diff get_data/kegg_glycan/2 @ 1:0a5e0df17054 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_data/kegg_glycan/2	Fri May 06 08:05:48 2016 -0400
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+
+from KEGG searches as follows should work
+
+
+/find/genes/shiga+toxin	  	for keywords "shiga" and "toxin"
+/find/genes/"shiga toxin"	  	for keywords "shiga toxin"
+
+these do not function on all databases esp. enzyme
+
+http://rest.kegg.jp/find/enzyme/deoxy+1.1.1 AND works
+http://rest.kegg.jp/find/enzyme/"deoxy%201.1.1" OR does not work
+http://rest.kegg.jp/find/enzyme/"deoxy 1.1.1" OR does not work
+
+0
+http://rest.kegg.jp/find/enzyme/ec:2.4.99.1+ec:2.4.99.6 AND works but return nothing as no overlap
+http://rest.kegg.jp/find/enzyme/"ec:2.4.99.1 ec:2.4.99.6" OR doesn't work
+http://rest.kegg.jp/find/enzyme/ec:2.4.99.  works
+
+ ../../../virtualpy/bin/python findKEGG.py  -d enzyme -q 2.4.99.1+2.4.99.6 . works but return None in python. which breaks file writing. rather fix this.
+
+
+
+
+
+# updated notes on KEGG behaviour
+
+True for release  Release 78.0+/05-05, May 16 (see http://rest.kegg.jp/info/genes)
+
+multiple complex queries are not recommended.
+
+Using the shiga toxin example from http://www.genome.jp/kegg/rest/keggapi.html
+/find/genes/shiga+toxin	  	for keywords "shiga" and "toxin"
+/find/genes/"shiga toxin"	  	for keywords "shiga toxin"
+
+## AND example
+/find/genes/shiga+toxin	  	for keywords "shiga" and "toxin"
+http://rest.kegg.jp/find/genes/shiga+toxin
+
+## OR example
+/find/genes/"shiga toxin"	  	for keywords "shiga toxin"
+http://rest.kegg.jp/find/genes/"shiga%20toxin"
+
+## BROKEN AND
+http://rest.kegg.jp/find/genes/"shiga+toxin"
+If query is in put in quotes.
+ this result is the same as OR.
+
+## BROKEN OR
+http://rest.kegg.jp/find/genes/shiga%20toxin
+If query is not placed in quotations.
+ this result is the same as AND.
+
+# Recommendation 
+Do not combine AND with OR queries