Mercurial > repos > chrisb > gap_all_glycan_tools

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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author chrisb
date Fri, 06 May 2016 08:05:48 -0400
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1
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2 from KEGG searches as follows should work
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3
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4
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5 /find/genes/shiga+toxin for keywords "shiga" and "toxin"
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6 /find/genes/"shiga toxin" for keywords "shiga toxin"
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7
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8 these do not function on all databases esp. enzyme
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9
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10 http://rest.kegg.jp/find/enzyme/deoxy+1.1.1 AND works
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11 http://rest.kegg.jp/find/enzyme/"deoxy%201.1.1" OR does not work
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12 http://rest.kegg.jp/find/enzyme/"deoxy 1.1.1" OR does not work
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13
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14 0
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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
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16 http://rest.kegg.jp/find/enzyme/"ec:2.4.99.1 ec:2.4.99.6" OR doesn't work
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17 http://rest.kegg.jp/find/enzyme/ec:2.4.99. works
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18
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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.
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23
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24
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25 # updated notes on KEGG behaviour
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26
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27 True for release Release 78.0+/05-05, May 16 (see http://rest.kegg.jp/info/genes)
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28
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29 multiple complex queries are not recommended.
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30
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31 Using the shiga toxin example from http://www.genome.jp/kegg/rest/keggapi.html
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32 /find/genes/shiga+toxin for keywords "shiga" and "toxin"
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33 /find/genes/"shiga toxin" for keywords "shiga toxin"
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34
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35 ## AND example
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36 /find/genes/shiga+toxin for keywords "shiga" and "toxin"
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37 http://rest.kegg.jp/find/genes/shiga+toxin
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38
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39 ## OR example
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40 /find/genes/"shiga toxin" for keywords "shiga toxin"
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41 http://rest.kegg.jp/find/genes/"shiga%20toxin"
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42
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43 ## BROKEN AND
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44 http://rest.kegg.jp/find/genes/"shiga+toxin"
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45 If query is in put in quotes.
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46 this result is the same as OR.
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47
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48 ## BROKEN OR
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49 http://rest.kegg.jp/find/genes/shiga%20toxin
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50 If query is not placed in quotations.
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51 this result is the same as AND.
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52
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53 # Recommendation
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54 Do not combine AND with OR queries