[BioRuby-cvs] bioruby/doc KEGG_API.rd, 1.4, 1.5 KEGG_API.rd.ja, 1.10, 1.11
Katayama Toshiaki
k at dev.open-bio.org
Wed Dec 27 13:40:47 UTC 2006
Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv10850
Modified Files:
KEGG_API.rd KEGG_API.rd.ja
Log Message:
* obsoleted comments are removed
Index: KEGG_API.rd.ja
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/KEGG_API.rd.ja,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** KEGG_API.rd.ja 27 Dec 2006 13:32:40 -0000 1.10
--- KEGG_API.rd.ja 27 Dec 2006 13:40:45 -0000 1.11
***************
*** 69,78 ****
* ((<get_reverse_best_neighbors_by_gene>))
* ((<get_paralogs_by_gene>))
- # * ((<get_neighbors_by_gene>))
- # * ((<get_similarity_between_genes>))
* ((<Motif>))
* ((<get_motifs_by_gene>))
* ((<get_genes_by_motifs>))
- # * ((<KO, OC, PC>))
* ((<KO>))
* ((<get_ko_by_gene>))
--- 69,75 ----
***************
*** 80,86 ****
* ((<get_genes_by_ko_class>))
* ((<get_genes_by_ko>))
- # * ((<get_oc_members_by_gene>))
- # * ((<get_pc_members_by_gene>))
- # * ((<get_ko_members>))
* ((<PATHWAY>))
* ((<¥Ñ¥¹¥¦¥§¥¤¤Ø¤Î¿§¤Å¤±>))
--- 77,80 ----
***************
*** 1136,1153 ****
* ((<URL:http://www.genome.jp/kegg/ssdb/>))
- #--- get_neighbors_by_gene(string:genes_id, string:org, int:offset, int:limit)
- #
- #»ØÄꤷ¤¿ genes_id ¤Î°äÅÁ»Ò¤Ë¥Û¥â¥í¥¸¡¼¤Î¤¢¤ëÁ´°äÅÁ»Ò¤ò»ØÄꤷ¤¿À¸Êª¤«¤é
- #¸¡º÷¤·¤Þ¤¹¡£¤Þ¤¿ org ¤Ë 'all' ¤ò»ØÄꤹ¤ë¤ÈÁ´À¸Êª¼ï¤«¤é¸¡º÷¤·¤Þ¤¹¡£
- #
- #ÌáÃÍ¡§
- # ArrayOfSSDBRelation
- #
- #Î㡧
- # # ÂçIJ¶Ý¤Î°äÅÁ»Ò b0002 ¤ËÁêƱÀ¤Î¤¢¤ë°äÅÁ»Ò¤òÁ´¤Æ¸¡º÷¤·¤Æ¡¢·ë²Ì¤Î£±ÈÖ
- # # ¤«¤é£±£°ÈÖÌܤޤǤòÊÖ¤·¤Þ¤¹
- # get_neighbors_by_gene('eco:b0002', 'all' 1, 10)
- # # ¼¡¤Î£±£°¸Ä¤ò offset = offset + limit ¤È¤·¤Æ¼è¤ê¤Þ¤¹
- # get_neighbors_by_gene('eco:b0002', 'all' 11, 10)
--- get_best_best_neighbors_by_gene(string:genes_id, int:offset, int:limit)
--- 1130,1133 ----
***************
*** 1199,1212 ****
get_paralogs_by_gene('eco:b0002', 11, 10)
- #--- get_similarity_between_genes(string:genes_id1, string:genes_id2)
- #
- #»ØÄꤷ¤¿£²¤Ä¤Î°äÅÁ»Ò´Ö¤Î Smith-Waterman ¥¹¥³¥¢¤ò´Þ¤à¥Ç¡¼¥¿¤òÊÖ¤·¤Þ¤¹¡£
- #
- #ÌáÃÍ¡§
- # SSDBRelation
- #
- #Î㡧
- # # ÂçIJ¶Ý¤Î b0002 °äÅÁ»Ò¤È b3940 °äÅÁ»Ò´Ö¤Î¥¹¥³¥¢¤ä¥¢¥é¥¤¥á¥ó¥ÈÎΰè¤òÆÀ¤ë
- # get_similarity_between_genes('eco:b0002', 'eco:b3940')
==== Motif
--- 1179,1182 ----
***************
*** 1255,1268 ****
get_ko_by_gene('eco:b0002')
- #--- get_ko_members(string:ko_id)
- #
- #»ØÄꤷ¤¿ ko_id ¤Î KO ¥¨¥ó¥È¥ê¤Ë´Þ¤Þ¤ì¤ë°äÅÁ»Ò¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
- #
- #ÌáÃÍ¡§
- # ArrayOfstring (genes_id)
- #
- #Î㡧
- # # KO ÈÖ¹æ K02208 ¤Î¥¢¥µ¥¤¥ó¤µ¤ì¤Æ¤¤¤ë°äÅÁ»Ò¤Î¥ê¥¹¥È
- # get_ko_by_gene('ko:K02598')
--- get_ko_by_ko_class(string:ko_class_id)
--- 1225,1228 ----
***************
*** 1303,1329 ****
get_genes_by_ko('ko:K00010', 'all')
- #--- get_oc_members_by_gene(string:genes_id, int:offset, int:limit)
- #
- #»ØÄꤷ¤¿°äÅÁ»Ò¤ÈƱ¤¸ OC ¤Ë°¤¹¤ë°äÅÁ»Ò¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
- #
- #ÌáÃÍ¡§
- # ArrayOfstring (genes_id)
- #
- #Î㡧
- # # eco:b0002 °äÅÁ»Ò¤ÈƱ¤¸¥ª¡¼¥½¥í¥°¥¯¥é¥¹¥¿¡¼¤Ë´Þ¤Þ¤ì¤ë°äÅÁ»Ò¤Î¥ê¥¹¥È
- # get_oc_members_by_gene('eco:b0002', 1, 10)
- # get_oc_members_by_gene('eco:b0002', 11, 10)
- #--- get_pc_members_by_gene(string:genes_id, int:offset, int:limit)
- #
- #»ØÄꤷ¤¿°äÅÁ»Ò¤ÈƱ¤¸ PC ¤Ë°¤¹¤ë°äÅÁ»Ò¤Î¥ê¥¹¥È¤òÊÖ¤·¤Þ¤¹¡£
- #
- #ÌáÃÍ¡§
- # ArrayOfstring (genes_id)
- #
- #Î㡧
- # # eco:b0002 °äÅÁ»Ò¤ÈƱ¤¸¥Ñ¥é¥í¥°¥¯¥é¥¹¥¿¡¼¤Ë´Þ¤Þ¤ì¤ë°äÅÁ»Ò¤Î¥ê¥¹¥È
- # get_pc_members_by_gene('eco:b0002', 1, 10)
- # get_pc_members_by_gene('eco:b0002', 11, 10)
==== PATHWAY
--- 1263,1267 ----
Index: KEGG_API.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/KEGG_API.rd,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** KEGG_API.rd 27 Dec 2006 13:32:39 -0000 1.4
--- KEGG_API.rd 27 Dec 2006 13:40:45 -0000 1.5
***************
*** 118,127 ****
* ((<get_reverse_best_neighbors_by_gene>))
* ((<get_paralogs_by_gene>))
- # * ((<get_neighbors_by_gene>))
- # * ((<get_similarity_between_genes>))
* ((<Motif>))
* ((<get_motifs_by_gene>))
* ((<get_genes_by_motifs>))
- # * ((<KO, OC, PC>))
* ((<KO>))
* ((<get_ko_by_gene>))
--- 118,124 ----
***************
*** 129,135 ****
* ((<get_genes_by_ko_class>))
* ((<get_genes_by_ko>))
- # * ((<get_oc_members_by_gene>))
- # * ((<get_pc_members_by_gene>))
- # * ((<get_ko_members>))
* ((<PATHWAY>))
* ((<Coloring pathways>))
--- 126,129 ----
***************
*** 706,724 ****
length2 amino acid length of the genes_id2 (int)
- #Notice (26 Nov, 2004):
- #
- #We found a serious bug with the 'best_flag_1to2' and 'best_flag_2to1'
- #fields in the SSDBRelation data type. The methods returning the
- #SSDBRelation (and ArrayOfSSDBRelation) data type had returned the
- #opposite values of the intended results with the both fields.
- #The following methods had been affected by this bug:
- #
- ## * get_neighbors_by_gene
- # * get_best_neighbors_by_gene
- # * get_reverse_best_neighbors_by_gene
- # * get_paralogs_by_gene
- ## * get_similarity_between_genes
- #
- #This problem is fixed in the KEGG API version 3.2.
+ ArrayOfSSDBRelation
--- 700,703 ----
***************
*** 1165,1182 ****
* ((<URL:http://www.genome.jp/kegg/ssdb/>))
- #--- get_neighbors_by_gene(string:genes_id, string:org, int:offset, int:limit)
- #
- #Search homologous genes of the user specified 'genes_id' from specified
- #organism (or from all organisms if 'all' is given as org).
- #
- #Return value:
- # ArrayOfSSDBRelation
- #
- #Examples:
- # # This will search all homologous genes of E. coli gene 'b0002'
- # # in the SSDB and returns the first ten results.
- # get_neighbors_by_gene('eco:b0002', 'all', 1, 10)
- # # Next ten results.
- # get_neighbors_by_gene('eco:b0002', 'all', 11, 10)
--- get_best_best_neighbors_by_gene(string:genes_id, int:offset, int:limit)
--- 1144,1147 ----
***************
*** 1228,1242 ****
get_paralogs_by_gene('eco:b0002', 11, 10)
- #--- get_similarity_between_genes(string:genes_id1, string:genes_id2)
- #
- #Returns data containing Smith-Waterman score and alignment positions
- #between the two genes.
- #
- #Return value:
- # SSDBRelation
- #
- #Example:
- # # Returns a 'sw_score' between two E. coli genes 'b0002' and 'b3940'
- # get_similarity_between_genes('eco:b0002', 'eco:b3940')
==== Motif
--- 1193,1196 ----
***************
*** 1282,1295 ****
get_ko_by_gene('eco:b0002')
- #--- get_ko_members(string:ko_id)
- #
- #Returns all genes assigned to the given KO entry.
- #
- #Return value:
- # ArrayOfstring (genes_id)
- #
- #Example
- # # Returns genes_ids those which belong to KO entry 'ko:K02598'.
- # get_ko_members('ko:K02598')
--- get_ko_by_ko_class(string:ko_class_id)
--- 1236,1239 ----
***************
*** 1331,1359 ****
get_genes_by_ko('ko:K00010', 'all')
- #--- get_oc_members_by_gene(string:genes_id, int:offset, int:limit)
- #
- #Search all members of the same OC (KEGG Ortholog Cluster) to which given
- #genes_id belongs.
- #
- #Return value:
- # ArrayOfstring (genes_id)
- #
- #Example
- # # Returns genes belonging to the same OC with eco:b0002 gene.
- # get_oc_members_by_gene('eco:b0002', 1, 10)
- # get_oc_members_by_gene('eco:b0002', 11, 10)
- #--- get_pc_members_by_gene(string:genes_id, int:offset, int:limit)
- #
- #Search all members of the same PC (KEGG Paralog Cluster) to which given
- #genes_id belongs.
- #
- #Return value:
- # ArrayOfstring (genes_id)
- #
- #Example
- # # Returns genes belonging to the same PC with eco:b0002 gene.
- # get_pc_members_by_gene('eco:b0002', 1, 10)
- # get_pc_members_by_gene('eco:b0002', 11, 10)
==== PATHWAY
--- 1275,1279 ----
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