/lib/bio/io/flatfile/index.rb +1381 -0
- data/lib/bio/io/flatfile/indexer.rb +805 -0
- data/lib/bio/io/flatfile/splitter.rb +297 -0
- data/lib/bio/io/higet.rb +73 -0
- data/lib/bio/io/hinv.rb +442 -0
- data/lib/bio/io/keggapi.rb +805 -0
- data/lib/bio/io/ncbirest.rb +733 -0
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +307 -0
- data/lib/bio/io/registry.rb +292 -0
- data/lib/bio/io/soapwsdl.rb +119 -0
- data/lib/bio/io/sql.rb +186 -0
- data/lib/bio/location.rb +867 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +960 -0
- data/lib/bio/reference.rb +602 -0
- data/lib/bio/sequence.rb +456 -0
- data/lib/bio/sequence/aa.rb +152 -0
- data/lib/bio/sequence/adapter.rb +108 -0
- data/lib/bio/sequence/common.rb +310 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/dblink.rb +54 -0
- data/lib/bio/sequence/format.rb +358 -0
- data/lib/bio/sequence/format_raw.rb +23 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +491 -0
- data/lib/bio/shell.rb +44 -0
- data/lib/bio/shell/core.rb +578 -0
- data/lib/bio/shell/demo.rb +146 -0
- data/lib/bio/shell/interface.rb +218 -0
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +71 -0
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +218 -0
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +105 -0
- data/lib/bio/shell/plugin/flatfile.rb +101 -0
- data/lib/bio/shell/plugin/keggapi.rb +181 -0
- data/lib/bio/shell/plugin/midi.rb +430 -0
- data/lib/bio/shell/plugin/obda.rb +45 -0
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +247 -0
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +102 -0
- data/lib/bio/tree.rb +852 -0
- data/lib/bio/util/color_scheme.rb +191 -0
- data/lib/bio/util/color_scheme/buried.rb +59 -0
- data/lib/bio/util/color_scheme/helix.rb +59 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +64 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +31 -0
- data/lib/bio/util/color_scheme/strand.rb +59 -0
- data/lib/bio/util/color_scheme/taylor.rb +50 -0
- data/lib/bio/util/color_scheme/turn.rb +59 -0
- data/lib/bio/util/color_scheme/zappo.rb +50 -0
- data/lib/bio/util/contingency_table.rb +370 -0
- data/lib/bio/util/restriction_enzyme.rb +228 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
- data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +200 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/aaindex/DAYM780301 +30 -0
- data/test/data/aaindex/PRAM900102 +20 -0
- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
- data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
- data/test/data/blast/2.2.15.blastp.m7 +876 -0
- data/test/data/blast/b0002.faa +15 -0
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- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/blast/blastp-multi.m7 +188 -0
- data/test/data/command/echoarg2.bat +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/embl/AB090716.embl.rel89 +63 -0
- data/test/data/fasta/example1.txt +75 -0
- data/test/data/fasta/example2.txt +21 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/paml/codeml/control_file.txt +30 -0
- data/test/data/paml/codeml/output.txt +78 -0
- data/test/data/paml/codeml/rates +217 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/rpsblast/misc.rpsblast +193 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/functional/bio/appl/test_pts1.rb +115 -0
- data/test/functional/bio/io/test_ensembl.rb +229 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -0
- data/test/functional/bio/sequence/test_output_embl.rb +51 -0
- data/test/functional/bio/test_command.rb +301 -0
- data/test/runner.rb +14 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_ncbioptions.rb +112 -0
- data/test/unit/bio/appl/blast/test_report.rb +1135 -0
- data/test/unit/bio/appl/blast/test_rpsblast.rb +398 -0
- data/test/unit/bio/appl/genscan/test_report.rb +182 -0
- data/test/unit/bio/appl/hmmer/test_report.rb +342 -0
- data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
- data/test/unit/bio/appl/mafft/test_report.rb +63 -0
- data/test/unit/bio/appl/paml/codeml/test_rates.rb +45 -0
- data/test/unit/bio/appl/paml/codeml/test_report.rb +45 -0
- data/test/unit/bio/appl/paml/test_codeml.rb +174 -0
- data/test/unit/bio/appl/sosui/test_report.rb +81 -0
- data/test/unit/bio/appl/targetp/test_report.rb +146 -0
- data/test/unit/bio/appl/test_blast.rb +277 -0
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_psort.rb +57 -0
- data/test/unit/bio/appl/test_pts1.rb +77 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +126 -0
- data/test/unit/bio/data/test_aa.rb +90 -0
- data/test/unit/bio/data/test_codontable.rb +107 -0
- data/test/unit/bio/data/test_na.rb +80 -0
- data/test/unit/bio/db/embl/test_common.rb +117 -0
- data/test/unit/bio/db/embl/test_embl.rb +214 -0
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +203 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1812 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +31 -0
- data/test/unit/bio/db/kegg/test_genes.rb +45 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +152 -0
- data/test/unit/bio/db/test_aaindex.rb +197 -0
- data/test/unit/bio/db/test_fasta.rb +250 -0
- data/test/unit/bio/db/test_gff.rb +1190 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_medline.rb +127 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +364 -0
- data/test/unit/bio/db/test_prosite.rb +1437 -0
- data/test/unit/bio/db/test_rebase.rb +101 -0
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/db/test_url.rb +36 -0
- data/test/unit/bio/io/flatfile/test_autodetection.rb +375 -0
- data/test/unit/bio/io/flatfile/test_buffer.rb +251 -0
- data/test/unit/bio/io/flatfile/test_splitter.rb +369 -0
- data/test/unit/bio/io/test_ddbjxml.rb +80 -0
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +42 -0
- data/test/unit/bio/io/test_flatfile.rb +505 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +115 -0
- data/test/unit/bio/sequence/test_common.rb +373 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -0
- data/test/unit/bio/sequence/test_dblink.rb +58 -0
- data/test/unit/bio/sequence/test_na.rb +330 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +185 -0
- data/test/unit/bio/test_alignment.rb +1025 -0
- data/test/unit/bio/test_command.rb +349 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +144 -0
- data/test/unit/bio/test_location.rb +599 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +499 -0
- data/test/unit/bio/test_reference.rb +252 -0
- data/test/unit/bio/test_sequence.rb +329 -0
- data/test/unit/bio/test_shell.rb +18 -0
- data/test/unit/bio/test_tree.rb +593 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +101 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
- data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
- data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
- data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
- data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
- data/test/unit/bio/util/test_color_scheme.rb +33 -0
- data/test/unit/bio/util/test_contingency_table.rb +94 -0
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +245 -0
- metadata +543 -0
@@ -0,0 +1,50 @@
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#
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# bio/util/color_scheme/taylor.rb - Taylor color codings for amino acids
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#
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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# License:: The Ruby License
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#
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# $Id: taylor.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
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#
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require 'bio/util/color_scheme'
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module Bio::ColorScheme
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class Taylor < Simple #:nodoc:
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#########
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protected
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#########
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@colors = {
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'A' => 'CCFF00',
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'C' => 'FFFF00',
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'D' => 'FF0000',
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'E' => 'FF0066',
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'F' => '00FF66',
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'G' => 'FF9900',
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'H' => '0066FF',
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'I' => '66FF00',
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'K' => '6600FF',
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'L' => '33FF00',
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'M' => '00FF00',
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'N' => 'CC00FF',
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'P' => 'FFCC00',
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'Q' => 'FF00CC',
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'R' => '0000FF',
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'S' => 'FF3300',
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'T' => 'FF6600',
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'U' => 'FFFFFF',
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'V' => '99FF00',
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'W' => '00CCFF',
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'Y' => '00FFCC',
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'B' => 'FFFFFF',
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'X' => 'FFFFFF',
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'Z' => 'FFFFFF',
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}
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@colors.default = 'FFFFFF' # return white by default
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end
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end
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#
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# bio/util/color_scheme/turn.rb - Color codings for turn propensity
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#
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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# License:: The Ruby License
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#
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# $Id: turn.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
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#
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require 'bio/util/color_scheme'
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module Bio::ColorScheme
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class Turn < Score #:nodoc:
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#########
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protected
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#########
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def self.score_to_rgb_hex(score, min, max)
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percent = score_to_percent(score, min, max)
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rgb_percent_to_hex(percent, 1.0-percent, 1.0-percent)
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end
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@colors = {}
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@scores = {
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'A' => 0.66,
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'C' => 1.19,
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'D' => 1.46,
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'E' => 0.74,
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'F' => 0.6,
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'G' => 1.56,
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'H' => 0.95,
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'I' => 0.47,
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'K' => 1.01,
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'L' => 0.59,
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'M' => 0.6,
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'N' => 1.56,
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'P' => 1.52,
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'Q' => 0.98,
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'R' => 0.95,
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'S' => 1.43,
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'T' => 0.96,
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'U' => 0,
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'V' => 0.5,
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'W' => 0.96,
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'Y' => 1.14,
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'B' => 1.51,
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'X' => 1.0,
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'Z' => 0.86,
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}
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@min = 0.47
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@max = 1.56
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@scores.each { |k,s| @colors[k] = score_to_rgb_hex(s, @min, @max) }
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@colors.default = 'FFFFFF' # return white by default
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end
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end
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#
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# bio/util/color_scheme/zappo.rb - Zappo color codings for amino acids
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#
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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# License:: The Ruby License
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#
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# $Id: zappo.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
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#
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require 'bio/util/color_scheme'
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module Bio::ColorScheme
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class Zappo < Simple #:nodoc:
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#########
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protected
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#########
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@colors = {
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'A' => 'FFAFAF',
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'C' => 'FFFF00',
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'D' => 'FF0000',
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'E' => 'FF0000',
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'F' => 'FFC800',
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'G' => 'FF00FF',
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'H' => 'FF0000',
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'I' => 'FFAFAF',
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'K' => '6464FF',
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'L' => 'FFAFAF',
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'M' => 'FFAFAF',
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'N' => '00FF00',
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'P' => 'FF00FF',
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'Q' => '00FF00',
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'R' => '6464FF',
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'S' => '00FF00',
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'T' => '00FF00',
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'U' => 'FFFFFF',
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'V' => 'FFAFAF',
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'W' => 'FFC800',
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'Y' => 'FFC800',
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'B' => 'FFFFFF',
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'X' => 'FFFFFF',
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'Z' => 'FFFFFF',
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}
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@colors.default = 'FFFFFF' # return white by default
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end
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end
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#
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# bio/util/contingency_table.rb - Statistical contingency table analysis for aligned sequences
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#
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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# License:: The Ruby License
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#
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# $Id: contingency_table.rb,v 1.7 2007/04/05 23:35:41 trevor Exp $
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#
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module Bio #:nodoc:
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#
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# bio/util/contingency_table.rb - Statistical contingency table analysis for aligned sequences
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#
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
|
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# License:: The Ruby License
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#
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# = Description
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#
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# The Bio::ContingencyTable class provides basic statistical contingency table
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# analysis for two positions within aligned sequences.
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#
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# When ContingencyTable is instantiated the set of characters in the
|
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# aligned sequences may be passed to it as an array. This is
|
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# important since it uses these characters to create the table's rows
|
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# and columns. If this array is not passed it will use it's default
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# of an amino acid and nucleotide alphabet in lowercase along with the
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# clustal spacer '-'.
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#
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# To get data from the table the most used functions will be
|
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# chi_square and contingency_coefficient:
|
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#
|
35
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# ctable = Bio::ContingencyTable.new()
|
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# ctable['a']['t'] += 1
|
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# # .. put more values into the table
|
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# puts ctable.chi_square
|
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# puts ctable.contingency_coefficient # between 0.0 and 1.0
|
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#
|
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# The contingency_coefficient represents the degree of correlation of
|
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# change between two sequence positions in a multiple-sequence
|
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# alignment. 0.0 indicates no correlation, 1.0 is the maximum
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# correlation.
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#
|
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#
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# = Further Reading
|
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#
|
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# * http://en.wikipedia.org/wiki/Contingency_table
|
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# * http://www.physics.csbsju.edu/stats/exact.details.html
|
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# * Numerical Recipes in C by Press, Flannery, Teukolsky, and Vetterling
|
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#
|
53
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# = Usage
|
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#
|
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# What follows is an example of ContingencyTable in typical usage
|
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# analyzing results from a clustal alignment.
|
57
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#
|
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# require 'bio'
|
59
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#
|
60
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# seqs = {}
|
61
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# max_length = 0
|
62
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# Bio::ClustalW::Report.new( IO.read('sample.aln') ).to_a.each do |entry|
|
63
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# data = entry.data.strip
|
64
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# seqs[entry.definition] = data.downcase
|
65
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# max_length = data.size if max_length == 0
|
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# raise "Aligned sequences must be the same length!" unless data.size == max_length
|
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# end
|
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#
|
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# VERBOSE = true
|
70
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# puts "i\tj\tchi_square\tcontingency_coefficient" if VERBOSE
|
71
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# correlations = {}
|
72
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#
|
73
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# 0.upto(max_length - 1) do |i|
|
74
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# (i+1).upto(max_length - 1) do |j|
|
75
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+
# ctable = Bio::ContingencyTable.new()
|
76
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# seqs.each_value { |seq| ctable.table[ seq[i].chr ][ seq[j].chr ] += 1 }
|
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#
|
78
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# chi_square = ctable.chi_square
|
79
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# contingency_coefficient = ctable.contingency_coefficient
|
80
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# puts [(i+1), (j+1), chi_square, contingency_coefficient].join("\t") if VERBOSE
|
81
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#
|
82
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# correlations["#{i+1},#{j+1}"] = contingency_coefficient
|
83
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# correlations["#{j+1},#{i+1}"] = contingency_coefficient # Both ways are accurate
|
84
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+
# end
|
85
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+
# end
|
86
|
+
#
|
87
|
+
# require 'yaml'
|
88
|
+
# File.new('results.yml', 'a+') { |f| f.puts correlations.to_yaml }
|
89
|
+
#
|
90
|
+
#
|
91
|
+
# = Tutorial
|
92
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+
#
|
93
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+
# ContingencyTable returns the statistical significance of change
|
94
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+
# between two positions in an alignment. If you would like to see how
|
95
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+
# every possible combination of positions in your alignment compares
|
96
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+
# to one another you must set this up yourself. Hopefully the
|
97
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# provided examples will help you get started without too much
|
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# trouble.
|
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#
|
100
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# def lite_example(sequences, max_length, characters)
|
101
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+
#
|
102
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+
# %w{i j chi_square contingency_coefficient}.each { |x| print x.ljust(12) }
|
103
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+
# puts
|
104
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+
#
|
105
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# 0.upto(max_length - 1) do |i|
|
106
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+
# (i+1).upto(max_length - 1) do |j|
|
107
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+
# ctable = Bio::ContingencyTable.new( characters )
|
108
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+
# sequences.each do |seq|
|
109
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+
# i_char = seq[i].chr
|
110
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+
# j_char = seq[j].chr
|
111
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+
# ctable.table[i_char][j_char] += 1
|
112
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+
# end
|
113
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# chi_square = ctable.chi_square
|
114
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# contingency_coefficient = ctable.contingency_coefficient
|
115
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+
# [(i+1), (j+1), chi_square, contingency_coefficient].each { |x| print x.to_s.ljust(12) }
|
116
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+
# puts
|
117
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+
# end
|
118
|
+
# end
|
119
|
+
#
|
120
|
+
# end
|
121
|
+
#
|
122
|
+
# allowed_letters = Array.new
|
123
|
+
# allowed_letters = 'abcdefghijk'.split('')
|
124
|
+
#
|
125
|
+
# seqs = Array.new
|
126
|
+
# seqs << 'abcde'
|
127
|
+
# seqs << 'abcde'
|
128
|
+
# seqs << 'aacje'
|
129
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+
# seqs << 'aacae'
|
130
|
+
#
|
131
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+
# length_of_every_sequence = seqs[0].size # 5 letters long
|
132
|
+
#
|
133
|
+
# lite_example(seqs, length_of_every_sequence, allowed_letters)
|
134
|
+
#
|
135
|
+
#
|
136
|
+
# Producing the following results:
|
137
|
+
#
|
138
|
+
# i j chi_square contingency_coefficient
|
139
|
+
# 1 2 0.0 0.0
|
140
|
+
# 1 3 0.0 0.0
|
141
|
+
# 1 4 0.0 0.0
|
142
|
+
# 1 5 0.0 0.0
|
143
|
+
# 2 3 0.0 0.0
|
144
|
+
# 2 4 4.0 0.707106781186548
|
145
|
+
# 2 5 0.0 0.0
|
146
|
+
# 3 4 0.0 0.0
|
147
|
+
# 3 5 0.0 0.0
|
148
|
+
# 4 5 0.0 0.0
|
149
|
+
#
|
150
|
+
# The position i=2 and j=4 has a high contingency coefficient
|
151
|
+
# indicating that the changes at these positions are related. Note
|
152
|
+
# that i and j are arbitrary, this could be represented as i=4 and j=2
|
153
|
+
# since they both refer to position two and position four in the
|
154
|
+
# alignment. Here are some more examples:
|
155
|
+
#
|
156
|
+
# seqs = Array.new
|
157
|
+
# seqs << 'abcde'
|
158
|
+
# seqs << 'abcde'
|
159
|
+
# seqs << 'aacje'
|
160
|
+
# seqs << 'aacae'
|
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|
+
# seqs << 'akcfe'
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162
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+
# seqs << 'akcfe'
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+
#
|
164
|
+
# length_of_every_sequence = seqs[0].size # 5 letters long
|
165
|
+
#
|
166
|
+
# lite_example(seqs, length_of_every_sequence, allowed_letters)
|
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|
+
#
|
168
|
+
#
|
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+
# Results:
|
170
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+
#
|
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|
+
# i j chi_square contingency_coefficient
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172
|
+
# 1 2 0.0 0.0
|
173
|
+
# 1 3 0.0 0.0
|
174
|
+
# 1 4 0.0 0.0
|
175
|
+
# 1 5 0.0 0.0
|
176
|
+
# 2 3 0.0 0.0
|
177
|
+
# 2 4 12.0 0.816496580927726
|
178
|
+
# 2 5 0.0 0.0
|
179
|
+
# 3 4 0.0 0.0
|
180
|
+
# 3 5 0.0 0.0
|
181
|
+
# 4 5 0.0 0.0
|
182
|
+
#
|
183
|
+
# Here we can see that the strength of the correlation of change has
|
184
|
+
# increased when more data is added with correlated changes at the
|
185
|
+
# same positions.
|
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|
+
#
|
187
|
+
# seqs = Array.new
|
188
|
+
# seqs << 'abcde'
|
189
|
+
# seqs << 'abcde'
|
190
|
+
# seqs << 'kacje' # changed first letter
|
191
|
+
# seqs << 'aacae'
|
192
|
+
# seqs << 'akcfa' # changed last letter
|
193
|
+
# seqs << 'akcfe'
|
194
|
+
#
|
195
|
+
# length_of_every_sequence = seqs[0].size # 5 letters long
|
196
|
+
#
|
197
|
+
# lite_example(seqs, length_of_every_sequence, allowed_letters)
|
198
|
+
#
|
199
|
+
#
|
200
|
+
# Results:
|
201
|
+
#
|
202
|
+
# i j chi_square contingency_coefficient
|
203
|
+
# 1 2 2.4 0.534522483824849
|
204
|
+
# 1 3 0.0 0.0
|
205
|
+
# 1 4 6.0 0.707106781186548
|
206
|
+
# 1 5 0.24 0.196116135138184
|
207
|
+
# 2 3 0.0 0.0
|
208
|
+
# 2 4 12.0 0.816496580927726
|
209
|
+
# 2 5 2.4 0.534522483824849
|
210
|
+
# 3 4 0.0 0.0
|
211
|
+
# 3 5 0.0 0.0
|
212
|
+
# 4 5 2.4 0.534522483824849
|
213
|
+
#
|
214
|
+
# With random changes it becomes more difficult to identify correlated
|
215
|
+
# changes, yet positions two and four still have the highest
|
216
|
+
# correlation as indicated by the contingency coefficient. The best
|
217
|
+
# way to improve the accuracy of your results, as is often the case
|
218
|
+
# with statistics, is to increase the sample size.
|
219
|
+
#
|
220
|
+
#
|
221
|
+
# = A Note on Efficiency
|
222
|
+
#
|
223
|
+
# ContingencyTable is slow. It involves many calculations for even a
|
224
|
+
# seemingly small five-string data set. Even worse, it's very
|
225
|
+
# dependent on matrix traversal, and this is done with two dimensional
|
226
|
+
# hashes which dashes any hope of decent speed.
|
227
|
+
#
|
228
|
+
# Finally, half of the matrix is redundant and positions could be
|
229
|
+
# summed with their companion position to reduce calculations. For
|
230
|
+
# example the positions (5,2) and (2,5) could both have their values
|
231
|
+
# added together and just stored in (2,5) while (5,2) could be an
|
232
|
+
# illegal position. Also, positions (1,1), (2,2), (3,3), etc. will
|
233
|
+
# never be used.
|
234
|
+
#
|
235
|
+
# The purpose of this package is flexibility and education. The code
|
236
|
+
# is short and to the point in aims of achieving that purpose. If the
|
237
|
+
# BioRuby project moves towards C extensions in the future a
|
238
|
+
# professional caliber version will likely be created.
|
239
|
+
#
|
240
|
+
|
241
|
+
class ContingencyTable
|
242
|
+
# Since we're making this math-notation friendly here is the layout of @table:
|
243
|
+
# * @table[row][column]
|
244
|
+
# * @table[i][j]
|
245
|
+
# * @table[y][x]
|
246
|
+
attr_accessor :table
|
247
|
+
attr_reader :characters
|
248
|
+
|
249
|
+
# Create a ContingencyTable that has characters_in_sequence.size rows and
|
250
|
+
# characters_in_sequence.size columns for each row
|
251
|
+
#
|
252
|
+
# ---
|
253
|
+
# *Arguments*
|
254
|
+
# * +characters_in_sequences+: (_optional_) The allowable characters that will be present in the aligned sequences.
|
255
|
+
# *Returns*:: +ContingencyTable+ object to be filled with values and calculated upon
|
256
|
+
def initialize(characters_in_sequences = nil)
|
257
|
+
@characters = ( characters_in_sequences or %w{a c d e f g h i k l m n p q r s t v w y - x u} )
|
258
|
+
tmp = Hash[*@characters.collect { |v| [v, 0] }.flatten]
|
259
|
+
@table = Hash[*@characters.collect { |v| [v, tmp.dup] }.flatten]
|
260
|
+
end
|
261
|
+
|
262
|
+
# Report the sum of all values in a given row
|
263
|
+
#
|
264
|
+
# ---
|
265
|
+
# *Arguments*
|
266
|
+
# * +i+: Row to sum
|
267
|
+
# *Returns*:: +Integer+ sum of row
|
268
|
+
def row_sum(i)
|
269
|
+
total = 0
|
270
|
+
@table[i].each { |k, v| total += v }
|
271
|
+
total
|
272
|
+
end
|
273
|
+
|
274
|
+
# Report the sum of all values in a given column
|
275
|
+
#
|
276
|
+
# ---
|
277
|
+
# *Arguments*
|
278
|
+
# * +j+: Column to sum
|
279
|
+
# *Returns*:: +Integer+ sum of column
|
280
|
+
def column_sum(j)
|
281
|
+
total = 0
|
282
|
+
@table.each { |row_key, column| total += column[j] }
|
283
|
+
total
|
284
|
+
end
|
285
|
+
|
286
|
+
# Report the sum of all values in all columns.
|
287
|
+
#
|
288
|
+
# * This is the same thing as asking for the sum of all values in the table.
|
289
|
+
#
|
290
|
+
# ---
|
291
|
+
# *Arguments*
|
292
|
+
# * _none_
|
293
|
+
# *Returns*:: +Integer+ sum of all columns
|
294
|
+
def column_sum_all
|
295
|
+
total = 0
|
296
|
+
@characters.each { |j| total += column_sum(j) }
|
297
|
+
total
|
298
|
+
end
|
299
|
+
|
300
|
+
# Report the sum of all values in all rows.
|
301
|
+
#
|
302
|
+
# * This is the same thing as asking for the sum of all values in the table.
|
303
|
+
#
|
304
|
+
# ---
|
305
|
+
# *Arguments*
|
306
|
+
# * _none_
|
307
|
+
# *Returns*:: +Integer+ sum of all rows
|
308
|
+
def row_sum_all
|
309
|
+
total = 0
|
310
|
+
@characters.each { |i| total += row_sum(i) }
|
311
|
+
total
|
312
|
+
end
|
313
|
+
alias table_sum_all row_sum_all
|
314
|
+
|
315
|
+
# Calculate _e_, the _expected_ value.
|
316
|
+
#
|
317
|
+
# ---
|
318
|
+
# *Arguments*
|
319
|
+
# * +i+: row
|
320
|
+
# * +j+: column
|
321
|
+
# *Returns*:: +Float+ e(sub:ij) = (r(sub:i)/N) * (c(sub:j))
|
322
|
+
def expected(i, j)
|
323
|
+
(row_sum(i).to_f / table_sum_all) * column_sum(j)
|
324
|
+
end
|
325
|
+
|
326
|
+
# Report the chi square of the entire table
|
327
|
+
#
|
328
|
+
# ---
|
329
|
+
# *Arguments*
|
330
|
+
# * _none_
|
331
|
+
# *Returns*:: +Float+ chi square value
|
332
|
+
def chi_square
|
333
|
+
total = 0
|
334
|
+
c = @characters
|
335
|
+
max = c.size - 1
|
336
|
+
@characters.each do |i| # Loop through every row in the ContingencyTable
|
337
|
+
@characters.each do |j| # Loop through every column in the ContingencyTable
|
338
|
+
total += chi_square_element(i, j)
|
339
|
+
end
|
340
|
+
end
|
341
|
+
total
|
342
|
+
end
|
343
|
+
|
344
|
+
# Report the chi-square relation of two elements in the table
|
345
|
+
#
|
346
|
+
# ---
|
347
|
+
# *Arguments*
|
348
|
+
# * +i+: row
|
349
|
+
# * +j+: column
|
350
|
+
# *Returns*:: +Float+ chi-square of an intersection
|
351
|
+
def chi_square_element(i, j)
|
352
|
+
eij = expected(i, j)
|
353
|
+
return 0 if eij == 0
|
354
|
+
( @table[i][j] - eij )**2 / eij
|
355
|
+
end
|
356
|
+
|
357
|
+
# Report the contingency coefficient of the table
|
358
|
+
#
|
359
|
+
# ---
|
360
|
+
# *Arguments*
|
361
|
+
# * _none_
|
362
|
+
# *Returns*:: +Float+ contingency_coefficient of the table
|
363
|
+
def contingency_coefficient
|
364
|
+
c_s = chi_square
|
365
|
+
Math.sqrt(c_s / (table_sum_all + c_s) )
|
366
|
+
end
|
367
|
+
|
368
|
+
end # ContingencyTable
|
369
|
+
end # Bio
|
370
|
+
|