Thanks for your help..
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EC file parsing
Dear all
I have some issue with the below data:
ENTRY EC 1.1.1.35 Enzyme
NAME 3-hydroxyacyl-CoA dehydrogenase;
beta-hydroxyacyl dehydrogenase;
beta-keto-reductase;
3-keto reductase;
3-hydroxyacyl coenzyme A dehydrogenase;
beta-hydroxyacyl-coenzyme A synthetase;
beta-hydroxyacylcoenzyme A dehydrogenase;
beta-hydroxybutyrylcoenzyme A dehydrogenase;
3-hydroxyacetyl-coenzyme A dehydrogenase;
L-3-hydroxyacyl coenzyme A dehydrogenase;
L-3-hydroxyacyl CoA dehydrogenase;
beta-hydroxyacyl CoA dehydrogenase;
3beta-hydroxyacyl coenzyme A dehydrogenase;
3-hydroxybutyryl-CoA dehydrogenase;
beta-ketoacyl-CoA reductase;
beta-hydroxy acid dehydrogenase;
3-L-hydroxyacyl-CoA dehydrogenase;
3-hydroxyisobutyryl-CoA dehydrogenase;
1-specific DPN-linked beta-hydroxybutyric dehydrogenase
CLASS Oxidoreductases;
Acting on the CH-OH group of donors;
With NAD+ or NADP+ as acceptor
How can I parse all the multi-line entries of this file like ENTRY, NAME, and CLASS with multi-line entries mentioned above?
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Ram
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sharmatina189059 •
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sharmatina189059 •
2 answers
Code (this code would not print enzyme in first column i.e Entry column):
$ awk -F " " '{if ($1=="") {$1=prev} prev=$1};{gsub(" +","\t")}1' test.txt | datamash -g 1 collapse 2| datamash transpose > test2.txt
output:
ENTRY NAME CLASS
EC 1.1.1.35 3-hydroxyacyl-CoA dehydrogenase;,beta-hydroxyacyl dehydrogenase;,beta-keto-reductase;,3-keto reductase;,3-hydroxyacyl coenzyme A dehydrogenase;,beta-hydroxyacyl-coenzyme A synthetase;,beta-hydroxyacylcoenzyme A dehydrogenase;,beta-hydroxybutyrylcoenzyme A dehydrogenase;,3-hydroxyacetyl-coenzyme A dehydrogenase;,L-3-hydroxyacyl coenzyme A dehydrogenase;,L-3-hydroxyacyl CoA dehydrogenase;,beta-hydroxyacyl CoA dehydrogenase;,3beta-hydroxyacyl coenzyme A dehydrogenase;,3-hydroxybutyryl-CoA dehydrogenase;,beta-ketoacyl-CoA reductase;,beta-hydroxy acid dehydrogenase;,3-L-hydroxyacyl-CoA dehydrogenase;,3-hydroxyisobutyryl-CoA dehydrogenase;,1-specific DPN-linked beta-hydroxybutyric dehydrogenase Oxidoreductases;,Acting on the CH-OH group of donors;,With NAD+ or NADP+ as acceptor
If you don't mind enzyme in first column, then the code is:
$ awk -F " " '{if ($1=="") {$1=prev} prev=$1}1' test.txt | awk '{$1=$1; sub(" ","\t")}1' | datamash -g1 collapse 2 | datamash transpose
input:
$ cat test.txt
ENTRY EC 1.1.1.35 Enzyme
NAME 3-hydroxyacyl-CoA dehydrogenase;
beta-hydroxyacyl dehydrogenase;
beta-keto-reductase;
3-keto reductase;
3-hydroxyacyl coenzyme A dehydrogenase;
beta-hydroxyacyl-coenzyme A synthetase;
beta-hydroxyacylcoenzyme A dehydrogenase;
beta-hydroxybutyrylcoenzyme A dehydrogenase;
3-hydroxyacetyl-coenzyme A dehydrogenase;
L-3-hydroxyacyl coenzyme A dehydrogenase;
L-3-hydroxyacyl CoA dehydrogenase;
beta-hydroxyacyl CoA dehydrogenase;
3beta-hydroxyacyl coenzyme A dehydrogenase;
3-hydroxybutyryl-CoA dehydrogenase;
beta-ketoacyl-CoA reductase;
beta-hydroxy acid dehydrogenase;
3-L-hydroxyacyl-CoA dehydrogenase;
3-hydroxyisobutyryl-CoA dehydrogenase;
1-specific DPN-linked beta-hydroxybutyric dehydrogenase
CLASS Oxidoreductases;
Acting on the CH-OH group of donors;
With NAD+ or NADP+ as acceptor
Is there a way to retrieve substrate , Product, enzyme class and interacting pathway using KEGG API and script if you have multiple number of EC numbers and Reaction number from KEGG. EC 1.1.1.35 EC 1.1.1.100 and so on
and rn:R1135 rn:R05233
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I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:
Please give an example of the desired output.
This does not work..I need all corresponding entries..
Eh? I didn't propose a solution. I think you reacted on the wrong comment.
It prints only single line output..I need multi-line output.
@OP: Please post expected output.
Again, I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below: