Extract KEGG Enzyme data
0
0
Entering edit mode
6.9 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 • 1.3k views
ADD COMMENT
0
Entering edit mode

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 :)

ADD REPLY
0
Entering edit mode
 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.

ADD REPLY

Login before adding your answer.

Traffic: 2968 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6