bio 0.7.0
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- data/bin/bioruby +107 -0
- data/bin/br_biofetch.rb +59 -0
- data/bin/br_bioflat.rb +294 -0
- data/bin/br_biogetseq.rb +57 -0
- data/bin/br_pmfetch.rb +431 -0
- data/doc/BioRuby.rd.ja +225 -0
- data/doc/Changes-0.7.rd +236 -0
- data/doc/Design.rd.ja +341 -0
- data/doc/KEGG_API.rd +1437 -0
- data/doc/KEGG_API.rd.ja +1399 -0
- data/doc/TODO.rd.ja +138 -0
- data/doc/Tutorial.rd +1138 -0
- data/doc/Tutorial.rd.ja +2110 -0
- data/etc/bioinformatics/seqdatabase.ini +210 -0
- data/lib/bio.rb +256 -0
- data/lib/bio/alignment.rb +1906 -0
- data/lib/bio/appl/bl2seq/report.rb +350 -0
- data/lib/bio/appl/blast.rb +269 -0
- data/lib/bio/appl/blast/format0.rb +1402 -0
- data/lib/bio/appl/blast/format8.rb +95 -0
- data/lib/bio/appl/blast/report.rb +652 -0
- data/lib/bio/appl/blast/rexml.rb +151 -0
- data/lib/bio/appl/blast/wublast.rb +553 -0
- data/lib/bio/appl/blast/xmlparser.rb +222 -0
- data/lib/bio/appl/blat/report.rb +392 -0
- data/lib/bio/appl/clustalw.rb +191 -0
- data/lib/bio/appl/clustalw/report.rb +154 -0
- data/lib/bio/appl/emboss.rb +68 -0
- data/lib/bio/appl/fasta.rb +262 -0
- data/lib/bio/appl/fasta/format10.rb +428 -0
- data/lib/bio/appl/fasta/format6.rb +37 -0
- data/lib/bio/appl/genscan/report.rb +570 -0
- data/lib/bio/appl/hmmer.rb +129 -0
- data/lib/bio/appl/hmmer/report.rb +556 -0
- data/lib/bio/appl/mafft.rb +222 -0
- data/lib/bio/appl/mafft/report.rb +119 -0
- data/lib/bio/appl/psort.rb +555 -0
- data/lib/bio/appl/psort/report.rb +473 -0
- data/lib/bio/appl/sim4.rb +134 -0
- data/lib/bio/appl/sim4/report.rb +501 -0
- data/lib/bio/appl/sosui/report.rb +166 -0
- data/lib/bio/appl/spidey/report.rb +604 -0
- data/lib/bio/appl/targetp/report.rb +283 -0
- data/lib/bio/appl/tmhmm/report.rb +238 -0
- data/lib/bio/command.rb +166 -0
- data/lib/bio/data/aa.rb +354 -0
- data/lib/bio/data/codontable.rb +740 -0
- data/lib/bio/data/na.rb +226 -0
- data/lib/bio/db.rb +340 -0
- data/lib/bio/db/aaindex.rb +280 -0
- data/lib/bio/db/embl/common.rb +332 -0
- data/lib/bio/db/embl/embl.rb +446 -0
- data/lib/bio/db/embl/sptr.rb +954 -0
- data/lib/bio/db/embl/swissprot.rb +32 -0
- data/lib/bio/db/embl/trembl.rb +31 -0
- data/lib/bio/db/embl/uniprot.rb +32 -0
- data/lib/bio/db/fantom.rb +604 -0
- data/lib/bio/db/fasta.rb +869 -0
- data/lib/bio/db/genbank/common.rb +299 -0
- data/lib/bio/db/genbank/ddbj.rb +34 -0
- data/lib/bio/db/genbank/genbank.rb +354 -0
- data/lib/bio/db/genbank/genpept.rb +73 -0
- data/lib/bio/db/genbank/refseq.rb +31 -0
- data/lib/bio/db/gff.rb +106 -0
- data/lib/bio/db/go.rb +497 -0
- data/lib/bio/db/kegg/brite.rb +51 -0
- data/lib/bio/db/kegg/cell.rb +88 -0
- data/lib/bio/db/kegg/compound.rb +130 -0
- data/lib/bio/db/kegg/enzyme.rb +125 -0
- data/lib/bio/db/kegg/expression.rb +173 -0
- data/lib/bio/db/kegg/genes.rb +293 -0
- data/lib/bio/db/kegg/genome.rb +362 -0
- data/lib/bio/db/kegg/glycan.rb +213 -0
- data/lib/bio/db/kegg/keggtab.rb +418 -0
- data/lib/bio/db/kegg/kgml.rb +299 -0
- data/lib/bio/db/kegg/ko.rb +178 -0
- data/lib/bio/db/kegg/reaction.rb +97 -0
- data/lib/bio/db/litdb.rb +131 -0
- data/lib/bio/db/medline.rb +317 -0
- data/lib/bio/db/nbrf.rb +199 -0
- data/lib/bio/db/pdb.rb +38 -0
- data/lib/bio/db/pdb/atom.rb +60 -0
- data/lib/bio/db/pdb/chain.rb +117 -0
- data/lib/bio/db/pdb/model.rb +106 -0
- data/lib/bio/db/pdb/pdb.rb +1682 -0
- data/lib/bio/db/pdb/residue.rb +122 -0
- data/lib/bio/db/pdb/utils.rb +234 -0
- data/lib/bio/db/prosite.rb +616 -0
- data/lib/bio/db/rebase.rb +417 -0
- data/lib/bio/db/transfac.rb +387 -0
- data/lib/bio/feature.rb +201 -0
- data/lib/bio/io/brdb.rb +103 -0
- data/lib/bio/io/das.rb +471 -0
- data/lib/bio/io/dbget.rb +212 -0
- data/lib/bio/io/ddbjxml.rb +614 -0
- data/lib/bio/io/fastacmd.rb +123 -0
- data/lib/bio/io/fetch.rb +114 -0
- data/lib/bio/io/flatfile.rb +496 -0
- data/lib/bio/io/flatfile/bdb.rb +266 -0
- data/lib/bio/io/flatfile/index.rb +1308 -0
- data/lib/bio/io/flatfile/indexer.rb +778 -0
- data/lib/bio/io/higet.rb +92 -0
- data/lib/bio/io/keggapi.rb +863 -0
- data/lib/bio/io/pubmed.rb +189 -0
- data/lib/bio/io/registry.rb +308 -0
- data/lib/bio/io/soapwsdl.rb +114 -0
- data/lib/bio/io/sql.rb +428 -0
- data/lib/bio/location.rb +650 -0
- data/lib/bio/pathway.rb +991 -0
- data/lib/bio/reference.rb +308 -0
- data/lib/bio/sequence.rb +593 -0
- data/lib/bio/shell.rb +51 -0
- data/lib/bio/shell/core.rb +512 -0
- data/lib/bio/shell/plugin/codon.rb +228 -0
- data/lib/bio/shell/plugin/entry.rb +85 -0
- data/lib/bio/shell/plugin/flatfile.rb +119 -0
- data/lib/bio/shell/plugin/keggapi.rb +187 -0
- data/lib/bio/shell/plugin/midi.rb +448 -0
- data/lib/bio/shell/plugin/obda.rb +63 -0
- data/lib/bio/shell/plugin/seq.rb +238 -0
- data/lib/bio/shell/session.rb +214 -0
- data/lib/bio/util/color_scheme.rb +214 -0
- data/lib/bio/util/color_scheme/buried.rb +78 -0
- data/lib/bio/util/color_scheme/helix.rb +78 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +83 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +50 -0
- data/lib/bio/util/color_scheme/strand.rb +78 -0
- data/lib/bio/util/color_scheme/taylor.rb +69 -0
- data/lib/bio/util/color_scheme/turn.rb +78 -0
- data/lib/bio/util/color_scheme/zappo.rb +69 -0
- data/lib/bio/util/contingency_table.rb +337 -0
- data/lib/bio/util/sirna.rb +306 -0
- data/lib/bioruby.rb +34 -0
- data/sample/biofetch.rb +475 -0
- data/sample/color_scheme_na.rb +99 -0
- data/sample/dbget +37 -0
- data/sample/fasta2tab.rb +99 -0
- data/sample/fsplit.rb +51 -0
- data/sample/gb2fasta.rb +31 -0
- data/sample/gb2tab.rb +325 -0
- data/sample/gbtab2mysql.rb +161 -0
- data/sample/genes2nuc.rb +33 -0
- data/sample/genes2pep.rb +33 -0
- data/sample/genes2tab.rb +81 -0
- data/sample/genome2rb.rb +29 -0
- data/sample/genome2tab.rb +76 -0
- data/sample/goslim.rb +311 -0
- data/sample/gt2fasta.rb +47 -0
- data/sample/pmfetch.rb +42 -0
- data/sample/pmsearch.rb +42 -0
- data/sample/psortplot_html.rb +222 -0
- data/sample/ssearch2tab.rb +96 -0
- data/sample/tdiary.rb +158 -0
- data/sample/tfastx2tab.rb +100 -0
- data/sample/vs-genes.rb +212 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/blast/eco:b0002.faa +15 -0
- data/test/data/blast/eco:b0002.faa.m0 +128 -0
- data/test/data/blast/eco:b0002.faa.m7 +65 -0
- data/test/data/blast/eco:b0002.faa.m8 +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/runner.rb +10 -0
- data/test/unit/bio/appl/blast/test_report.rb +427 -0
- data/test/unit/bio/appl/blast/test_xmlparser.rb +400 -0
- data/test/unit/bio/appl/genscan/test_report.rb +195 -0
- data/test/unit/bio/appl/sosui/test_report.rb +94 -0
- data/test/unit/bio/appl/targetp/test_report.rb +159 -0
- data/test/unit/bio/appl/test_blast.rb +159 -0
- data/test/unit/bio/appl/test_fasta.rb +142 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +139 -0
- data/test/unit/bio/data/test_aa.rb +103 -0
- data/test/unit/bio/data/test_codontable.rb +120 -0
- data/test/unit/bio/data/test_na.rb +89 -0
- data/test/unit/bio/db/embl/test_common.rb +130 -0
- data/test/unit/bio/db/embl/test_embl.rb +227 -0
- data/test/unit/bio/db/embl/test_sptr.rb +268 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +44 -0
- data/test/unit/bio/db/kegg/test_genes.rb +58 -0
- data/test/unit/bio/db/test_fasta.rb +263 -0
- data/test/unit/bio/db/test_gff.rb +140 -0
- data/test/unit/bio/db/test_prosite.rb +1450 -0
- data/test/unit/bio/io/test_ddbjxml.rb +87 -0
- data/test/unit/bio/io/test_soapwsdl.rb +45 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +175 -0
- data/test/unit/bio/test_alignment.rb +1028 -0
- data/test/unit/bio/test_command.rb +71 -0
- data/test/unit/bio/test_db.rb +109 -0
- data/test/unit/bio/test_feature.rb +128 -0
- data/test/unit/bio/test_location.rb +51 -0
- data/test/unit/bio/test_pathway.rb +485 -0
- data/test/unit/bio/test_sequence.rb +386 -0
- data/test/unit/bio/test_shell.rb +31 -0
- data/test/unit/bio/util/test_color_scheme.rb +45 -0
- data/test/unit/bio/util/test_contingency_table.rb +106 -0
- data/test/unit/bio/util/test_sirna.rb +258 -0
- metadata +295 -0
data/doc/KEGG_API.rd.ja
ADDED
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=begin
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$Id: KEGG_API.rd.ja,v 1.7 2005/08/31 13:29:01 k Exp $
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Copyright (C) 2003-2005 Toshiaki Katayama <k@bioruby.org>
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= KEGG API
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KEGG API �ϥץ������ʤɤ��� KEGG �����Ѥ��뤿��Υ����֥����ӥ��Ǥ���
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��Ⱦ�Ǥϡ�KEGG �ǡ����١�������������������긡�������ꤹ�뤿���
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KEGG API ��Ȥ���ˡ���������ޤ�����Ⱦ�Υ�ե���� KEGG API ������ǽ��
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���⤷�ޤ�����Ȥ��Ƽ�� Ruby �����ȤäƲ��⤷�ޤ�����SOAP �� WSDL ��
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�������ȤΤǤ�������Perl, Python, Java �ʤɡˤǤ���д�ñ�� KEGG API ��
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���Ѥ��뤳�Ȥ��Ǥ��ޤ���
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== �ܼ�
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* ((<����ȥ����������>))
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* ((<KEGG API �λȤ���>))
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* ((<Ruby ��>))
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* ((<Perl ��>))
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* ((<Python ��>))
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* ((<Java ��>))
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* ((<KEGG API ��ե����>))
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* ((<WSDL �ե�����>))
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* ((<�Ѹ������>))
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* ((<����ͤΥǡ�����>))
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* ((<SSDBRelation ��>)), ((<ArrayOfSSDBRelation ��>))
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* ((<MotifResult ��>)), ((<ArrayOfMotifResult ��>))
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* ((<Definition ��>)), ((<ArrayOfDefinition ��>))
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* ((<LinkDBRelation ��>)), ((<ArrayOfLinkDBRelation ��>))
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* ((<��åɰ���>))
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* ((<�����>))
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* ((<list_databases>)),
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((<list_organisms>)),
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((<list_pathways>))
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* ((<DBGET>))
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* ((<binfo>)),
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((<bfind>)),
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((<bget>)),
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((<btit>))
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* ((<LinkDB>))
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* ((<get_linkdb_by_entry>))
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* ((<SSDB>))
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* ((<get_best_best_neighbors_by_gene>)),
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((<get_best_neighbors_by_gene>)),
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((<get_reverse_best_neighbors_by_gene>)),
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((<get_paralogs_by_gene>))
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# * ((<get_neighbors_by_gene>)),
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# ((<get_similarity_between_genes>))
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* ((<Motif>))
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* ((<get_motifs_by_gene>)),
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((<get_genes_by_motifs>))
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* ((<KO, OC, PC>))
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* ((<get_ko_by_gene>)),
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((<get_ko_by_ko_class>)),
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((<get_genes_by_ko_class>)),
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((<get_genes_by_ko>)),
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((<get_oc_members_by_gene>)),
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((<get_pc_members_by_gene>))
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# ((<get_ko_members>)),
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* ((<PATHWAY>))
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* ((<mark_pathway_by_objects>)),
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((<color_pathway_by_objects>)),
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((<get_html_of_marked_pathway_by_objects>)),
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((<get_html_of_colored_pathway_by_objects>))
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* ((<get_genes_by_pathway>)),
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((<get_enzymes_by_pathway>)),
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((<get_compounds_by_pathway>)),
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((<get_glycans_by_pathway>)),
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((<get_reactions_by_pathway>)),
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((<get_kos_by_pathway>))
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* ((<get_pathways_by_genes>)),
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((<get_pathways_by_enzymes>)),
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((<get_pathways_by_compounds>)),
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((<get_pathways_by_glycans>)),
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((<get_pathways_by_reactions>)),
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((<get_pathways_by_kos>))
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* ((<get_linked_pathways>))
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* ((<get_genes_by_enzyme>)),
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((<get_enzymes_by_gene>))
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* ((<get_enzymes_by_compound>)),
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((<get_enzymes_by_glycan>)),
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((<get_enzymes_by_reaction>)),
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((<get_compounds_by_enzyme>)),
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((<get_compounds_by_reaction>)),
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((<get_glycans_by_enzyme>)),
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((<get_glycans_by_reaction>)),
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((<get_reactions_by_enzyme>)),
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((<get_reactions_by_compound>)),
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((<get_reactions_by_glycan>))
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* ((<GENES>))
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* ((<get_genes_by_organism>))
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* ((<GENOME>))
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* ((<get_number_of_genes_by_organism>))
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* ((<LIGAND>))
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* ((<convert_mol_to_kcf>))
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== ����ȥ����������
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�����֥����ӥ��Ȥϡ����饤����Ȥ��������ͥåȤ�𤷤ƥ����Ф�
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���ꡢ�����Ф��ץ������μ¹Է�̤饤����Ȥ��֤����Ȥߤǡ�����Ū�ˤ�
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�����֥ڡ����ǻȤ��� HTTP �ץ��ȥ���ȡ���¤����ĥǡ�����ɽ����ˡ�Ȥ���
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��ڤ��Ƥ��� XML �ޡ������å�ʸ��������Ѥ�����Τ�ؤ��ޤ���
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�����֥����ӥ��ϥץ�����फ�����ѤǤ��뤿�ᡢ���Ū�˸�����Ԥä��ꡢ
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���������ͤ��Ѥ����͡������ưŪ�˽��������ꤹ��Τ˸����Ƥ��ޤ���
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���Τ��ᡢ������ŷ��������䤤��碌��Google �ؤ�ʣ�縡���ʤɤǤ�Ȥ���
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���ޤ���
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HTTP ���Ѥ�����åȤˤϡ�ï�Ǥ�Ȥ��뤳�Ȥ�ե�������������ʤɤ����¤�
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�����ˤ������Ȥ����ꡢXML �����ˤϴ�Ϣ���Ѥ�·�äƤ��뤳�Ȥ�ʣ���ʥǡ���
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��¤��ɽ���Ǥ���Ȥ��ä��ݥ���Ȥ�����ޤ���
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�����֥����ӥ��Ǥ� XML ��Ϣ���Ѥ���Ǥ� SOAP �� WSDL ��Ȥ����Ȥ�¿���ʤä�
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���ޤ���SOAP �ϥ��饤����Ȥȥ����Ф����Ȥꤹ���å�������ɽ����ˡ��
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ɸ�ಽ������Τǡ������� Simple Object Access Method ��ά�Ȥ���Ƥ��ޤ���
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(���� Service Oriented Access Protocol �Ȥ������Ȥ⤢��褦�Ǥ�)��
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WSDL �� SOAP �˴�Ť������ӥ���ԥ塼������ñ�����ѤǤ���褦�ˤ���
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����Τ�Τǡ�Web Service Description Language ��ά�ȤʤäƤ��ޤ���
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KEGG API �Ϥ����ε��Ѥ�Ȥäơ���ʬ�ζ�̣��������Ҥ�ѥ��������ʤɤ�
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�����ͳ�˸�����������Ϥ��Ѥ����ꤹ�뤿��μ��ʤ����ޤ����桼����
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KEGG ��¿���ε�ǽ�����֥ڡ�����å���������˼�ʬ�Υץ�������
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�椫�鼡���ȼ¹Ԥ��뤳�Ȥ��Ǥ���褦�ˤʤ�ޤ���
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KEGG API �˴ؤ���ǿ��ξ���ϰʲ��� URL �������뤳�Ȥ��Ǥ��ޤ���
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* ((<URL:http://www.genome.jp/kegg/soap/>))
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+
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131
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+
== KEGG API �λȤ���
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+
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133
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+
�ʲ��Ǥ� Ruby, Perl, Python, Java �γƸ���ˤ�� KEGG API �δ�ñ�ʻȤ�����
|
134
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+
�Ҳ𤷤ޤ����Ƹ���� SOAP �� WSDL ����饤�֥����ɲå��ȡ��뤹��
|
135
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+
ɬ�פ�����ޤ���
|
136
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+
|
137
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+
=== Ruby ��
|
138
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+
|
139
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+
Ruby 1.8.1 �ʹߤǤϡ�ɸ��� SOAP ��Ȥ������Ǥ��ޤ��Τ��ɲå��ȡ�
|
140
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+
���ɬ�פ���ޤ���
|
141
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+
|
142
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+
Ruby 1.8.0 �Ǥ�
|
143
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+
((<SOAP4R|URL:http://raa.ruby-lang.org/list.rhtml?name=soap4r>)),
|
144
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+
((<devel-logger|URL:http://raa.ruby-lang.org/list.rhtml?name=devel-logger>)),
|
145
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+
((<http-access2|URL:http://raa.ruby-lang.org/list.rhtml?name=http-access2>))
|
146
|
+
�ʤɤΥ饤�֥��ȡ��뤹��ɬ�פ�����ޤ���
|
147
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+
|
148
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+
Ruby 1.6.8 �ξ��Ϥ���� SOAP4R ��ɬ�פȤ���¾�Υ饤�֥�� (date2, uconv,
|
149
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+
XML �Υѡ����ʤ�) �⥤�ȡ��뤹��ɬ�פ�����ޤ��Τǡ����餫���� SOAP4R
|
150
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+
�Υɥ�����Ȥ˽��ä�����Ƥ����ޤ���
|
151
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+
|
152
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+
�ʲ��Υ���ץ륳���ɤϡ���IJ�ݤ� b0002 �����ҤȺǤ���Ʊ���ι⤤������
|
153
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+
��Smith-Waterman �������ι⤤��� 5 �ĸ�������ɽ������ץ������Ǥ���
|
154
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+
|
155
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+
#!/usr/bin/env ruby
|
156
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+
|
157
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+
require 'soap/wsdlDriver'
|
158
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+
|
159
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+
wsdl = "http://soap.genome.jp/KEGG.wsdl"
|
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+
serv = SOAP::WSDLDriverFactory.new(wsdl).create_driver
|
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+
serv.generate_explicit_type = true # SOAP �� Ruby �η��Ѵ���ͭ���ˤ���
|
162
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+
|
163
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+
start = 1
|
164
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+
max_results = 5
|
165
|
+
|
166
|
+
top5 = serv.get_best_neighbors_by_gene('eco:b0002', start, max_results)
|
167
|
+
top5.each do |hit|
|
168
|
+
print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
|
169
|
+
end
|
170
|
+
|
171
|
+
�ץ���������� 'get_best_neighbors_by_gene' �ϡ�KEGG �� SSDB �ǡ���
|
172
|
+
�١�����Ȥä� KEGG �� GENES �˴ޤޤ�Ƥ������ʪ����椫��Ǥ���Ʊ��
|
173
|
+
�ι⤤�����Ҥ�õ���Ƥ��� API �Ǥ�����̤ϼ��Τ褦��ɽ������ޤ���
|
174
|
+
|
175
|
+
eco:b0002 eco:b0002 5283
|
176
|
+
eco:b0002 ecj:JW0001 5283
|
177
|
+
eco:b0002 sfx:S0002 5271
|
178
|
+
eco:b0002 sfl:SF0002 5271
|
179
|
+
eco:b0002 ecc:c0003 5269
|
180
|
+
|
181
|
+
���ޤ�ư���ʤ����ϡ�
|
182
|
+
|
183
|
+
serv = SOAP::WSDLDriverFactory.new(wsdl).create_driver
|
184
|
+
serv.wiredump_dev = STDERR # �����ιԤ����
|
185
|
+
serv.generate_explicit_type = true
|
186
|
+
|
187
|
+
�Τ褦�� wiredump_dev �� STDERR ����ꤷ���Ԥ��ɲä��Ƽ¹Ԥ��뤳�Ȥǡ�
|
188
|
+
�����ФȤΤ���꤬ɸ�२�顼�˽��Ϥ���ޤ���
|
189
|
+
|
190
|
+
KEGG API v3.0 ���顢�����Ф���ô��ڤ���������ॢ���Ȥ��ɤ���Ū�ǡ�
|
191
|
+
���̤η�̤��֤���åɤˤ� start, max_results ������Ƴ�����졢���٤�
|
192
|
+
�������̤ο������¤����褦�ˤʤ�ޤ��������Τ��ᡢ�����Υ��
|
193
|
+
�ɤ����Ƥη�̤����뤿��ˤϥ롼�פ��Ѥ���ɬ�פ�����ޤ���
|
194
|
+
|
195
|
+
#!/usr/bin/env ruby
|
196
|
+
|
197
|
+
require 'soap/wsdlDriver'
|
198
|
+
|
199
|
+
wsdl = "http://soap.genome.jp/KEGG.wsdl"
|
200
|
+
serv = SOAP::WSDLDriverFactory.new(wsdl).create_driver
|
201
|
+
serv.generate_explicit_type = true
|
202
|
+
|
203
|
+
start = 1
|
204
|
+
max_results = 100
|
205
|
+
|
206
|
+
loop do
|
207
|
+
results = serv.get_best_neighbors_by_gene('eco:b0002', start, max_results)
|
208
|
+
break unless results # ��̤��֤äƤ��ʤ���н�λ
|
209
|
+
results.each do |hit|
|
210
|
+
print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
|
211
|
+
end
|
212
|
+
start += max_results
|
213
|
+
end
|
214
|
+
|
215
|
+
WSDL ���Ѥ��Ƥ��뤿�ᡢ��������Ǥ� Ruby �ξ��Ͻ�ʬ�˴�ñ�˽�
|
216
|
+
������((<BioRuby|URL:http://bioruby.org/>)) ��Ȥ��Ȥ���˥��å����
|
217
|
+
���Ȥ��Ǥ��ޤ���
|
218
|
+
|
219
|
+
#!/usr/bin/env ruby
|
220
|
+
|
221
|
+
require 'bio'
|
222
|
+
|
223
|
+
serv = Bio::KEGG::API.new
|
224
|
+
|
225
|
+
results = serv.get_all_best_neighbors_by_gene('eco:b0002')
|
226
|
+
results.each do |hit|
|
227
|
+
print hit.genes_id1, "\t", hit.genes_id2, "\t", hit.sw_score, "\n"
|
228
|
+
end
|
229
|
+
|
230
|
+
BioRuby �Ǥ� 'get_all_best_neighbors_by_gene' ��åɤ��������Ƥ��ꡢ
|
231
|
+
��ư�Ǿ嵭����Υ롼�פ�����Ƥη�̤��֤��Ƥ���ޤ����ޤ�������
|
232
|
+
������̾���Υꥹ�Ȥ��Ϥ����б������ͤ�������֤��Ƥ���� filter ���
|
233
|
+
�ɤ�Ȥ����Ȥ�Ǥ��ޤ���
|
234
|
+
|
235
|
+
#!/usr/bin/env ruby
|
236
|
+
|
237
|
+
require 'bio'
|
238
|
+
|
239
|
+
serv = Bio::KEGG::API.new
|
240
|
+
|
241
|
+
results = serv.get_all_best_neighbors_by_gene('eco:b0002')
|
242
|
+
|
243
|
+
# �ߤ����ͤ�������̾�Υڥ��� SW �����������ξ�����
|
244
|
+
fields = [:genes_id1, :genes_id2, :sw_score]
|
245
|
+
results.each do |hit|
|
246
|
+
puts hit.filter(fields).join("\t")
|
247
|
+
end
|
248
|
+
|
249
|
+
# ���줾��ΰ����Ҥǥ��饤���Ȥ��줿�ݥ������ʤɤ�ɽ����������
|
250
|
+
fields1 = [:genes_id1, :start_position1, :end_position1, :best_flag_1to2]
|
251
|
+
fields2 = [:genes_id2, :start_position2, :end_position2, :best_flag_2to1]
|
252
|
+
results.each do |hit|
|
253
|
+
print "> score: ", hit.sw_score, ", identity: ", hit.identity, "\n"
|
254
|
+
print "1:\t", hit.filter(fields1).join("\t"), "\n"
|
255
|
+
print "2:\t", hit.filter(fields2).join("\t"), "\n"
|
256
|
+
end
|
257
|
+
|
258
|
+
���ϡ���IJ�� (eco) ���Ф��� KEGG �ѥ��������ΰ������֤���Ǥ���
|
259
|
+
|
260
|
+
#!/usr/bin/env ruby
|
261
|
+
|
262
|
+
require 'bio'
|
263
|
+
|
264
|
+
serv = Bio::KEGG::API.new
|
265
|
+
|
266
|
+
list = serv.list_pathways("eco")
|
267
|
+
list.each do |path|
|
268
|
+
print path.entry_id, "\t", path.definition, "\n"
|
269
|
+
end
|
270
|
+
|
271
|
+
ArrayOfDefinition �����֤����Τǡ����줾��ˤĤ��� Definition ������
|
272
|
+
�� entry_id (�ѥ���������ID) �� definition (�ѥ��������Υ����ȥ�) ���
|
273
|
+
��Ф��ޤ������ SSDB ����⡢�¤� SSDBRelation �������� genes_id1 ��
|
274
|
+
sw_score �ʤɤ���Ф��Ƥ����ΤǤ����ˡ�
|
275
|
+
|
276
|
+
�Ǹ����ϡ���IJ�ݤΰ����� b1002 �� b2388 ���б�����ܥå����˿����դ�
|
277
|
+
���ѥ������� eco00010 �β������������ơ��ե��������¸������Ǥ���
|
278
|
+
|
279
|
+
#!/usr/bin/env ruby
|
280
|
+
|
281
|
+
require 'bio'
|
282
|
+
|
283
|
+
serv = Bio::KEGG::API.new
|
284
|
+
|
285
|
+
genes = ["eco:b1002", "eco:b2388"]
|
286
|
+
url = serv.mark_pathway_by_objects("path:eco00010", genes)
|
287
|
+
|
288
|
+
puts url
|
289
|
+
|
290
|
+
# BioRuby �ξ�硢���������������¸����Τ� save_image ��åɤ��Ȥ���
|
291
|
+
serv.save_image(url, "filename.gif")
|
292
|
+
|
293
|
+
=== Perl ��
|
294
|
+
|
295
|
+
Perl �Ǥϡ��ʲ��Υ饤�֥����ɲå��ȡ��뤷�Ƥ���ɬ�פ�����ޤ���
|
296
|
+
|
297
|
+
* ((<SOAP::Lite|URL://soaplite.com/>))
|
298
|
+
* ((<MIME-Base64|URL:http://search.cpan.org/author/GAAS/MIME-Base64/>))
|
299
|
+
* ((<libwww-perl|URL:http://search.cpan.org/author/GAAS/libwww-perl/>))
|
300
|
+
* ((<URI|URL:http://search.cpan.org/author/GAAS/URI/>))
|
301
|
+
|
302
|
+
�ʲ���Ruby �κǽ�����Ʊ��������¹Ԥ��륵��ץ륳���ɤǤ���
|
303
|
+
|
304
|
+
#!/usr/bin/env perl
|
305
|
+
|
306
|
+
use SOAP::Lite;
|
307
|
+
|
308
|
+
$wsdl = 'http://soap.genome.jp/KEGG.wsdl';
|
309
|
+
|
310
|
+
$serv = SOAP::Lite -> service($wsdl);
|
311
|
+
|
312
|
+
$start = 1;
|
313
|
+
$max_results = 5;
|
314
|
+
|
315
|
+
$top5 = $serv->get_best_neighbors_by_gene('eco:b0002', $start, $max_results);
|
316
|
+
|
317
|
+
foreach $hit (@{$top5}) {
|
318
|
+
print "$hit->{genes_id1}\t$hit->{genes_id2}\t$hit->{sw_score}\n";
|
319
|
+
}
|
320
|
+
|
321
|
+
Ʊ��������IJ�ݤ� KEGG �ѥ��������Υꥹ�Ȥ��֤���Ǥ���
|
322
|
+
|
323
|
+
#!/usr/bin/env perl
|
324
|
+
|
325
|
+
use SOAP::Lite;
|
326
|
+
|
327
|
+
$wsdl = 'http://soap.genome.jp/KEGG.wsdl';
|
328
|
+
|
329
|
+
$results = SOAP::Lite
|
330
|
+
-> service($wsdl)
|
331
|
+
-> list_pathways("eco");
|
332
|
+
|
333
|
+
foreach $path (@{$results}) {
|
334
|
+
print "$path->{entry_id}\t$path->{definition}\n";
|
335
|
+
}
|
336
|
+
|
337
|
+
SOAP::Lite �Ǥϰ�����������Ϥ����ˤϡ�
|
338
|
+
|
339
|
+
SOAP::Data->type(array => [value1, value2, .. ])
|
340
|
+
|
341
|
+
�Τ褦���Ѵ�����ɬ�פ�����Τ����դ�ɬ�פǤ������Ȥ��Хѥ��������ؤο�
|
342
|
+
�Ť��ǰ����ҤΥꥹ�Ȥ��Ϥ����ϡ�
|
343
|
+
|
344
|
+
#!/usr/bin/env perl
|
345
|
+
|
346
|
+
use SOAP::Lite;
|
347
|
+
|
348
|
+
$wsdl = 'http://soap.genome.jp/KEGG.wsdl';
|
349
|
+
|
350
|
+
$serv = SOAP::Lite -> service($wsdl);
|
351
|
+
|
352
|
+
$genes = SOAP::Data->type(array => ["eco:b1002", "eco:b2388"]);
|
353
|
+
|
354
|
+
$result = $serv -> mark_pathway_by_objects("path:eco00010", $genes);
|
355
|
+
|
356
|
+
print $result;
|
357
|
+
|
358
|
+
�Τ褦�ˤʤ�ޤ���
|
359
|
+
|
360
|
+
|
361
|
+
=== Python ��
|
362
|
+
|
363
|
+
Python �Ǥϰʲ��Υ饤�֥����ɲå��ȡ��뤷�Ƥ���ɬ�פ�����ޤ���
|
364
|
+
|
365
|
+
* ((<SOAPpy|URL:http://pywebsvcs.sourceforge.net/>))
|
366
|
+
|
367
|
+
�ޤ���SOAPpy ����¸���Ƥ��뤤���Ĥ��Υѥå����� (fpconst, PyXML �ʤ�) ��
|
368
|
+
ɬ�פˤʤ�ޤ���
|
369
|
+
|
370
|
+
�ʲ���KEGG/PATHWAY �� 00020 �֤Υѥ��������˺ܤäƤ�����IJ�ݤΰ����Ҥ�
|
371
|
+
�ꥹ�Ȥ��֤�����ץ륳���ɤǤ���
|
372
|
+
|
373
|
+
#!/usr/bin/env python
|
374
|
+
|
375
|
+
from SOAPpy import WSDL
|
376
|
+
|
377
|
+
wsdl = 'http://soap.genome.jp/KEGG.wsdl'
|
378
|
+
serv = WSDL.Proxy(wsdl)
|
379
|
+
|
380
|
+
results = serv.get_genes_by_pathway('path:eco00020')
|
381
|
+
print results
|
382
|
+
|
383
|
+
|
384
|
+
=== Java ��
|
385
|
+
|
386
|
+
Java �Ǥ� Apache Axis �饤�֥��� axis-1.2alpha ��꿷�����С������
|
387
|
+
(axis-1_1 �ǤϤ��ޤ�ư���ޤ���ˤ����ꤷ�ơ�ɬ�פ� jar �ե������Ŭ��
|
388
|
+
�ʥǥ��쥯�ȥ���֤��Ƥ���ɬ�פ�����ޤ���
|
389
|
+
|
390
|
+
* ((<Apache Axis|URL:http://ws.apache.org/axis/>))
|
391
|
+
|
392
|
+
���Ȥ��� Apache Axis �С������ axis-1_2beta �ΥХ��ʥ����ۤξ�硢
|
393
|
+
axis-1_2beta/lib �ʲ��ˤ��� jar �ե�����ȡ�����Υǥ��쥯��
|
394
|
+
��˥��ԡ����ޤ���
|
395
|
+
|
396
|
+
% cp axis-1_2beta/lib/* /path/to/lib/
|
397
|
+
|
398
|
+
�ʲ��Τ褦�˼¹Ԥ��� WSDL ���� KEGG API �ѤΥ��饹��ư�������ޤ���
|
399
|
+
�ޤ����������줿�ե�������Զ���ľ������ˡ�
|
400
|
+
((<axisfix.pl|URL:http://www.genome.jp/kegg/soap/support/axisfix.pl>))
|
401
|
+
������ץȤ����ꤷ�Ƥ����ޤ���
|
402
|
+
|
403
|
+
% java -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/commons-logging.jar:/path/to/lib/commons-discovery.jar:/path/to/lib/saaj.jar:/path/to/lib/wsdl4j.jar:. org.apache.axis.wsdl.WSDL2Java -p keggapi http://soap.genome.jp/KEGG.wsdl
|
404
|
+
% perl -i axisfix.pl keggapi/KEGGBindingStub.java
|
405
|
+
% javac -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/wsdl4j.jar:. keggapi/KEGGLocator.java
|
406
|
+
% jar cvf keggapi.jar keggapi/*
|
407
|
+
% javadoc -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar -d keggapi_javadoc keggapi/*.java
|
408
|
+
|
409
|
+
javadoc �αѸ��Ǥ�ɬ�פʾ��� javadoc �� -locale en_US ���ץ�����
|
410
|
+
�Ĥ��Ƽ¹Ԥ��ޤ���
|
411
|
+
|
412
|
+
�ʲ��ϡ�Python �����Ʊ�ͤˡ����ꤷ�� KEGG/PATHWAY �˺ܤäƤ�������Ҥ�
|
413
|
+
�ꥹ�Ȥ�ɽ�����륵��ץ륳���ɤǤ���
|
414
|
+
|
415
|
+
import keggapi.*;
|
416
|
+
|
417
|
+
class GetGenesByPathway {
|
418
|
+
public static void main(String[] args) throws Exception {
|
419
|
+
KEGGLocator locator = new KEGGLocator();
|
420
|
+
KEGGPortType serv = locator.getKEGGPort();
|
421
|
+
|
422
|
+
String query = args[0];
|
423
|
+
String[] results = serv.get_genes_by_pathway(query);
|
424
|
+
|
425
|
+
for (int i = 0; i < results.length; i++) {
|
426
|
+
System.out.println(results[i]);
|
427
|
+
}
|
428
|
+
}
|
429
|
+
}
|
430
|
+
|
431
|
+
���ϡ�SSDBRelation ����������äƤ�����Ǥ���
|
432
|
+
|
433
|
+
import keggapi.*;
|
434
|
+
|
435
|
+
class GetBestNeighborsByGene {
|
436
|
+
public static void main(String[] args) throws Exception {
|
437
|
+
KEGGLocator locator = new KEGGLocator();
|
438
|
+
KEGGPortType serv = locator.getKEGGPort();
|
439
|
+
|
440
|
+
String query = args[0];
|
441
|
+
SSDBRelation[] results = null;
|
442
|
+
|
443
|
+
results = serv.get_best_neighbors_by_gene(query, 1, 50);
|
444
|
+
|
445
|
+
for (int i = 0; i < results.length; i++) {
|
446
|
+
String gene1 = results[i].getGenes_id1();
|
447
|
+
String gene2 = results[i].getGenes_id2();
|
448
|
+
int score = results[i].getSw_score();
|
449
|
+
System.out.println(gene1 + "\t" + gene2 + "\t" + score);
|
450
|
+
}
|
451
|
+
}
|
452
|
+
}
|
453
|
+
|
454
|
+
���Υץ������ϰʲ��Τ褦�� -classpath ���ץ����� keggapi.jar �ե�
|
455
|
+
�����ä��ƥ���ѥ��롢�¹Ԥ��ޤ���
|
456
|
+
|
457
|
+
% javac -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/wsdl4j.jar:/path/to/keggapi.jar GetBestNeighborsByGene.java
|
458
|
+
|
459
|
+
% java -classpath /path/to/lib/axis.jar:/path/to/lib/jaxrpc.jar:/path/to/lib/commons-logging.jar:/path/to/lib/commons-discovery.jar:/path/to/lib/saaj.jar:/path/to/lib/wsdl4j.jar:/path/to/keggapi.jar:. GetBestNeighborsByGene eco:b0002
|
460
|
+
|
461
|
+
�Ķ��ѿ� CLASSPATH ����ꤷ�Ƥ����ȡ�Ĺ�����ץ���������ɬ�פ���
|
462
|
+
���ʤ�ޤ���
|
463
|
+
|
464
|
+
bash �ޤ��� zsh �ξ�硧
|
465
|
+
|
466
|
+
% for i in /path/to/lib/*.jar
|
467
|
+
do
|
468
|
+
CLASSPATH="${CLASSPATH}:${i}"
|
469
|
+
done
|
470
|
+
% export CLASSPATH
|
471
|
+
|
472
|
+
tcsh �ξ�硧
|
473
|
+
|
474
|
+
% foreach i ( /path/to/lib/*.jar )
|
475
|
+
setenv CLASSPATH ${CLASSPATH}:${i}
|
476
|
+
end
|
477
|
+
|
478
|
+
¾������ͤȷ����Ȥ��ͤμ��Ф����ʤɤˤĤ��Ƥϡ�WSDL2Java �ˤ������
|
479
|
+
���줿�ʲ��Υɥ�����ȤȤ��Ƥ���������
|
480
|
+
|
481
|
+
* ((<URL:http://www.genome.jp/kegg/soap/doc/keggapi_javadoc_ja/>))
|
482
|
+
|
483
|
+
|
484
|
+
== KEGG API ��ե����
|
485
|
+
|
486
|
+
�ʲ��Ǥϡ�KEGG API ��Ȥ��Τ�ɬ�פʾ�������ƤΥ�åɤ���⤷�ޤ���
|
487
|
+
|
488
|
+
=== WSDL �ե�����
|
489
|
+
|
490
|
+
SOAP �Ǥϡ������Ф��ɤΤ褦�ʥ�åɤ���äƤ��뤫�ΤäƤ���ɬ�פ�
|
491
|
+
����ޤ�����WSDL ��Ȥ��Ȥ��μ���ư���Ǥ��ޤ���WSDL �ե������
|
492
|
+
�������ƥ��饤����ȥɥ饤�Ф���������Ȥ����ޤǡ��̾�� SOAP/WSDL ��
|
493
|
+
�饤�֥�꤬�������Ƥ����Ϥ��Ǥ���KEGG API �� WSDL �ե�����ϰʲ���
|
494
|
+
URL �ˤ���ޤ���
|
495
|
+
|
496
|
+
* ((<URL:http://soap.genome.jp/KEGG.wsdl>))
|
497
|
+
|
498
|
+
=== �Ѹ������
|
499
|
+
|
500
|
+
�ʲ��β���ǽФƤ��� KEGG ��Ϣ�Ѹ�������Ƥ����ޤ���
|
501
|
+
|
502
|
+
* org �� KEGG �˴ޤޤ�Ƥ�����ʪ��줾�죳ʸ�������ɤ�
|
503
|
+
ɽ��������Τǡ�eco ����IJ�ݡ�sce ���в����ʤɤȤʤäƤ��ޤ���
|
504
|
+
��ʸ�������ɤΥꥹ�Ȥ� list_organisms ��åɤ�ʲ��Υڡ�����
|
505
|
+
���Ȥ��Ƥ���������
|
506
|
+
|
507
|
+
* ((<URL:http://www.genome.jp/kegg/catalog/org_list.html>))
|
508
|
+
|
509
|
+
* db �� GenomeNet ������Ƥ���ǡ����١���̾�Ǥ����ǡ����١���̾��
|
510
|
+
�ꥹ�ȤˤĤ��Ƥ� list_databases ��åɤȤ��Ƥ���������
|
511
|
+
|
512
|
+
* entry_id �� db_name �ȥ���ȥ�̾�� ':' �Ƿ�礷�����ƤΥǡ����١����֤�
|
513
|
+
��ˡ����� ID �Ǥ������Ȥ��� embl:J00231 �� EMBL �Υ���ȥ� J00231 ��
|
514
|
+
�ؤ��ޤ���entry_id �ϡ��ʲ��� genes_id, enzyme_id, compound_id,
|
515
|
+
glycan_id, reaction_id, pathway_id, motif_id �ʤɤ�ޤߤޤ���
|
516
|
+
|
517
|
+
* genes_id �� keggorg �Ȱ�����̾�� ':' �Ƿ�礷�� KEGG �ΰ����� ID �Ǥ���
|
518
|
+
eco:b0001 ����IJ�ݤΰ����� b0001 ��ؤ��ޤ���
|
519
|
+
|
520
|
+
* enzyme_id �� ec: ��Ĥ��������ֹ�� ID �Ǥ���ec:1.1.1.1 �Ϲ����ֹ�
|
521
|
+
1.1.1.1 �ι��ǤǤ��륢�륳���롦�ǥҥɥ����ʡ�����ؤ��ޤ���
|
522
|
+
|
523
|
+
* compound_id �� cpd: ��Ĥ�������ʪ�� ID �Ǥ���cpd:C00158 �ϲ���ʪ�ֹ�
|
524
|
+
C00158 �β���ʪ�Ǥ��륯�������ؤ��ޤ���
|
525
|
+
|
526
|
+
* glycan_id �� gl: ��Ĥ�������ʪ�� ID �Ǥ���gl:G00050 �������ֹ�
|
527
|
+
G00050 �������Ǥ��� Paragloboside ��ؤ��ޤ���
|
528
|
+
|
529
|
+
* reaction_id �� REACTION �ǡ����١����Υ���ȥ��ֹ�ǡ�rn:R00959 ��
|
530
|
+
�ꥢ��������ֹ� R00959 ��ȿ�� (cpd:C00103 �� cpd:00668 �֤��Ѵ�) ��
|
531
|
+
�ؤ��ޤ���
|
532
|
+
|
533
|
+
* pathway_id �� KEGG/PATHWAY �ǡ����١����Υѥ��������ֹ�ǡ��ѥ�������
|
534
|
+
�ֹ�Υץ�ե��å����� map �ξ��ϥ�ե���ѥ���������keggorg ��
|
535
|
+
���Ϥ�����ʪ��λ��İ����Ҥκܤä��ѥ���������ɽ���ޤ����㤨��
|
536
|
+
path:map00020 �ϥ�ե���ѥ��������� 00020 �֤�path:eco00020 ��
|
537
|
+
��IJ�ݤΥѥ������� 00020 �֤�ؤ��ޤ���
|
538
|
+
|
539
|
+
* motif_id �ϥ�����եǡ����١����Υ���ȥ�̾�ǡ�pf:DnaJ �� Pfam �Υ���ȥ�
|
540
|
+
DnaJ ��ؤ��ޤ���'pf' ��¾��'ps' �� PROSITE, 'bl' �� BLOCS, 'pr' ��
|
541
|
+
PRINTS, 'pd' �� PRODOM ��ؤ��ޤ���
|
542
|
+
|
543
|
+
* ko_id �� KO (KEGG Orthology) �ǡ����١����Υ���ȥ��ֹ�ǡ�ko:K02598
|
544
|
+
�� KO �ֹ� K02598 �� nitrite transporter NirC �Υ������������ʰ�����
|
545
|
+
���롼�פ�ؤ��ޤ���
|
546
|
+
|
547
|
+
* ko_class_id �� KO ����Ū��ʬ�ष���Ƴ��ءʥ��饹�ˤ� ID �ǡ�
|
548
|
+
'01110' �� Carbohydrate Metabolism ���饹�ˤʤ�ޤ���
|
549
|
+
KO ���饹�� KO �ֹ�Υꥹ�Ȥϰʲ��Υڡ����Ȥ��Ƥ���������
|
550
|
+
|
551
|
+
* ((<URL:http://www.genome.jp/dbget-bin/get_htext?KO>))
|
552
|
+
|
553
|
+
* start, max_results �ϰ��٤��֤äƤ����̤ο�����ꤹ�륪�ץ����ǡ�
|
554
|
+
start ���ܤ��� max_results �Ĥη�̤�������ޤ������Ƥη�̤�����ˤ�
|
555
|
+
start = start + max_results �Ȥ��ƶ��������֤äƤ���ޤǷ����֤�
|
556
|
+
��åɤ�ƤӤޤ���
|
557
|
+
|
558
|
+
* fg_color_list �ϥѥ��������ؤο��Ť��ǥ��֥������Ȥ��Ȥ�ʸ����������
|
559
|
+
������ꤹ������Ǥ���
|
560
|
+
|
561
|
+
* fg_color_list �ϥѥ��������ؤο��Ť��ǥ��֥������Ȥ��Ȥ��طʤ�
|
562
|
+
������ꤹ������Ǥ���
|
563
|
+
|
564
|
+
=== ����ͤΥǡ�����
|
565
|
+
|
566
|
+
KEGG API �Υ�åɤ�ʸ����ʤ�ñ����ͤ��֤���Τ����Ǥʤ���ʣ���ʥǡ���
|
567
|
+
��¤����ä��ͤ��֤����⤢�ꡢ���Τ���Υǡ��������������Ƥ��ޤ���
|
568
|
+
API �Υ�åɤˤ��ʸ����ʤɤΡ˷�̤��ʤ��ä���硢���ˤ�äưʲ���
|
569
|
+
����ͤ��֤���ޤ���
|
570
|
+
* �������� -- ��Ȥ�� ArrayOfOBJ �ʥ��֥������Ȥ�����ˤ��֤���åɤξ��
|
571
|
+
* ����ʸ���� -- ��Ȥ�� String ��ʸ����ˤ��֤���åɤξ��
|
572
|
+
* -1 -- ��Ȥ�� int �ʿ��͡ˤ��֤���åɤξ��
|
573
|
+
* NULL -- ��Ȥ�Ȱʲ���������줿���֥������ȤΤɤ줫���֤���åɤξ��
|
574
|
+
|
575
|
+
+ SSDBRelation ��
|
576
|
+
|
577
|
+
SSDB �ǡ����١����γƥե�����ɤ��б������ͤ����ä��ǡ������Ǥ���
|
578
|
+
|
579
|
+
genes_id1 ������� genes_id (string)
|
580
|
+
genes_id2 �������åȤ� genes_id (string)
|
581
|
+
sw_score genes_id1 �� genes_id2 �֤� Smith-Waterman ������ (int)
|
582
|
+
bit_score genes_id1 �� genes_id2 �֤� bit ������ (float)
|
583
|
+
identity genes_id1 �� genes_id2 �֤� �����ǥ�ƥ��ƥ� (float)
|
584
|
+
overlap genes_id1 �� genes_id2 �Υ����С���å��ΰ��Ĺ�� (int)
|
585
|
+
start_position1 genes_id1 �Υ��饤���Ȥγ��ϻĴ���� (int)
|
586
|
+
end_position1 genes_id1 �Υ��饤���Ȥν�ü�Ĵ���� (int)
|
587
|
+
start_position2 genes_id2 �Υ��饤���Ȥγ��ϻĴ���� (int)
|
588
|
+
end_position2 genes_id2 �Υ��饤���Ȥν�ü�Ĵ���� (int)
|
589
|
+
best_flag_1to2 genes_id1 ���鸫�� genes_id2 ���٥��ȥҥåȤ� (boolean)
|
590
|
+
best_flag_2to1 genes_id2 ���鸫�� genes_id1 ���٥��ȥҥåȤ� (boolean)
|
591
|
+
definition1 genes_id1 �Υǥե��˥����ʸ���� (string)
|
592
|
+
definition2 genes_id2 �Υǥե��˥����ʸ���� (string)
|
593
|
+
length1 genes_id1 �Υ��ߥλ������Ĺ�� (int)
|
594
|
+
length2 genes_id2 �Υ��ߥλ������Ĺ�� (int)
|
595
|
+
|
596
|
+
+ ArrayOfSSDBRelation ��
|
597
|
+
|
598
|
+
ʣ���� SSDBRelation ���ǡ�����ޤ�����Ǥ���
|
599
|
+
|
600
|
+
+ MotifResult ��
|
601
|
+
|
602
|
+
motif_id ������եǡ����١����Υ���ȥ� ID (string)
|
603
|
+
definition ������դΥǥե��˥���� (string)
|
604
|
+
genes_id ������դ���äƤ�������Ҥ� genes_id (string)
|
605
|
+
start_position ������դγ��ϻĴ���� (int)
|
606
|
+
end_position ������դν�λ�Ĵ���� (int)
|
607
|
+
score ������� (PROSITE Profile, TIGRFAM) ������ (float)
|
608
|
+
evalue ������� (Pfam) �� E-value (double)
|
609
|
+
|
610
|
+
����score �� evalue �Τ������б������ͤ�̵����ΤˤĤ��Ƥ� -1 ���֤��ޤ���
|
611
|
+
|
612
|
+
+ ArrayOfMotifResult ��
|
613
|
+
|
614
|
+
ʣ���� MotifResult ���ǡ�����ޤ�����Ǥ���
|
615
|
+
|
616
|
+
+ Definition ��
|
617
|
+
|
618
|
+
entry_id �ǡ����١�������ȥ��ID (string)
|
619
|
+
definition ����ȥ�Υǥե��˥������� (string)
|
620
|
+
|
621
|
+
+ ArrayOfDefinition ��
|
622
|
+
|
623
|
+
ʣ���� Definitioin ���ǡ�����ޤ�����Ǥ���
|
624
|
+
|
625
|
+
+ LinkDBRelation ��
|
626
|
+
|
627
|
+
entry_id1 �ǡ����١����Υ���ȥ� ID (string)
|
628
|
+
entry_id2 �ǡ����١����Υ���ȥ� ID (string)
|
629
|
+
type "direct" �ޤ��� "indirect" �Υ�μ��� (string)
|
630
|
+
path ��η�ϩ (string)
|
631
|
+
|
632
|
+
+ ArrayOfLinkDBRelation ��
|
633
|
+
|
634
|
+
ʣ���� LinkDBRelation ���ǡ�����ޤ�����Ǥ���
|
635
|
+
|
636
|
+
=== ��åɰ���
|
637
|
+
|
638
|
+
�ʲ���KEGG API ������åɤΥꥹ�ȤǤ�����åɤˤϥ������֤���Τ�
|
639
|
+
�ƥǡ����١������Ф����Τ�����ޤ������ߡ�KEGG �ˤ���ǡ����١����Τ���
|
640
|
+
KEGG API ���оݤȤʤäƤ����Τ� SSDB, PATHWAY, GENES, LIGAND �Ǥ�������
|
641
|
+
�ʳ��Υǡ����١����ؤ��б����åɤ��ɲä�缡�����ʤ�ͽ��Ǥ���
|
642
|
+
|
643
|
+
�ʲ�����Ǥϡ������ʤɤ� Ruby �����ɽ������äƽ�Ƥ��ޤ������ºݤ�
|
644
|
+
�������ä˥ꥹ�Ȥ��Ϥ����ʤɡˤϻ��Ѥ������ˤ�äưۤʤ��ǽ��������ޤ���
|
645
|
+
|
646
|
+
|
647
|
+
==== �����
|
648
|
+
|
649
|
+
�ǿ��Υǡ����١�������ʤɤ��֤�����Υ�åɤǤ���
|
650
|
+
|
651
|
+
--- list_databases
|
652
|
+
|
653
|
+
KEGG �����Ƥ��륲�Υ�ͥåȤǸ������ѤǤ���ǡ����١����ΰ������֤��ޤ���
|
654
|
+
|
655
|
+
���͡�
|
656
|
+
ArrayOfDefinition (db, definition)
|
657
|
+
|
658
|
+
--- list_organisms
|
659
|
+
|
660
|
+
���� KEGG �˴ޤޤ�Ƥ�����ʪ�� (org) �Υꥹ�Ȥ��֤��ޤ���
|
661
|
+
|
662
|
+
���͡�
|
663
|
+
ArrayOfDefinition (org, definition)
|
664
|
+
|
665
|
+
--- list_pathways(org)
|
666
|
+
|
667
|
+
���� KEGG �˴ޤޤ�Ƥ�����ꤷ����ʪ�Υѥ��������Υꥹ�Ȥ��֤��ޤ���������
|
668
|
+
'map' �Ȥ���ʸ�����Ϳ����ȥ�ե���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
669
|
+
|
670
|
+
���͡�
|
671
|
+
ArrayOfDefinition (pathway_id, definition)
|
672
|
+
|
673
|
+
|
674
|
+
==== DBGET
|
675
|
+
|
676
|
+
DBGET �����ƥ���Ф����åɤΰ����Ǥ���DBGET �ˤĤ��ƾܤ����ϰʲ���
|
677
|
+
�ڡ����Ȥ��Ƥ���������
|
678
|
+
|
679
|
+
* ((<URL:http://www.genome.jp/dbget/dbget_manual.html>))
|
680
|
+
|
681
|
+
--- binfo(string)
|
682
|
+
|
683
|
+
���ꤷ���ǡ����١����Υ���ȥ���乹�����ʤɾܤ����ǿ�������֤��ޤ���
|
684
|
+
'all' ���Ϥ������Ѳ�ǽ�����ƤΥǡ����١����ξ�����֤��ޤ���
|
685
|
+
binfo ���ޥ�ɤؤΰ�����ʸ������Ϥ��ޤ���
|
686
|
+
|
687
|
+
���͡�
|
688
|
+
string
|
689
|
+
|
690
|
+
�㡧
|
691
|
+
# GenBank �ǡ����١����κǿ�����
|
692
|
+
binfo('gb')
|
693
|
+
# ���ƤΥǡ����١����κǿ�����
|
694
|
+
binfo('all')
|
695
|
+
|
696
|
+
--- bfind(string)
|
697
|
+
|
698
|
+
DBGET �� bfind ���ޥ�ɤؤΥ�åѡ��Ǥ���������ɤˤ�ꥨ��ȥ��
|
699
|
+
�������뤳�Ȥ��Ǥ��ޤ������٤�Ϳ�����륭����ɤο��� 100 �İʲ���
|
700
|
+
���¤���Ƥ��ޤ���
|
701
|
+
|
702
|
+
���͡�
|
703
|
+
string
|
704
|
+
|
705
|
+
�㡧
|
706
|
+
# �ǥե��˥����� E-cadherin �� human ����� GenBank �Υ���ȥ��
|
707
|
+
bfind("gb E-cadherin human")
|
708
|
+
|
709
|
+
|
710
|
+
--- bget(string)
|
711
|
+
|
712
|
+
���ꤷ�� entry_id �Υ���ȥ���֤��ޤ���GENES �ΰ����ҥ���ȥ��Ϥ��ᡢ
|
713
|
+
���Υ�ͥåȤ� DBGET �����ƥ������Ƥ����͡��ʥǡ����١���
|
714
|
+
(list_databases ��) �Υ���ȥ�����Ƽ����Ǥ��ޤ���bget ���ޥ�ɤؤ�
|
715
|
+
���ޥ�ɥ饤�ץ�����ʸ������Ϥ��ޤ������٤˼����Ǥ��륨��ȥ��
|
716
|
+
���� 100 �İʲ������¤���Ƥ��ޤ���
|
717
|
+
|
718
|
+
���͡�
|
719
|
+
string
|
720
|
+
|
721
|
+
�㡧
|
722
|
+
# ʣ���Υ���ȥ�����
|
723
|
+
bget("eco:b0002 bsu:BG10065 cpd:C00209")
|
724
|
+
# FASTA �ե����ޥåȤΥ��ߥλ���������
|
725
|
+
bget("-f -n a eco:b0002 bsu:BG10065")
|
726
|
+
# FASTA �ե����ޥåȤα�����������
|
727
|
+
bget("-f -n n eco:b0002 hin:tRNA-Cys-1")
|
728
|
+
|
729
|
+
--- btit(string)
|
730
|
+
|
731
|
+
DBGET �� btit ���ޥ�ɤؤΥ�åѡ��Ǥ������ꤷ������ȥ�� ID ���б���
|
732
|
+
��ǥե��˥������֤��ޤ������٤�Ϳ�����륨��ȥ�ο��� 100 �İʲ���
|
733
|
+
���¤���Ƥ��ޤ���
|
734
|
+
|
735
|
+
���͡�
|
736
|
+
string
|
737
|
+
|
738
|
+
�㡧
|
739
|
+
# ����飴�Ĥΰ����ҤΥǥե��˥�����
|
740
|
+
btit("hsa:1798 mmu:13478 dme:CG5287-PA cel:Y60A3A.14")
|
741
|
+
|
742
|
+
|
743
|
+
==== LinkDB
|
744
|
+
|
745
|
+
--- get_linkdb_by_entry(entry_id, db, start, max_results)
|
746
|
+
|
747
|
+
���ꤷ�� entry_id ����ľ�ܤޤ��ϴ���Ū�˥����Ƥ��륨��ȥ�η�ϩ��
|
748
|
+
db �ǻ��ꤷ���ǡ����١����ˤ��ɤ��ޤǸ������ޤ���
|
749
|
+
|
750
|
+
���͡�
|
751
|
+
ArrayOfLinkDBRelation
|
752
|
+
|
753
|
+
�㡧
|
754
|
+
# E. coli �ΰ����� b0002 �����Τ��ɤ�� KEGG/PATHWAY �Υ���ȥ��
|
755
|
+
get_linkdb_by_entry('eco:b0002', 'pathway', 1, 10)
|
756
|
+
get_linkdb_by_entry('eco:b0002', 'pathway', 11, 10)
|
757
|
+
|
758
|
+
|
759
|
+
==== SSDB
|
760
|
+
|
761
|
+
SSDB �ǡ����١������Ф����åɤΰ����Ǥ���SSDB �� KEGG/GENES �˴ޤޤ��
|
762
|
+
����ʪ��������Ҵ֤� ssearch ���Ѥ��� Smith-Waterman ���르�ꥺ���
|
763
|
+
��븡����Ԥä���̤ȡ��������ҤΥ�����ո�����̤���Ͽ�����ǡ����١����ǡ�
|
764
|
+
���֤Τ�����������餫���Ὢ��äƤ��뤿���®�ʸ�������ǽ�ˤʤäƤ��ޤ���
|
765
|
+
|
766
|
+
KEGG �����Υ�����η�ޤä���ʪ����濴���оݤȤ��Ƥ��뤳�Ȥȡ�Smith-
|
767
|
+
Waterman �������ˤ����Ӥ��Ǥ��뤳�Ȥ��饪����������ѥ�����ط��ˤ���
|
768
|
+
�����Ҥ�õ������ʪ���ͭ�ΰ����Ҥθ�����Ϥ����͡��ʱ��Ѥ��ͤ����ޤ���
|
769
|
+
|
770
|
+
SSDB �ǡ����١����ˤĤ��ƾܤ����ϰʲ��Υڡ����Ȥ��Ƥ���������
|
771
|
+
|
772
|
+
* ((<URL:http://www.genome.jp/kegg/ssdb/>))
|
773
|
+
|
774
|
+
#--- get_neighbors_by_gene(genes_id, org, start, max_results)
|
775
|
+
#
|
776
|
+
#���ꤷ�� genes_id �ΰ����Ҥ˥ۥ�������Τ����������Ҥ���ꤷ����ʪ����
|
777
|
+
#�������ޤ����ޤ� org �� 'all' ����ꤹ�������ʪ�狼�鸡�����ޤ���
|
778
|
+
#
|
779
|
+
#���͡�
|
780
|
+
# ArrayOfSSDBRelation
|
781
|
+
#
|
782
|
+
#�㡧
|
783
|
+
# # ��IJ�ݤΰ����� b0002 ����Ʊ���Τ�������Ҥ����Ƹ������ơ���̤Σ���
|
784
|
+
# # ���飱�����ܤޤǤ��֤��ޤ�
|
785
|
+
# get_neighbors_by_gene('eco:b0002', 'all' 1, 10)
|
786
|
+
# # ���Σ����Ĥ� start = start + max_results �Ȥ��Ƽ��ޤ�
|
787
|
+
# get_neighbors_by_gene('eco:b0002', 'all' 11, 10)
|
788
|
+
|
789
|
+
--- get_best_best_neighbors_by_gene(genes_id, start, max_results)
|
790
|
+
|
791
|
+
������ȥ������åȤ� best-best �δط��ˤ�������Ҥ��������ޤ���
|
792
|
+
|
793
|
+
���͡�
|
794
|
+
ArrayOfSSDBRelation
|
795
|
+
|
796
|
+
�㡧
|
797
|
+
# ��IJ�ݤΰ����� b0002 ��������ʪ��� best-best �δط��ˤ��������
|
798
|
+
get_best_best_neighbors_by_gene('eco:b0002', 1, 10)
|
799
|
+
get_best_best_neighbors_by_gene('eco:b0002', 11, 10)
|
800
|
+
|
801
|
+
--- get_best_neighbors_by_gene(genes_id, start, max_results)
|
802
|
+
|
803
|
+
�����꤫�鸫�ƥ٥��ȥҥåȤδط��ˤ�������Ҥ��������ޤ���
|
804
|
+
|
805
|
+
���͡�
|
806
|
+
ArrayOfSSDBRelation
|
807
|
+
|
808
|
+
�㡧
|
809
|
+
# ��IJ�ݤΰ����� b0002 ��������ʪ��� best neighbor �δط��ˤ��������
|
810
|
+
get_best_neighbors_by_gene('eco:b0002', 1, 10)
|
811
|
+
get_best_neighbors_by_gene('eco:b0002', 11, 10)
|
812
|
+
|
813
|
+
--- get_reverse_best_neighbors_by_gene(genes_id, start, max_results)
|
814
|
+
|
815
|
+
�������å�¦����ʪ�狼�鸫�ƥ����꤬�٥��ȥҥåȤȤʤ�����Ҥ����ޤ���
|
816
|
+
|
817
|
+
���͡�
|
818
|
+
ArrayOfSSDBRelation
|
819
|
+
|
820
|
+
�㡧
|
821
|
+
# ��IJ�ݤΰ����� b0002 �� reverse best neighbor �δط��ˤ��������
|
822
|
+
get_reverse_best_neighbors_by_gene('eco:b0002', 1, 10)
|
823
|
+
get_reverse_best_neighbors_by_gene('eco:b0002', 11, 10)
|
824
|
+
|
825
|
+
--- get_paralogs_by_gene(genes_id, start, max_results)
|
826
|
+
|
827
|
+
�������Ʊ����ʪ����ǥѥ���������Ҥ����ޤ���
|
828
|
+
|
829
|
+
���͡�
|
830
|
+
ArrayOfSSDBRelation
|
831
|
+
|
832
|
+
�㡧
|
833
|
+
# ��IJ�ݤΰ����� b0002 �ȥѥ�����δط��ˤ��������
|
834
|
+
get_paralogs_by_gene('eco:b0002', 1, 10)
|
835
|
+
get_paralogs_by_gene('eco:b0002', 11, 10)
|
836
|
+
|
837
|
+
#--- get_similarity_between_genes(genes_id1, genes_id2)
|
838
|
+
#
|
839
|
+
#���ꤷ�����Ĥΰ����Ҵ֤� Smith-Waterman ��������ޤ�ǡ������֤��ޤ���
|
840
|
+
#
|
841
|
+
#���͡�
|
842
|
+
# SSDBRelation
|
843
|
+
#
|
844
|
+
#�㡧
|
845
|
+
# # ��IJ�ݤ� b0002 �����Ҥ� b3940 �����Ҵ֤Υ������䥢�饤�����ΰ������
|
846
|
+
# get_similarity_between_genes('eco:b0002', 'eco:b3940')
|
847
|
+
|
848
|
+
|
849
|
+
==== Motif
|
850
|
+
|
851
|
+
--- get_motifs_by_gene(genes_id, db)
|
852
|
+
|
853
|
+
���ꤷ�������Ҥ�¸�ߤ��������դΥꥹ�Ȥ��֤��ޤ���������եǡ����١���
|
854
|
+
�Υꥹ�Ȥˤϡ�Pfam (pfam), TIGRFAM (tfam), PROSITE pattern (pspt), PROSITE
|
855
|
+
profile (pspf) �ޤ��Ϥ�������� (all) ��������ޤ���
|
856
|
+
|
857
|
+
���͡�
|
858
|
+
ArrayOfMotifResult
|
859
|
+
|
860
|
+
�㡧
|
861
|
+
# ��IJ�ݤΰ����� b0002 ����Pfam������դΥꥹ��
|
862
|
+
get_motifs_by_gene('eco:b0002', 'pfam')
|
863
|
+
|
864
|
+
--- get_genes_by_motifs(motif_id_list, start, max_results)
|
865
|
+
|
866
|
+
���ꤷ��������դ����ƻ��İ����Ҥ����ޤ���
|
867
|
+
|
868
|
+
���͡�
|
869
|
+
ArrayOfDefinition (genes_id, definition)
|
870
|
+
|
871
|
+
�㡧
|
872
|
+
# Pfam �� DnaJ �� Prosite �� DNAJ_2 �˥ҥåȤ�������Ҥ�
|
873
|
+
list = ['pf:DnaJ', 'ps:DNAJ_2']
|
874
|
+
get_genes_by_motifs(list, 1, 10)
|
875
|
+
get_genes_by_motifs(list, 11, 10)
|
876
|
+
|
877
|
+
|
878
|
+
==== KO, OC, PC
|
879
|
+
|
880
|
+
KO (KEGG orthology), OC (KEGG ortholog cluster), PC (KEGG paralog cluster) ��
|
881
|
+
��������뤿��Υ�åɤǤ���KO �ϥ���졼����줿���������������ҷ���
|
882
|
+
OC �� PC �ϵ���Ū�˥��饹������줿��Ʊ���Τ�������ҷ��Υǡ����١����Ǥ���
|
883
|
+
|
884
|
+
--- get_ko_by_gene(genes_id)
|
885
|
+
|
886
|
+
���ꤷ�������Ҥ˥�������Ƥ��� KO �Υ���ȥ��ֹ�������֤��ޤ���
|
887
|
+
|
888
|
+
���͡�
|
889
|
+
ArrayOfstring (ko_id)
|
890
|
+
|
891
|
+
�㡧
|
892
|
+
# eco:b0002 �����Ҥ˥�������Ƥ��� KO �Υꥹ��
|
893
|
+
get_ko_by_gene('eco:b0002')
|
894
|
+
|
895
|
+
#--- get_ko_members(ko_id)
|
896
|
+
#
|
897
|
+
#���ꤷ�� ko_id �� KO ����ȥ�˴ޤޤ������ҤΥꥹ�Ȥ��֤��ޤ���
|
898
|
+
#
|
899
|
+
#���͡�
|
900
|
+
# ArrayOfstring (genes_id)
|
901
|
+
#
|
902
|
+
#�㡧
|
903
|
+
# # KO �ֹ� K02208 �Υ�������Ƥ�������ҤΥꥹ��
|
904
|
+
# get_ko_by_gene('ko:K02598')
|
905
|
+
|
906
|
+
--- get_ko_by_ko_class(ko_class_id)
|
907
|
+
|
908
|
+
���ꤷ�� ko_class_id �˴ޤޤ�� ko_id �Υꥹ�Ȥ��֤��ޤ���
|
909
|
+
|
910
|
+
���͡�
|
911
|
+
ArrayOfDefinition (ko_id)
|
912
|
+
|
913
|
+
�㡧
|
914
|
+
# KO class '01196' �˴ޤޤ�� KO �Υꥹ��
|
915
|
+
get_ko_by_ko_class('01196')
|
916
|
+
|
917
|
+
--- get_genes_by_ko_class(ko_class_id, org, start, max_results)
|
918
|
+
|
919
|
+
���ꤷ����ʪ��� ko_class_id �˴ޤޤ������ҤΥꥹ�Ȥ��֤��ޤ���
|
920
|
+
|
921
|
+
���͡�
|
922
|
+
ArrayOfDefinition (genes_id, definition)
|
923
|
+
|
924
|
+
�㡧
|
925
|
+
# KO ���饹 '00930' �˴ޤޤ��ҥȰ����ҤΥꥹ��
|
926
|
+
get_genes_by_ko_class('00903', 'hsa' , 1, 100)
|
927
|
+
|
928
|
+
--- get_genes_by_ko(ko_id, org)
|
929
|
+
|
930
|
+
���ꤷ����ʪ��� ko_id �˴ޤޤ������ҤΥꥹ�Ȥ��֤��ޤ���
|
931
|
+
��ʪ�拾���ɤ� all ����ꤹ�������ʪ��ΰ����Ҥ��֤��ޤ���
|
932
|
+
|
933
|
+
���͡�
|
934
|
+
ArrayOfDefinition (genes_id, definition)
|
935
|
+
|
936
|
+
�㡧
|
937
|
+
# KO �ֹ� 'K00001' �˴ޤޤ����IJ�ݰ����ҤΥꥹ��
|
938
|
+
get_genes_by_ko('ko:K00010', 'eco')
|
939
|
+
|
940
|
+
# KO �ֹ� 'K00010' �˴ޤޤ������ʪ��ΰ����ҥꥹ��
|
941
|
+
get_genes_by_ko('ko:K00010', 'all')
|
942
|
+
|
943
|
+
--- get_oc_members_by_gene(genes_id, start, max_results)
|
944
|
+
|
945
|
+
���ꤷ�������Ҥ�Ʊ�� OC ��°��������ҤΥꥹ�Ȥ��֤��ޤ���
|
946
|
+
|
947
|
+
���͡�
|
948
|
+
ArrayOfstring (genes_id)
|
949
|
+
|
950
|
+
�㡧
|
951
|
+
# eco:b0002 �����Ҥ�Ʊ���������������饹�����˴ޤޤ������ҤΥꥹ��
|
952
|
+
get_oc_members_by_gene('eco:b0002', 1, 10)
|
953
|
+
get_oc_members_by_gene('eco:b0002', 11, 10)
|
954
|
+
|
955
|
+
--- get_pc_members_by_gene(genes_id, start, max_results)
|
956
|
+
|
957
|
+
���ꤷ�������Ҥ�Ʊ�� PC ��°��������ҤΥꥹ�Ȥ��֤��ޤ���
|
958
|
+
|
959
|
+
���͡�
|
960
|
+
ArrayOfstring (genes_id)
|
961
|
+
|
962
|
+
�㡧
|
963
|
+
# eco:b0002 �����Ҥ�Ʊ���ѥ�������饹�����˴ޤޤ������ҤΥꥹ��
|
964
|
+
get_pc_members_by_gene('eco:b0002', 1, 10)
|
965
|
+
get_pc_members_by_gene('eco:b0002', 11, 10)
|
966
|
+
|
967
|
+
|
968
|
+
==== PATHWAY
|
969
|
+
|
970
|
+
PATHWAY �ǡ����١������Ф����åɤΰ����Ǥ���PATHWAY �ǡ����١�����
|
971
|
+
�Ĥ��ƾܤ����ϰʲ��Υڡ����Ȥ��Ƥ���������
|
972
|
+
|
973
|
+
* ((<URL:http://www.genome.jp/kegg/kegg2.html#pathway>))
|
974
|
+
|
975
|
+
+ �ѥ��������ؤο��Ť�
|
976
|
+
|
977
|
+
--- mark_pathway_by_objects(pathway_id, object_id_list)
|
978
|
+
|
979
|
+
���ꤷ����ʪ��ǡ�Ϳ����줿�ѥ��������ޥåפ�Ϳ����줿���֥�������
|
980
|
+
�ʰ����ҡ�����ʪ�������ֹ�ˤ��б������Ȥ˿���Ĥ���������������
|
981
|
+
������ URL ���֤��ޤ���
|
982
|
+
|
983
|
+
���͡�
|
984
|
+
string (URL)
|
985
|
+
|
986
|
+
�㡧
|
987
|
+
# ��IJ�ݤΥѥ������� path:eco00260 ��ΰ����� eco:b0002 �� Homoserine
|
988
|
+
# �� cpd:C00263 ���б�����ܥå������֤��忧���������� URL
|
989
|
+
obj_list = ['eco:b0002', 'cpd:C00263']
|
990
|
+
mark_pathway_by_objects('path:eco00260', obj_list)
|
991
|
+
|
992
|
+
--- color_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
|
993
|
+
|
994
|
+
���ꤷ���ѥ���������Ϳ����줿���֥������ȡʰ����ҡ�����ʪ�����ǡˤ��Ф���
|
995
|
+
ʸ�����Ȥ� fg_color_list �ǻ��ꤷ�������طʤ� bg_color_list �ǻ��ꤷ������
|
996
|
+
�Ĥ��������������������� URL ���֤��ޤ���object_id_list �� fg_color_list,
|
997
|
+
bg_color_list �����Ǥο��Ƚ��֤�·����褦�����դ���ɬ�פ�����ޤ���
|
998
|
+
|
999
|
+
���͡�
|
1000
|
+
string (URL)
|
1001
|
+
|
1002
|
+
�㡧
|
1003
|
+
# �ѥ������� path:eco00053 ��˺ܤäƤ�����IJ�ݤΰ����� eco:b0207 ��
|
1004
|
+
# �طʤ��֡�ʸ�����Ȥ��Ĥ��忧����eco:b1300 ���طʤ���ʸ�����Ȥ��Ф�
|
1005
|
+
# �忧���������� URL ���֤��ޤ���
|
1006
|
+
obj_list = ['eco:b0207', 'eco:b1300']
|
1007
|
+
fg_list = ['blue', '#00ff00']
|
1008
|
+
bg_list = ['#ff0000', 'yellow']
|
1009
|
+
color_pathway_by_objects('path:eco00053', obj_list, fg_list, bg_list)
|
1010
|
+
|
1011
|
+
--- get_html_of_marked_pathway_by_objects(pathway_id, object_id_list)
|
1012
|
+
|
1013
|
+
����������˥���å��֥�ޥåפ�ޤ� HTML �ڡ����� URL ���֤�
|
1014
|
+
�С������� 'mark_pathway_by_objects' ��åɤǤ���
|
1015
|
+
|
1016
|
+
���͡�
|
1017
|
+
string (URL)
|
1018
|
+
|
1019
|
+
�㡧
|
1020
|
+
# ��IJ�ݤΥѥ������� '00970' �Ρ������� 'eco:b4258'������ʪ 'cpd:C00135'
|
1021
|
+
# KO �ֹ� 'ko:K01881' ���ֿ��ǥޡ�����Ĥ��������Υ���å��֥�ޥåפ�
|
1022
|
+
# ɽ������ HTML �� URL ���֤�
|
1023
|
+
obj_list = ['eco:b4258', 'cpd:C00135', 'ko:K01881']
|
1024
|
+
get_html_of_marked_pathway_by_objects('path:eco00970', obj_list)
|
1025
|
+
|
1026
|
+
--- get_html_of_colored_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
|
1027
|
+
|
1028
|
+
����������˥���å��֥�ޥåפ�ޤ� HTML �ڡ����� URL ���֤�
|
1029
|
+
�С������� 'color_pathway_by_object' ��åɤǤ���
|
1030
|
+
|
1031
|
+
���͡�
|
1032
|
+
string (URL)
|
1033
|
+
|
1034
|
+
�㡧
|
1035
|
+
# ��IJ�ݤΥѥ������� '00970' �Ρ������� 'eco:b4258' �����Ϥ˳���������ʪ
|
1036
|
+
# 'cpd:C00135' ���Ϥ��С�KO �ֹ� 'ko:K01881' �����Ϥ��Ĥο��Ť���
|
1037
|
+
# �����Υ���å��֥�ޥåפ�ɽ������ HTML �� URL ���֤�
|
1038
|
+
obj_list = ['eco:b4258', 'cpd:C00135', 'ko:K01881']
|
1039
|
+
fg_list = ['gray', '#00ff00', 'blue']
|
1040
|
+
bg_list = ['#ff0000', 'yellow', 'orange']
|
1041
|
+
get_html_of_colored_pathway_by_objects('path:eco00970', obj_list, fg_list, bg_list)
|
1042
|
+
|
1043
|
+
+ �ѥ���������Υ��֥������ȸ���
|
1044
|
+
|
1045
|
+
--- get_genes_by_pathway(pathway_id)
|
1046
|
+
|
1047
|
+
���ꤷ���ѥ���������˺ܤäƤ�������ҤΥꥹ�Ȥ��֤��ޤ�����ʪ��̾��
|
1048
|
+
pathway_id �˴ޤޤ�� keggorg �ǻ��ꤷ�ޤ���
|
1049
|
+
|
1050
|
+
���͡�
|
1051
|
+
ArrayOfstring (genes_id)
|
1052
|
+
|
1053
|
+
�㡧
|
1054
|
+
# ��IJ�ݤΥѥ������� 00020 �֤˺ܤäƤ�������ҤΥꥹ��
|
1055
|
+
get_genes_by_pathway('path:eco00020')
|
1056
|
+
|
1057
|
+
--- get_enzymes_by_pathway(pathway_id)
|
1058
|
+
|
1059
|
+
���ꤷ���ѥ��������˺ܤäƤ�������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
1060
|
+
|
1061
|
+
���͡�
|
1062
|
+
ArrayOfstring (enzyme_id)
|
1063
|
+
|
1064
|
+
�㡧
|
1065
|
+
# ��IJ�ݤΥѥ������� 00020 �֤˺ܤäƤ�������ֹ�Υꥹ��
|
1066
|
+
get_enzymes_by_pathway('path:eco00020')
|
1067
|
+
|
1068
|
+
--- get_compounds_by_pathway(pathway_id)
|
1069
|
+
|
1070
|
+
���ꤷ���ѥ��������˺ܤäƤ��벽��ʪ�Υꥹ�Ȥ��֤��ޤ���
|
1071
|
+
|
1072
|
+
���͡�
|
1073
|
+
ArrayOfstring (compound_id)
|
1074
|
+
|
1075
|
+
�㡧
|
1076
|
+
# ��IJ�ݤΥѥ������� 00020 �˺ܤäƤ��벽��ʪ�Υꥹ��
|
1077
|
+
get_compounds_by_pathway('path:eco00020')
|
1078
|
+
|
1079
|
+
--- get_glycans_by_pathway(pathway_id)
|
1080
|
+
|
1081
|
+
���ꤷ���ѥ��������˺ܤäƤ��������Υꥹ�Ȥ��֤��ޤ���
|
1082
|
+
|
1083
|
+
���͡�
|
1084
|
+
ArrayOfstring (glycan_id)
|
1085
|
+
|
1086
|
+
�㡧
|
1087
|
+
# ��IJ�ݤΥѥ������� 00510 �˺ܤäƤ��������Υꥹ��
|
1088
|
+
get_glycans_by_pathway('path:eco00510')
|
1089
|
+
|
1090
|
+
--- get_reactions_by_pathway(pathway_id)
|
1091
|
+
|
1092
|
+
���ꤷ���ѥ��������˺ܤäƤ���ꥢ��������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
1093
|
+
|
1094
|
+
���͡�
|
1095
|
+
ArrayOfstring (reaction_id)
|
1096
|
+
|
1097
|
+
�㡧
|
1098
|
+
# ��IJ�ݤΥѥ������� 00260 �֤˺ܤäƤ���ꥢ�������Υꥹ��
|
1099
|
+
get_reactions_by_pathways('path:eco00260')
|
1100
|
+
|
1101
|
+
--- get_kos_by_pathway(pathway_id)
|
1102
|
+
|
1103
|
+
���ꤷ���ѥ��������˺ܤäƤ��� KO �ֹ�Υꥹ�Ȥ��֤��ޤ���
|
1104
|
+
|
1105
|
+
���͡�
|
1106
|
+
ArrayOfstring (ko_id)
|
1107
|
+
|
1108
|
+
�㡧
|
1109
|
+
# �ҥȤΥѥ������� 00010 �˺ܤäƤ��� KO �ֹ�Υꥹ��
|
1110
|
+
get_kos_by_pathway('path:hsa00010')
|
1111
|
+
|
1112
|
+
|
1113
|
+
|
1114
|
+
+ ���֥������Ȥ���ѥ�����������
|
1115
|
+
|
1116
|
+
--- get_pathways_by_genes(genes_id_list)
|
1117
|
+
|
1118
|
+
���ꤷ�������Ҥ����ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1119
|
+
|
1120
|
+
���͡�
|
1121
|
+
ArrayOfstring (pathway_id)
|
1122
|
+
|
1123
|
+
�㡧
|
1124
|
+
# ��IJ�ݤΰ����� b0077 �� b0078 ��ξ���ܤäƤ���ѥ��������Υꥹ��
|
1125
|
+
get_pathways_by_genes(['eco:b0077', 'eco:b0078'])
|
1126
|
+
|
1127
|
+
--- get_pathways_by_enzymes(enzyme_id_list)
|
1128
|
+
|
1129
|
+
���ꤷ�������ֹ椬���ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1130
|
+
|
1131
|
+
���͡�
|
1132
|
+
ArrayOfstring (pathway_id)
|
1133
|
+
|
1134
|
+
�㡧
|
1135
|
+
# �����ֹ� 1.3.99.1 �ι��Ǥ��ܤäƤ���ѥ��������Υꥹ��
|
1136
|
+
get_pathways_by_enzymes(['ec:1.3.99.1'])
|
1137
|
+
|
1138
|
+
--- get_pathways_by_compounds(compound_id_list)
|
1139
|
+
|
1140
|
+
���ꤷ������ʪ�����ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1141
|
+
|
1142
|
+
���͡�
|
1143
|
+
ArrayOfstring (pathway_id)
|
1144
|
+
|
1145
|
+
�㡧
|
1146
|
+
# ����ʪ C00033 �� C00158 ��ξ���ܤäƤ���ѥ��������Υꥹ��
|
1147
|
+
get_pathways_by_compounds(['cpd:C00033', 'cpd:C00158'])
|
1148
|
+
|
1149
|
+
--- get_pathways_by_glycans(compound_id_list)
|
1150
|
+
|
1151
|
+
���ꤷ�����������ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1152
|
+
|
1153
|
+
���͡�
|
1154
|
+
ArrayOfstring (pathway_id)
|
1155
|
+
|
1156
|
+
�㡧
|
1157
|
+
# ���� G00009 �� G00011 ��ξ���ܤäƤ���ѥ��������Υꥹ��
|
1158
|
+
get_pathways_by_glycans(['gl:G00009', 'gl:G00011'])
|
1159
|
+
|
1160
|
+
--- get_pathways_by_reactions(reaction_id_list)
|
1161
|
+
|
1162
|
+
���ꤷ���ꥢ��������ֹ椬���ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1163
|
+
|
1164
|
+
���͡�
|
1165
|
+
ArrayOfstring (pathway_id)
|
1166
|
+
|
1167
|
+
�㡧
|
1168
|
+
# �ꥢ��������ֹ� rn:R00959, rn:R02740, rn:R00960, rn:R01786 �����Ƥ�
|
1169
|
+
# ȿ����ޤ�ѥ��������Υꥹ��
|
1170
|
+
get_pathways_by_reactions(['rn:R00959', 'rn:R02740', 'rn:R00960', 'rn:R01786'])
|
1171
|
+
|
1172
|
+
--- get_pathways_by_kos(ko_id_list, org)
|
1173
|
+
|
1174
|
+
���ꤷ����ʪ�� KO �ֹ椬���ƺܤäƤ���ѥ��������Υꥹ�Ȥ��֤��ޤ���
|
1175
|
+
|
1176
|
+
���͡�
|
1177
|
+
ArrayOfstring (pathway_id)
|
1178
|
+
|
1179
|
+
�㡧
|
1180
|
+
# KO �ֹ� 'ko:K00016' �� 'ko:K00382' ��ޤ�ҥȤΥѥ��������Υꥹ��
|
1181
|
+
get_pathways_by_kos(['ko:K00016', 'ko:K00382'], 'hsa')
|
1182
|
+
|
1183
|
+
# KO �ֹ� 'ko:K00016' �� 'ko:K00382' ��ޤ�����ʪ��Υѥ��������Υꥹ��
|
1184
|
+
get_pathways_by_kos(['ko:K00016', 'ko:K00382'], 'all')
|
1185
|
+
|
1186
|
+
|
1187
|
+
+ �ѥ��������֤δط�
|
1188
|
+
|
1189
|
+
--- get_linked_pathways(pathway_id)
|
1190
|
+
|
1191
|
+
���ꤷ���ѥ��������ֹ�Υѥ���������������Ƥ���ѥ���������
|
1192
|
+
�ꥹ�Ȥ��֤��ޤ���
|
1193
|
+
|
1194
|
+
���͡�
|
1195
|
+
ArrayOfstring (pathway_id)
|
1196
|
+
|
1197
|
+
�㡧
|
1198
|
+
# �ѥ������� path:eco00620 ��������Ƥ���ѥ��������Υꥹ��
|
1199
|
+
get_linked_pathways('path:eco00620')
|
1200
|
+
|
1201
|
+
|
1202
|
+
+ �����Ҥȹ����ֹ�δط�
|
1203
|
+
|
1204
|
+
--- get_genes_by_enzyme(enzyme_id, org)
|
1205
|
+
|
1206
|
+
�о���ʪ��ˤ����ơ����ꤷ�������ֹ����İ����ҤΥꥹ�Ȥ��֤��ޤ���
|
1207
|
+
|
1208
|
+
���͡�
|
1209
|
+
ArrayOfstring (genes_id)
|
1210
|
+
|
1211
|
+
�㡧
|
1212
|
+
# �����ֹ� 1.1.1.1 �������IJ�ݤΰ����ҤΥꥹ��
|
1213
|
+
get_genes_by_enzyme('ec:1.1.1.1', 'eco')
|
1214
|
+
|
1215
|
+
--- get_enzymes_by_gene(genes_id)
|
1216
|
+
|
1217
|
+
���ꤷ�������Ҥ��б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
1218
|
+
|
1219
|
+
���͡�
|
1220
|
+
ArrayOfstring (enzyme_id)
|
1221
|
+
|
1222
|
+
�㡧
|
1223
|
+
# ��IJ�ݰ����� 'eco:b0002' �ι����ֹ�Υꥹ��
|
1224
|
+
get_enzymes_by_gene(eco:b0002)
|
1225
|
+
|
1226
|
+
|
1227
|
+
+ ���ǡ�����ʪ���ꥢ�������δط�
|
1228
|
+
|
1229
|
+
--- get_enzymes_by_compound(compound_id)
|
1230
|
+
|
1231
|
+
���ꤷ������ʪ���б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
1232
|
+
|
1233
|
+
���͡�
|
1234
|
+
ArrayOfstring (compound_id)
|
1235
|
+
|
1236
|
+
�㡧
|
1237
|
+
# ����ʪ 'cpd:C00345' ����դ˴ؤ����ǤΥꥹ��
|
1238
|
+
get_enzymes_by_compound('cpd:C00345')
|
1239
|
+
|
1240
|
+
--- get_enzymes_by_glycan(compound_id)
|
1241
|
+
|
1242
|
+
���ꤷ���������б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
1243
|
+
|
1244
|
+
���͡�
|
1245
|
+
ArrayOfstring (glycan_id)
|
1246
|
+
|
1247
|
+
�㡧
|
1248
|
+
# ���� 'gl:G00001' ����դ˴ؤ����ǤΥꥹ��
|
1249
|
+
get_enzymes_by_glycan('gl:G00001')
|
1250
|
+
|
1251
|
+
--- get_enzymes_by_reaction(reaction_id)
|
1252
|
+
|
1253
|
+
���ꤷ���ꥢ��������ֹ���б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
1254
|
+
|
1255
|
+
���͡�
|
1256
|
+
ArrayOfstring (reaction_id)
|
1257
|
+
|
1258
|
+
�㡧
|
1259
|
+
# �ꥢ��������ֹ� R00100 ����Ĺ��ǤΥꥹ��
|
1260
|
+
get_enzymes_by_reaction('rn:R00100')
|
1261
|
+
|
1262
|
+
--- get_compounds_by_enzyme(enzyme_id)
|
1263
|
+
|
1264
|
+
���ꤷ�������ֹ���б����벽��ʪ�Υꥹ�Ȥ��֤��ޤ���
|
1265
|
+
|
1266
|
+
���͡�
|
1267
|
+
ArrayOfstring (compound_id)
|
1268
|
+
|
1269
|
+
�㡧
|
1270
|
+
# �����ֹ� 'ec:2.7.1.12' ����դ˴ؤ�벽��ʪ�Υꥹ��
|
1271
|
+
get_compounds_by_enzyme('ec:2.7.1.12')
|
1272
|
+
|
1273
|
+
--- get_compounds_by_reaction(reaction_id)
|
1274
|
+
|
1275
|
+
���ꤷ���ꥢ���������б����벽��ʪ�Υꥹ�Ȥ��֤��ޤ���
|
1276
|
+
|
1277
|
+
���͡�
|
1278
|
+
ArrayOfstring (compound_id)
|
1279
|
+
|
1280
|
+
�㡧
|
1281
|
+
# �ꥢ��������ֹ� 'rn:R00100' ��ȿ���˴ؤ�벽��ʪ�Υꥹ��
|
1282
|
+
get_compounds_by_reaction('rn:R00100')
|
1283
|
+
|
1284
|
+
--- get_glycans_by_enzyme(enzyme_id)
|
1285
|
+
|
1286
|
+
���ꤷ�������ֹ���б����������Υꥹ�Ȥ��֤��ޤ���
|
1287
|
+
|
1288
|
+
���͡�
|
1289
|
+
ArrayOfstring (glycan_id)
|
1290
|
+
|
1291
|
+
�㡧
|
1292
|
+
# �����ֹ� 'ec:2.4.1.141' ����դ˴ؤ�������Υꥹ��
|
1293
|
+
get_glycans_by_enzyme('ec:2.4.1.141')
|
1294
|
+
|
1295
|
+
--- get_glycans_by_reaction(reaction_id)
|
1296
|
+
|
1297
|
+
���ꤷ���ꥢ���������б����������Υꥹ�Ȥ��֤��ޤ���
|
1298
|
+
|
1299
|
+
���͡�
|
1300
|
+
ArrayOfstring (glycan_id)
|
1301
|
+
|
1302
|
+
�㡧
|
1303
|
+
# �ꥢ��������ֹ� 'rn:R06164' ��ȿ���˴ؤ�������Υꥹ��
|
1304
|
+
get_glycans_by_reaction('rn:R06164')
|
1305
|
+
|
1306
|
+
--- get_reactions_by_enzyme(enzyme_id)
|
1307
|
+
|
1308
|
+
���ꤷ�������ֹ���б�����ꥢ�������Υꥹ�Ȥ��֤��ޤ���
|
1309
|
+
|
1310
|
+
���͡�
|
1311
|
+
ArrayOfstring (reaction_id)
|
1312
|
+
|
1313
|
+
�㡧
|
1314
|
+
# �����ֹ� 'ec:2.7.1.12' ��ȿ���˴ؤ��ꥢ��������ֹ�Υꥹ��
|
1315
|
+
get_reactions_by_enzyme('ec:2.7.1.12')
|
1316
|
+
|
1317
|
+
--- get_reactions_by_compound(compound_id)
|
1318
|
+
|
1319
|
+
���ꤷ������ʪ���б�����ꥢ�������Υꥹ�Ȥ��֤��ޤ���
|
1320
|
+
|
1321
|
+
���͡�
|
1322
|
+
ArrayOfstring (reaction_id)
|
1323
|
+
|
1324
|
+
�㡧
|
1325
|
+
# ����ʪ 'cpd:C00199' �ο���ȿ���˴ؤ��ꥢ��������ֹ�Υꥹ��
|
1326
|
+
get_reactions_by_compound('cpd:C00199')
|
1327
|
+
|
1328
|
+
--- get_reactions_by_glycan(glycan_id)
|
1329
|
+
|
1330
|
+
���ꤷ���������б�����ꥢ�������Υꥹ�Ȥ��֤��ޤ���
|
1331
|
+
|
1332
|
+
���͡�
|
1333
|
+
ArrayOfstring (reaction_id)
|
1334
|
+
|
1335
|
+
�㡧
|
1336
|
+
# ���� 'gl:G00001' �ο���ȿ���˴ؤ��ꥢ��������ֹ�Υꥹ��
|
1337
|
+
get_reactions_by_glycan('gl:G00001')
|
1338
|
+
|
1339
|
+
|
1340
|
+
==== GENES
|
1341
|
+
|
1342
|
+
GENES �ǡ����١������Ф����åɤΰ����Ǥ���GENES �ǡ����١����ˤĤ���
|
1343
|
+
�ܤ����ϰʲ��Υڡ����Ȥ��Ƥ���������
|
1344
|
+
|
1345
|
+
* ((<URL:http://www.genome.jp/kegg/kegg2.html#genes>))
|
1346
|
+
|
1347
|
+
--- get_genes_by_organism(org, start, max_results)
|
1348
|
+
|
1349
|
+
���ꤷ����ʪ����� GENES ����ȥ�Τ�����start ���ܤ��� max_results ʬ��
|
1350
|
+
��̤��֤��ޤ���
|
1351
|
+
|
1352
|
+
���͡�
|
1353
|
+
ArrayOfstring (genes_id)
|
1354
|
+
|
1355
|
+
�㡧
|
1356
|
+
# ����ե륨�ݤΰ����ҥꥹ�Ȥ� 100 �Ĥ�������
|
1357
|
+
get_genes_by_organism('hin', 1, 100)
|
1358
|
+
get_genes_by_organism('hin', 101, 100)
|
1359
|
+
|
1360
|
+
|
1361
|
+
==== GENOME
|
1362
|
+
|
1363
|
+
GENOME �ǡ����١������Ф����åɤΰ����Ǥ���GENOME �ǡ����١����ˤĤ���
|
1364
|
+
�ܤ����ϰʲ��Υڡ����Ȥ��Ƥ���������
|
1365
|
+
|
1366
|
+
* ((<URL:http://www.genome.jp/kegg/kegg2.html#genome>))
|
1367
|
+
|
1368
|
+
--- get_number_of_genes_by_organism(org)
|
1369
|
+
|
1370
|
+
���ꤷ����ʪ�郎���İ����ҿ����֤��ޤ���
|
1371
|
+
|
1372
|
+
���͡�
|
1373
|
+
int
|
1374
|
+
|
1375
|
+
�㡧
|
1376
|
+
# ��IJ�ݤ����İ����Ҥο�
|
1377
|
+
get_number_of_genes_by_organism('eco')
|
1378
|
+
|
1379
|
+
|
1380
|
+
==== LIGAND
|
1381
|
+
|
1382
|
+
LIGAND �ǡ����١������Ф����åɤΰ����Ǥ���
|
1383
|
+
|
1384
|
+
--- convert_mol_to_kcf(mol_text)
|
1385
|
+
|
1386
|
+
MOL �ե����ޥåȤΥ���ȥ�� KCF �ե����ޥåȤ��Ѵ����ޤ���
|
1387
|
+
|
1388
|
+
���͡�
|
1389
|
+
String
|
1390
|
+
|
1391
|
+
�㡧
|
1392
|
+
convert_mol_to_kcf(mol_str)
|
1393
|
+
|
1394
|
+
|
1395
|
+
== Notes
|
1396
|
+
|
1397
|
+
Last updated: May 31, 2005
|
1398
|
+
|
1399
|
+
=end
|