Extract KEGG Enzyme data
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7.5 years ago

Hi Guyz Can someone tell me how to extract a enzyme file which looks like this (having thousands of entries)

ENTRY       EC 1.1.1.1                  Enzyme
NAME        alcohol dehydrogenase;
CLASS       Oxidoreductases;
ENTRY       EC 1.1.1.157                Enzyme
NAME        3-hydroxybutyryl-CoA dehydrogenase;
CLASS       Oxidoreductases;

and so on ..... I want a file like

Entry                         name                                                                                classs
EC1.1.1.1                  alcohol dehydrogenase                                                    Oxidoreductases;
Ec 1.1.1.157              3-hydroxybutyryl-CoA dehydrogenase;                           Oxidoreductases;

please do the needful...

genome • 1.4k views
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You should be able to find information you need via this previous thread: Enzyme (Ec Number) - Description Mapping

please do the needful...

I am afraid you will have to do the work yourself :)

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 import sys
 f=open(sys.argv[1])
 arr=[]
 for i in f:
     j = i.strip("\n").split('\t')[1]
     arr.append(j)
 print [arr[i:i + 3] for i in xrange(0, len(arr), 3)]

This should work for you, assuming that you files is tab seperated file.

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