Mercurial > repos > chrisb > gap_all_glycan_tools
comparison get_data/kegg_glycan/2 @ 1:0a5e0df17054 draft default tip
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| author | chrisb |
|---|---|
| date | Fri, 06 May 2016 08:05:48 -0400 |
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| 0:89592faa2875 | 1:0a5e0df17054 |
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| 1 | |
| 2 from KEGG searches as follows should work | |
| 3 | |
| 4 | |
| 5 /find/genes/shiga+toxin for keywords "shiga" and "toxin" | |
| 6 /find/genes/"shiga toxin" for keywords "shiga toxin" | |
| 7 | |
| 8 these do not function on all databases esp. enzyme | |
| 9 | |
| 10 http://rest.kegg.jp/find/enzyme/deoxy+1.1.1 AND works | |
| 11 http://rest.kegg.jp/find/enzyme/"deoxy%201.1.1" OR does not work | |
| 12 http://rest.kegg.jp/find/enzyme/"deoxy 1.1.1" OR does not work | |
| 13 | |
| 14 0 | |
| 15 http://rest.kegg.jp/find/enzyme/ec:2.4.99.1+ec:2.4.99.6 AND works but return nothing as no overlap | |
| 16 http://rest.kegg.jp/find/enzyme/"ec:2.4.99.1 ec:2.4.99.6" OR doesn't work | |
| 17 http://rest.kegg.jp/find/enzyme/ec:2.4.99. works | |
| 18 | |
| 19 ../../../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. | |
| 20 | |
| 21 | |
| 22 | |
| 23 | |
| 24 | |
| 25 # updated notes on KEGG behaviour | |
| 26 | |
| 27 True for release Release 78.0+/05-05, May 16 (see http://rest.kegg.jp/info/genes) | |
| 28 | |
| 29 multiple complex queries are not recommended. | |
| 30 | |
| 31 Using the shiga toxin example from http://www.genome.jp/kegg/rest/keggapi.html | |
| 32 /find/genes/shiga+toxin for keywords "shiga" and "toxin" | |
| 33 /find/genes/"shiga toxin" for keywords "shiga toxin" | |
| 34 | |
| 35 ## AND example | |
| 36 /find/genes/shiga+toxin for keywords "shiga" and "toxin" | |
| 37 http://rest.kegg.jp/find/genes/shiga+toxin | |
| 38 | |
| 39 ## OR example | |
| 40 /find/genes/"shiga toxin" for keywords "shiga toxin" | |
| 41 http://rest.kegg.jp/find/genes/"shiga%20toxin" | |
| 42 | |
| 43 ## BROKEN AND | |
| 44 http://rest.kegg.jp/find/genes/"shiga+toxin" | |
| 45 If query is in put in quotes. | |
| 46 this result is the same as OR. | |
| 47 | |
| 48 ## BROKEN OR | |
| 49 http://rest.kegg.jp/find/genes/shiga%20toxin | |
| 50 If query is not placed in quotations. | |
| 51 this result is the same as AND. | |
| 52 | |
| 53 # Recommendation | |
| 54 Do not combine AND with OR queries |