EC file parsing

Question

[sharmatina189059]

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?

[Pierre Lindenbaum]

 grep  -E '^(ENTRY|NAME|CLASS)'  input.txt | cut -c 10- | paste - - -

[sharmatina189059]

It prints only single line output..I need multi-line output.

[WouterDeCoster]

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.

[sharmatina189059]

This does not work..I need all corresponding entries..

[WouterDeCoster]

Eh? I didn't propose a solution. I think you reacted on the wrong comment.

[cpad0112]

@OP: Please post expected output.

[sharmatina189059]

ENTRY            NAME             CLASS
EC 1.1.1.35   3-hydroxyacyl-CoA dehydrogenase;          Oxidoreductases;
            Acting on the CH-OH group of donors;
            With NAD+ or NADP+ as acceptor
            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 d

[WouterDeCoster]

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:

[sharmatina189059]

ENTRY            NAME             CLASS
EC 1.1.1.35   3-hydroxyacyl-CoA dehydrogenase;          Oxidoreductases;Acting on the CH-OH group of donors;
        With NAD+ or NADP+ as acceptor
            Acting on the CH-OH group of donors;
            With NAD+ or NADP+ as acceptor
            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 d

Answer 1

[cpad0112]

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

[sharmatina189059]

Thanks for your help..

Answer 2

[sharmatina189059]

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