bio 0.7.1 → 1.0.0
Sign up to get free protection for your applications and to get access to all the features.
- data/bin/bioruby +71 -27
- data/bin/br_biofetch.rb +5 -17
- data/bin/br_bioflat.rb +14 -26
- data/bin/br_biogetseq.rb +6 -18
- data/bin/br_pmfetch.rb +6 -16
- data/doc/Changes-0.7.rd +35 -0
- data/doc/KEGG_API.rd +287 -172
- data/doc/KEGG_API.rd.ja +273 -160
- data/doc/Tutorial.rd +18 -9
- data/doc/Tutorial.rd.ja +656 -138
- data/lib/bio.rb +6 -24
- data/lib/bio/alignment.rb +5 -5
- data/lib/bio/appl/blast.rb +132 -98
- data/lib/bio/appl/blast/format0.rb +9 -19
- data/lib/bio/appl/blast/wublast.rb +5 -18
- data/lib/bio/appl/emboss.rb +40 -47
- data/lib/bio/appl/hmmer.rb +116 -82
- data/lib/bio/appl/hmmer/report.rb +509 -364
- data/lib/bio/appl/spidey/report.rb +7 -18
- data/lib/bio/data/na.rb +3 -21
- data/lib/bio/db.rb +3 -21
- data/lib/bio/db/aaindex.rb +147 -52
- data/lib/bio/db/embl/common.rb +27 -6
- data/lib/bio/db/embl/embl.rb +18 -10
- data/lib/bio/db/embl/sptr.rb +87 -67
- data/lib/bio/db/embl/swissprot.rb +32 -3
- data/lib/bio/db/embl/trembl.rb +32 -3
- data/lib/bio/db/embl/uniprot.rb +32 -3
- data/lib/bio/db/fasta.rb +327 -289
- data/lib/bio/db/medline.rb +25 -4
- data/lib/bio/db/nbrf.rb +12 -20
- data/lib/bio/db/pdb.rb +4 -1
- data/lib/bio/db/pdb/chemicalcomponent.rb +240 -0
- data/lib/bio/db/pdb/pdb.rb +13 -8
- data/lib/bio/db/rebase.rb +93 -97
- data/lib/bio/feature.rb +2 -31
- data/lib/bio/io/ddbjxml.rb +167 -139
- data/lib/bio/io/fastacmd.rb +89 -56
- data/lib/bio/io/flatfile.rb +994 -278
- data/lib/bio/io/flatfile/index.rb +257 -194
- data/lib/bio/io/flatfile/indexer.rb +37 -29
- data/lib/bio/reference.rb +147 -64
- data/lib/bio/sequence.rb +57 -417
- data/lib/bio/sequence/aa.rb +64 -0
- data/lib/bio/sequence/common.rb +175 -0
- data/lib/bio/sequence/compat.rb +68 -0
- data/lib/bio/sequence/format.rb +134 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +189 -0
- data/lib/bio/shell.rb +9 -23
- data/lib/bio/shell/core.rb +130 -125
- data/lib/bio/shell/demo.rb +143 -0
- data/lib/bio/shell/{session.rb → interface.rb} +42 -40
- data/lib/bio/shell/object.rb +52 -0
- data/lib/bio/shell/plugin/codon.rb +4 -22
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +34 -25
- data/lib/bio/shell/plugin/flatfile.rb +5 -23
- data/lib/bio/shell/plugin/keggapi.rb +11 -24
- data/lib/bio/shell/plugin/midi.rb +5 -23
- data/lib/bio/shell/plugin/obda.rb +4 -22
- data/lib/bio/shell/plugin/seq.rb +6 -24
- data/lib/bio/shell/rails/Rakefile +10 -0
- data/lib/bio/shell/rails/app/controllers/application.rb +4 -0
- data/lib/bio/shell/rails/app/controllers/shell_controller.rb +94 -0
- data/lib/bio/shell/rails/app/helpers/application_helper.rb +3 -0
- data/lib/bio/shell/rails/app/models/shell_connection.rb +30 -0
- data/lib/bio/shell/rails/app/views/layouts/shell.rhtml +37 -0
- data/lib/bio/shell/rails/app/views/shell/history.rhtml +5 -0
- data/lib/bio/shell/rails/app/views/shell/index.rhtml +2 -0
- data/lib/bio/shell/rails/app/views/shell/show.rhtml +13 -0
- data/lib/bio/shell/rails/config/boot.rb +19 -0
- data/lib/bio/shell/rails/config/database.yml +85 -0
- data/lib/bio/shell/rails/config/environment.rb +53 -0
- data/lib/bio/shell/rails/config/environments/development.rb +19 -0
- data/lib/bio/shell/rails/config/environments/production.rb +19 -0
- data/lib/bio/shell/rails/config/environments/test.rb +19 -0
- data/lib/bio/shell/rails/config/routes.rb +19 -0
- data/lib/bio/shell/rails/doc/README_FOR_APP +2 -0
- data/lib/bio/shell/rails/public/404.html +8 -0
- data/lib/bio/shell/rails/public/500.html +8 -0
- data/lib/bio/shell/rails/public/dispatch.cgi +10 -0
- data/lib/bio/shell/rails/public/dispatch.fcgi +24 -0
- data/lib/bio/shell/rails/public/dispatch.rb +10 -0
- data/lib/bio/shell/rails/public/favicon.ico +0 -0
- data/lib/bio/shell/rails/public/images/icon.png +0 -0
- data/lib/bio/shell/rails/public/images/rails.png +0 -0
- data/lib/bio/shell/rails/public/index.html +277 -0
- data/lib/bio/shell/rails/public/javascripts/controls.js +750 -0
- data/lib/bio/shell/rails/public/javascripts/dragdrop.js +584 -0
- data/lib/bio/shell/rails/public/javascripts/effects.js +854 -0
- data/lib/bio/shell/rails/public/javascripts/prototype.js +1785 -0
- data/lib/bio/shell/rails/public/robots.txt +1 -0
- data/lib/bio/shell/rails/public/stylesheets/main.css +187 -0
- data/lib/bio/shell/rails/script/about +3 -0
- data/lib/bio/shell/rails/script/breakpointer +3 -0
- data/lib/bio/shell/rails/script/console +3 -0
- data/lib/bio/shell/rails/script/destroy +3 -0
- data/lib/bio/shell/rails/script/generate +3 -0
- data/lib/bio/shell/rails/script/performance/benchmarker +3 -0
- data/lib/bio/shell/rails/script/performance/profiler +3 -0
- data/lib/bio/shell/rails/script/plugin +3 -0
- data/lib/bio/shell/rails/script/process/reaper +3 -0
- data/lib/bio/shell/rails/script/process/spawner +3 -0
- data/lib/bio/shell/rails/script/process/spinner +3 -0
- data/lib/bio/shell/rails/script/runner +3 -0
- data/lib/bio/shell/rails/script/server +42 -0
- data/lib/bio/shell/rails/test/test_helper.rb +28 -0
- data/lib/bio/shell/web.rb +90 -0
- data/lib/bio/util/contingency_table.rb +231 -225
- data/sample/any2fasta.rb +59 -0
- data/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -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/{eco:b0002.faa → b0002.faa} +0 -0
- data/test/data/blast/{eco:b0002.faa.m0 → b0002.faa.m0} +2 -2
- data/test/data/blast/{eco:b0002.faa.m7 → b0002.faa.m7} +1 -1
- data/test/data/blast/{eco:b0002.faa.m8 → b0002.faa.m8} +0 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_report.rb +15 -12
- data/test/unit/bio/appl/blast/test_xmlparser.rb +4 -4
- data/test/unit/bio/appl/hmmer/test_report.rb +355 -0
- data/test/unit/bio/appl/test_blast.rb +5 -5
- data/test/unit/bio/data/test_na.rb +9 -18
- data/test/unit/bio/db/pdb/test_pdb.rb +169 -0
- data/test/unit/bio/db/test_aaindex.rb +197 -0
- data/test/unit/bio/io/test_fastacmd.rb +55 -0
- data/test/unit/bio/sequence/test_aa.rb +102 -0
- data/test/unit/bio/sequence/test_common.rb +178 -0
- data/test/unit/bio/sequence/test_compat.rb +82 -0
- data/test/unit/bio/sequence/test_na.rb +242 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +29 -19
- data/test/unit/bio/test_alignment.rb +15 -7
- data/test/unit/bio/test_reference.rb +198 -0
- data/test/unit/bio/test_sequence.rb +4 -49
- data/test/unit/bio/test_shell.rb +2 -2
- metadata +118 -15
- data/lib/bio/io/brdb.rb +0 -103
- data/lib/bioruby.rb +0 -34
data/doc/KEGG_API.rd.ja
CHANGED
@@ -1,8 +1,8 @@
|
|
1
1
|
=begin
|
2
|
-
|
3
|
-
|
4
|
-
|
5
|
-
|
2
|
+
|
3
|
+
$Id: KEGG_API.rd.ja,v 1.8 2006/02/23 04:51:23 k Exp $
|
4
|
+
|
5
|
+
Copyright (C) 2003-2006 Toshiaki Katayama <k@bioruby.org>
|
6
6
|
|
7
7
|
= KEGG API
|
8
8
|
|
@@ -29,6 +29,7 @@ KEGG API
|
|
29
29
|
* ((<MotifResult ��>)), ((<ArrayOfMotifResult ��>))
|
30
30
|
* ((<Definition ��>)), ((<ArrayOfDefinition ��>))
|
31
31
|
* ((<LinkDBRelation ��>)), ((<ArrayOfLinkDBRelation ��>))
|
32
|
+
* ((<PathwayElement ��>)), ((<ArrayOfPathwayElement ��>))
|
32
33
|
* ((<��åɰ���>))
|
33
34
|
* ((<�����>))
|
34
35
|
* ((<list_databases>)),
|
@@ -38,9 +39,22 @@ KEGG API
|
|
38
39
|
* ((<binfo>)),
|
39
40
|
((<bfind>)),
|
40
41
|
((<bget>)),
|
41
|
-
((<btit>))
|
42
|
+
((<btit>)),
|
43
|
+
((<bconv>))
|
42
44
|
* ((<LinkDB>))
|
43
45
|
* ((<get_linkdb_by_entry>))
|
46
|
+
* ((<get_genes_by_enzyme>)),
|
47
|
+
((<get_enzymes_by_gene>))
|
48
|
+
* ((<get_enzymes_by_compound>)),
|
49
|
+
((<get_enzymes_by_glycan>)),
|
50
|
+
((<get_enzymes_by_reaction>)),
|
51
|
+
((<get_compounds_by_enzyme>)),
|
52
|
+
((<get_compounds_by_reaction>)),
|
53
|
+
((<get_glycans_by_enzyme>)),
|
54
|
+
((<get_glycans_by_reaction>)),
|
55
|
+
((<get_reactions_by_enzyme>)),
|
56
|
+
((<get_reactions_by_compound>)),
|
57
|
+
((<get_reactions_by_glycan>))
|
44
58
|
* ((<SSDB>))
|
45
59
|
* ((<get_best_best_neighbors_by_gene>)),
|
46
60
|
((<get_best_neighbors_by_gene>)),
|
@@ -62,9 +76,12 @@ KEGG API
|
|
62
76
|
* ((<PATHWAY>))
|
63
77
|
* ((<mark_pathway_by_objects>)),
|
64
78
|
((<color_pathway_by_objects>)),
|
79
|
+
((<color_pathway_by_elements>)),
|
65
80
|
((<get_html_of_marked_pathway_by_objects>)),
|
66
|
-
((<get_html_of_colored_pathway_by_objects>))
|
67
|
-
|
81
|
+
((<get_html_of_colored_pathway_by_objects>)),
|
82
|
+
((<get_html_of_colored_pathway_by_elements>))
|
83
|
+
* ((<get_elements_by_pathway>)),
|
84
|
+
((<get_genes_by_pathway>)),
|
68
85
|
((<get_enzymes_by_pathway>)),
|
69
86
|
((<get_compounds_by_pathway>)),
|
70
87
|
((<get_glycans_by_pathway>)),
|
@@ -77,18 +94,6 @@ KEGG API
|
|
77
94
|
((<get_pathways_by_reactions>)),
|
78
95
|
((<get_pathways_by_kos>))
|
79
96
|
* ((<get_linked_pathways>))
|
80
|
-
* ((<get_genes_by_enzyme>)),
|
81
|
-
((<get_enzymes_by_gene>))
|
82
|
-
* ((<get_enzymes_by_compound>)),
|
83
|
-
((<get_enzymes_by_glycan>)),
|
84
|
-
((<get_enzymes_by_reaction>)),
|
85
|
-
((<get_compounds_by_enzyme>)),
|
86
|
-
((<get_compounds_by_reaction>)),
|
87
|
-
((<get_glycans_by_enzyme>)),
|
88
|
-
((<get_glycans_by_reaction>)),
|
89
|
-
((<get_reactions_by_enzyme>)),
|
90
|
-
((<get_reactions_by_compound>)),
|
91
|
-
((<get_reactions_by_glycan>))
|
92
97
|
* ((<GENES>))
|
93
98
|
* ((<get_genes_by_organism>))
|
94
99
|
* ((<GENOME>))
|
@@ -633,6 +638,18 @@ SSDB
|
|
633
638
|
|
634
639
|
ʣ���� LinkDBRelation ���ǡ�����ޤ�����Ǥ���
|
635
640
|
|
641
|
+
+ PathwayElement ��
|
642
|
+
|
643
|
+
element_id �ѥ���������Υ��֥������Ȥ�ؤ���ˡ����� ID (int)
|
644
|
+
type ���֥������Ȥμ��� ("gene", "enzyme" �ʤ�) (string)
|
645
|
+
names ���֥������ȤˤĤ���줿̾���Υꥹ�� (ArrayOfstring)
|
646
|
+
components ���롼�פξ��ʤɴޤޤ�륪�֥������ȤΥꥹ�� (ArrayOfint)
|
647
|
+
|
648
|
+
+ ArrayOfPathwayElement ��
|
649
|
+
|
650
|
+
ʣ���� PathwayElement ���ǡ�����ޤ�����Ǥ���
|
651
|
+
|
652
|
+
|
636
653
|
=== ��åɰ���
|
637
654
|
|
638
655
|
�ʲ���KEGG API ������åɤΥꥹ�ȤǤ�����åɤˤϥ������֤���Τ�
|
@@ -739,6 +756,18 @@ DBGET
|
|
739
756
|
# ����飴�Ĥΰ����ҤΥǥե��˥�����
|
740
757
|
btit("hsa:1798 mmu:13478 dme:CG5287-PA cel:Y60A3A.14")
|
741
758
|
|
759
|
+
--- bconv(string)
|
760
|
+
|
761
|
+
�����ǡ����١����� ID �� KEGG �� ID ���Ѵ����ޤ����б����Ƥ��볰���ǡ���
|
762
|
+
�١����� NCBI Gene ID, NCBI GI, GenBank ID, UniProt ID �Ǥ���
|
763
|
+
��̤ϡ���������䤤��碌 ID ���Ѵ� ID �Υ����ڤ�ʸ����Ȥ����֤���ޤ���
|
764
|
+
|
765
|
+
���͡�
|
766
|
+
string
|
767
|
+
|
768
|
+
�㡧
|
769
|
+
# NCBI GI �� Gene ID �� KEGG genes_id ���Ѵ�
|
770
|
+
serv.bconv("ncbi-gi:10047086 ncbi-gi:10047090 ncbi-geneid:14751")
|
742
771
|
|
743
772
|
==== LinkDB
|
744
773
|
|
@@ -755,6 +784,143 @@ db
|
|
755
784
|
get_linkdb_by_entry('eco:b0002', 'pathway', 1, 10)
|
756
785
|
get_linkdb_by_entry('eco:b0002', 'pathway', 11, 10)
|
757
786
|
|
787
|
+
+ �����Ҥȹ����ֹ�δط�
|
788
|
+
|
789
|
+
--- get_genes_by_enzyme(enzyme_id, org)
|
790
|
+
|
791
|
+
�о���ʪ��ˤ����ơ����ꤷ�������ֹ����İ����ҤΥꥹ�Ȥ��֤��ޤ���
|
792
|
+
|
793
|
+
���͡�
|
794
|
+
ArrayOfstring (genes_id)
|
795
|
+
|
796
|
+
�㡧
|
797
|
+
# �����ֹ� 1.1.1.1 �������IJ�ݤΰ����ҤΥꥹ��
|
798
|
+
get_genes_by_enzyme('ec:1.1.1.1', 'eco')
|
799
|
+
|
800
|
+
--- get_enzymes_by_gene(genes_id)
|
801
|
+
|
802
|
+
���ꤷ�������Ҥ��б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
803
|
+
|
804
|
+
���͡�
|
805
|
+
ArrayOfstring (enzyme_id)
|
806
|
+
|
807
|
+
�㡧
|
808
|
+
# ��IJ�ݰ����� 'eco:b0002' �ι����ֹ�Υꥹ��
|
809
|
+
get_enzymes_by_gene(eco:b0002)
|
810
|
+
|
811
|
+
|
812
|
+
+ ���ǡ�����ʪ���ꥢ�������δط�
|
813
|
+
|
814
|
+
--- get_enzymes_by_compound(compound_id)
|
815
|
+
|
816
|
+
���ꤷ������ʪ���б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
817
|
+
|
818
|
+
���͡�
|
819
|
+
ArrayOfstring (compound_id)
|
820
|
+
|
821
|
+
�㡧
|
822
|
+
# ����ʪ 'cpd:C00345' ����դ˴ؤ����ǤΥꥹ��
|
823
|
+
get_enzymes_by_compound('cpd:C00345')
|
824
|
+
|
825
|
+
--- get_enzymes_by_glycan(compound_id)
|
826
|
+
|
827
|
+
���ꤷ���������б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
828
|
+
|
829
|
+
���͡�
|
830
|
+
ArrayOfstring (glycan_id)
|
831
|
+
|
832
|
+
�㡧
|
833
|
+
# ���� 'gl:G00001' ����դ˴ؤ����ǤΥꥹ��
|
834
|
+
get_enzymes_by_glycan('gl:G00001')
|
835
|
+
|
836
|
+
--- get_enzymes_by_reaction(reaction_id)
|
837
|
+
|
838
|
+
���ꤷ���ꥢ��������ֹ���б���������ֹ�Υꥹ�Ȥ��֤��ޤ���
|
839
|
+
|
840
|
+
���͡�
|
841
|
+
ArrayOfstring (reaction_id)
|
842
|
+
|
843
|
+
�㡧
|
844
|
+
# �ꥢ��������ֹ� R00100 ����Ĺ��ǤΥꥹ��
|
845
|
+
get_enzymes_by_reaction('rn:R00100')
|
846
|
+
|
847
|
+
--- get_compounds_by_enzyme(enzyme_id)
|
848
|
+
|
849
|
+
���ꤷ�������ֹ���б����벽��ʪ�Υꥹ�Ȥ��֤��ޤ���
|
850
|
+
|
851
|
+
���͡�
|
852
|
+
ArrayOfstring (compound_id)
|
853
|
+
|
854
|
+
�㡧
|
855
|
+
# �����ֹ� 'ec:2.7.1.12' ����դ˴ؤ�벽��ʪ�Υꥹ��
|
856
|
+
get_compounds_by_enzyme('ec:2.7.1.12')
|
857
|
+
|
858
|
+
--- get_compounds_by_reaction(reaction_id)
|
859
|
+
|
860
|
+
���ꤷ���ꥢ���������б����벽��ʪ�Υꥹ�Ȥ��֤��ޤ���
|
861
|
+
|
862
|
+
���͡�
|
863
|
+
ArrayOfstring (compound_id)
|
864
|
+
|
865
|
+
�㡧
|
866
|
+
# �ꥢ��������ֹ� 'rn:R00100' ��ȿ���˴ؤ�벽��ʪ�Υꥹ��
|
867
|
+
get_compounds_by_reaction('rn:R00100')
|
868
|
+
|
869
|
+
--- get_glycans_by_enzyme(enzyme_id)
|
870
|
+
|
871
|
+
���ꤷ�������ֹ���б����������Υꥹ�Ȥ��֤��ޤ���
|
872
|
+
|
873
|
+
���͡�
|
874
|
+
ArrayOfstring (glycan_id)
|
875
|
+
|
876
|
+
�㡧
|
877
|
+
# �����ֹ� 'ec:2.4.1.141' ����դ˴ؤ�������Υꥹ��
|
878
|
+
get_glycans_by_enzyme('ec:2.4.1.141')
|
879
|
+
|
880
|
+
--- get_glycans_by_reaction(reaction_id)
|
881
|
+
|
882
|
+
���ꤷ���ꥢ���������б����������Υꥹ�Ȥ��֤��ޤ���
|
883
|
+
|
884
|
+
���͡�
|
885
|
+
ArrayOfstring (glycan_id)
|
886
|
+
|
887
|
+
�㡧
|
888
|
+
# �ꥢ��������ֹ� 'rn:R06164' ��ȿ���˴ؤ�������Υꥹ��
|
889
|
+
get_glycans_by_reaction('rn:R06164')
|
890
|
+
|
891
|
+
--- get_reactions_by_enzyme(enzyme_id)
|
892
|
+
|
893
|
+
���ꤷ�������ֹ���б�����ꥢ�������Υꥹ�Ȥ��֤��ޤ���
|
894
|
+
|
895
|
+
���͡�
|
896
|
+
ArrayOfstring (reaction_id)
|
897
|
+
|
898
|
+
�㡧
|
899
|
+
# �����ֹ� 'ec:2.7.1.12' ��ȿ���˴ؤ��ꥢ��������ֹ�Υꥹ��
|
900
|
+
get_reactions_by_enzyme('ec:2.7.1.12')
|
901
|
+
|
902
|
+
--- get_reactions_by_compound(compound_id)
|
903
|
+
|
904
|
+
���ꤷ������ʪ���б�����ꥢ�������Υꥹ�Ȥ��֤��ޤ���
|
905
|
+
|
906
|
+
���͡�
|
907
|
+
ArrayOfstring (reaction_id)
|
908
|
+
|
909
|
+
�㡧
|
910
|
+
# ����ʪ 'cpd:C00199' �ο���ȿ���˴ؤ��ꥢ��������ֹ�Υꥹ��
|
911
|
+
get_reactions_by_compound('cpd:C00199')
|
912
|
+
|
913
|
+
--- get_reactions_by_glycan(glycan_id)
|
914
|
+
|
915
|
+
���ꤷ���������б�����ꥢ�������Υꥹ�Ȥ��֤��ޤ���
|
916
|
+
|
917
|
+
���͡�
|
918
|
+
ArrayOfstring (reaction_id)
|
919
|
+
|
920
|
+
�㡧
|
921
|
+
# ���� 'gl:G00001' �ο���ȿ���˴ؤ��ꥢ��������ֹ�Υꥹ��
|
922
|
+
get_reactions_by_glycan('gl:G00001')
|
923
|
+
|
758
924
|
|
759
925
|
==== SSDB
|
760
926
|
|
@@ -1008,6 +1174,45 @@ bg_color_list
|
|
1008
1174
|
bg_list = ['#ff0000', 'yellow']
|
1009
1175
|
color_pathway_by_objects('path:eco00053', obj_list, fg_list, bg_list)
|
1010
1176
|
|
1177
|
+
--- color_pathway_by_elements(pathway_id, element_id_list, fg_color_list, bg_color_list)
|
1178
|
+
|
1179
|
+
���ꤷ�� element_id ���б�����ѥ���������Υ��֥������ȡ�Ĺ������ݤʤɡ�
|
1180
|
+
���Ф���ʸ�����Ȥ� fg_color_list �ǻ��ꤷ�������طʤ� bg_color_list ��
|
1181
|
+
���ꤷ������Ĥ��������������������� URL ���֤��ޤ���object_id_list ��
|
1182
|
+
fg_color_list, bg_color_list �����Ǥο��Ƚ��֤�·����褦�����դ���
|
1183
|
+
ɬ�פ�����ޤ���
|
1184
|
+
|
1185
|
+
KEGG PATHWAY �Ǥϡ�ʣ���ΰ����Ҥ���ĤΥܥå����˳�����Ƥ��Ƥ����ꡢ
|
1186
|
+
�դˣ��Ĥΰ����Ҥ�ʣ���Υܥå����˳�����Ƥ��Ƥ��뤳�Ȥ�����ޤ���
|
1187
|
+
���Τ褦�ʾ�� color_pathway_by_objects ��åɤǤ��ɤ�ʬ���뤳�Ȥ�
|
1188
|
+
����ޤ���color_pathway_by_elements ��Ȥ����ȤDz��Ǥ��ޤ���
|
1189
|
+
|
1190
|
+
element_id �� KEGG PATHWAY �� XML ɽ���Ǥ��� KGML �� <entry> ������
|
1191
|
+
���ꤵ��롢�ѥ���������Υ���ե������������ˤĤ���줿��ˡ�����
|
1192
|
+
���ͤǤ����ѥ���������� element_id �� get_elements_by_pathway ��åɤ�
|
1193
|
+
PathwayElement ���֥������ȤΥꥹ�ȤȤ������뤳�Ȥ��Ǥ��ޤ���
|
1194
|
+
PathwayElement �� type �� name °���ˤ������ҡ����ǡ�����ʪ�ʤɤ�
|
1195
|
+
�б����ꡢelement_id ���ͤ�Ȥäƥ��֥������Ȥ����ꤷ�ޤ���
|
1196
|
+
|
1197
|
+
KGML �ˤĤ��ƾܤ����ϲ����Υڡ����Ȥ��Ƥ���������
|
1198
|
+
|
1199
|
+
* ((<URL:http://www.genome.jp/kegg/xml/>))
|
1200
|
+
|
1201
|
+
����͡�
|
1202
|
+
string (URL)
|
1203
|
+
|
1204
|
+
�㡧
|
1205
|
+
# ����ݤΥѥ������� path:bsu00010 ��˺ܤäƤ��롢
|
1206
|
+
# ������ bsu:BG11350 (element_id 78, ec:3.2.1.86) ������/���طʤ�
|
1207
|
+
# ������ bsu:BG11203 (element_id 79, ec:3.2.1.86) ������/���طʤ�
|
1208
|
+
# ������ bsu:BG11685 (element_id 51, ec:2.7.1.2) ������/���طʤ�
|
1209
|
+
# ������ bsu:BG11685 (element_id 47, ec:2.7.1.2) ������/���طʤ�
|
1210
|
+
# ���줾���忧���������� URL ���֤��ޤ���
|
1211
|
+
element_id_list = [ 78, 79, 51, 47 ]
|
1212
|
+
fg_list = [ '#ff0000', '#0000ff', '#ff0000', '#0000ff' ]
|
1213
|
+
bg_list = [ '#ffff00', '#ffff00', '#ffcc00', '#ffcc00' ]
|
1214
|
+
color_pathway_by_elements('path:bsu00010', element_id_list, fg_list, bg_list)
|
1215
|
+
|
1011
1216
|
--- get_html_of_marked_pathway_by_objects(pathway_id, object_id_list)
|
1012
1217
|
|
1013
1218
|
����������˥���å��֥�ޥåפ�ޤ� HTML �ڡ����� URL ���֤�
|
@@ -1026,7 +1231,7 @@ bg_color_list
|
|
1026
1231
|
--- get_html_of_colored_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
|
1027
1232
|
|
1028
1233
|
����������˥���å��֥�ޥåפ�ޤ� HTML �ڡ����� URL ���֤�
|
1029
|
-
�������� '
|
1234
|
+
�С������� 'color_pathway_by_objects' ��åɤǤ���
|
1030
1235
|
|
1031
1236
|
���͡�
|
1032
1237
|
string (URL)
|
@@ -1040,8 +1245,53 @@ bg_color_list
|
|
1040
1245
|
bg_list = ['#ff0000', 'yellow', 'orange']
|
1041
1246
|
get_html_of_colored_pathway_by_objects('path:eco00970', obj_list, fg_list, bg_list)
|
1042
1247
|
|
1248
|
+
--- get_html_of_colored_pathway_by_elements(pathway_id, element_id_list, fg_color_list, bg_color_list)
|
1249
|
+
|
1250
|
+
����������˥���å��֥�ޥåפ�ޤ� HTML �ڡ����� URL ���֤�
|
1251
|
+
�С������� 'color_pathway_by_elements' ��åɤǤ���
|
1252
|
+
|
1253
|
+
���͡�
|
1254
|
+
string (URL)
|
1255
|
+
|
1256
|
+
�㡧
|
1257
|
+
# ����ݤΥѥ������� path:bsu00010 ��˺ܤäƤ��롢
|
1258
|
+
# ������ bsu:BG11350 (element_id 78, ec:3.2.1.86) ������/���طʤ�
|
1259
|
+
# ������ bsu:BG11203 (element_id 79, ec:3.2.1.86) ������/���طʤ�
|
1260
|
+
# ������ bsu:BG11685 (element_id 51, ec:2.7.1.2) ������/���طʤ�
|
1261
|
+
# ������ bsu:BG11685 (element_id 47, ec:2.7.1.2) ������/���طʤ�
|
1262
|
+
# �忧���������Υ���å��֥�ޥåפ�ɽ������ HTML �� URL ���֤��ޤ���
|
1263
|
+
element_id_list = [ 78, 79, 51, 47 ]
|
1264
|
+
fg_list = [ '#ff0000', '#0000ff', '#ff0000', '#0000ff' ]
|
1265
|
+
bg_list = [ '#ffff00', '#ffff00', '#ffcc00', '#ffcc00' ]
|
1266
|
+
color_pathway_by_elements('path:bsu00010', element_id_list, fg_list, bg_list)
|
1267
|
+
|
1043
1268
|
+ �ѥ���������Υ��֥������ȸ���
|
1044
1269
|
|
1270
|
+
--- get_elements_by_pathway(pathway_id)
|
1271
|
+
|
1272
|
+
���ꤷ���ѥ���������˺ܤäƤ��륪�֥����������ǤΥꥹ�Ȥ��֤��ޤ���
|
1273
|
+
����ˡ�ˤĤ��Ƥ� color_pathway_by_elements ��åɤȤ��Ƥ���������
|
1274
|
+
|
1275
|
+
���͡�
|
1276
|
+
ArrayOfPathwayElement
|
1277
|
+
|
1278
|
+
�㡧
|
1279
|
+
# ����ݤΥѥ������� path:bsu00010 ��˺ܤäƤ��� PathwayElement ��
|
1280
|
+
# �ꥹ�Ȥ�������롣
|
1281
|
+
get_elements_by_pathway('path:bsu00010')
|
1282
|
+
|
1283
|
+
# Ruby �ǰ����� bsu:BG11350, bsu:BG11203 �� bsu:BG11685 �� element_id ��
|
1284
|
+
# Ĵ�٤��㡣
|
1285
|
+
elems = serv.get_elements_by_pathway('path:bsu00010')
|
1286
|
+
genes = [ 'bsu:BG11350', 'bsu:BG11203', 'bsu:BG11685' ]
|
1287
|
+
elems.each do |elem|
|
1288
|
+
genes.each do |gene|
|
1289
|
+
if elem.names.include?(gene)
|
1290
|
+
puts gene, elem.element_id
|
1291
|
+
end
|
1292
|
+
end
|
1293
|
+
end
|
1294
|
+
|
1045
1295
|
--- get_genes_by_pathway(pathway_id)
|
1046
1296
|
|
1047
1297
|
���ꤷ���ѥ���������˺ܤäƤ�������ҤΥꥹ�Ȥ��֤��ޤ�����ʪ��̾��
|
@@ -1096,7 +1346,7 @@ pathway_id
|
|
1096
1346
|
|
1097
1347
|
�㡧
|
1098
1348
|
# ��IJ�ݤΥѥ������� 00260 �֤˺ܤäƤ���ꥢ�������Υꥹ��
|
1099
|
-
|
1349
|
+
get_reactions_by_pathway('path:eco00260')
|
1100
1350
|
|
1101
1351
|
--- get_kos_by_pathway(pathway_id)
|
1102
1352
|
|
@@ -1199,144 +1449,6 @@ pathway_id
|
|
1199
1449
|
get_linked_pathways('path:eco00620')
|
1200
1450
|
|
1201
1451
|
|
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
1452
|
==== GENES
|
1341
1453
|
|
1342
1454
|
GENES �ǡ����١������Ф����åɤΰ����Ǥ���GENES �ǡ����١����ˤĤ���
|
@@ -1394,6 +1506,7 @@ MOL
|
|
1394
1506
|
|
1395
1507
|
== Notes
|
1396
1508
|
|
1397
|
-
Last updated:
|
1509
|
+
Last updated: Feb 17, 2006
|
1398
1510
|
|
1399
1511
|
=end
|
1512
|
+
|