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Full Discussion: Search for a pattern,extract value(s) from next line, extract lines having those extracted value(s)
Top Forums Shell Programming and Scripting Search for a pattern,extract value(s) from next line, extract lines having those extracted value(s) Post 302673837 by Vryali on Wednesday 18th of July 2012 12:54:28 PM
Old 07-18-2012
I'm not sure about everything you want to do, but I think this does most of it:

Code:
sed -n '/^[\ \t]*COMPND.*CYTOCHROME\ C.*/{n;p;}' out.test | awk -F":" '{print $2}' | sed 's/[\ \,]//g'

sed - print the line after it finds the line with the matching regex.
awk - print only the text after the colon, could change this if needed pretty simply.
sed - remove spaces & commas so now it'll just read: A, or AB, or AC, etc.

Here's the list of lines where the 5th argument matches your AB:
Code:
awk '$5 ~ "[AB]"' out.test             
HEADER ELECTRON TRANSPORT 18-MAR-98 1A7V  
 TITLE CYTOCHROME C' FROM RHODOPSEUDOMONAS PALUSTRIS  
 COMPND 3 CHAIN: A, B  
 SOURCE 2 ORGANISM_SCIENTIFIC: RHODOPSEUDOMONAS PALUSTRIS;  
 ATOM 1 N GLN A 1 45.346 45.040 5.004 1.00 90.15 N  
 ATOM 2 CA GLN A 1 45.068 43.614 4.669 1.00 89.25 C  
 ATOM 3 C GLN A 1 45.626 42.698 5.751 1.00 89.26 C  
 ATOM 4 O GLN A 1 46.326 43.158 6.652 1.00 89.60 O  
 ATOM 5 CB GLN A 1 45.662 43.254 3.302 0.20 89.81 C  
 ATOM 6 CG GLN A 1 45.062 44.027 2.134 0.20 89.99 C  
 ATOM 7 CD GLN A 1 43.546 43.995 2.137 0.20 89.88 C  
 ATOM 8 OE1 GLN A 1 42.909 44.738 2.883 0.20 89.97 O  
 ATOM 920 OG SER A 125 44.804 18.922 -1.607 1.00 91.77 O  
 ATOM 921 OXT SER A 125 43.350 14.761 -1.403 1.00 94.70 O  
 ATOM 923 N GLN B 1 11.868 35.655 8.087 1.00 91.68 N  
 ATOM 924 CA GLN B 1 13.224 35.969 8.625 1.00 90.25 C  
 ATOM 925 C GLN B 1 13.335 37.449 8.982 1.00 89.59 C  
 ATOM 926 O GLN B 1 12.346 38.180 8.909 1.00 89.38 O  
 ATOM 927 CB GLN B 1 14.309 35.585 7.611 0.20 91.63 C  
 ATOM 928 CG GLN B 1 15.059 34.291 7.944 0.20 89.78 C

Adding a grep above for ^[\ \t]*ATOM will give us just the atom lines, so now we just combine it all:

Code:
$ awk "\$5 ~ \"[$(sed -n '/^[\ \t]*COMPND.*CYTOCHROME\ C.*/{n;p;}' out.test | awk -F':' '{print $2}' | sed 's/[\ \,]//g')]\"" out.test | grep '^[\ \t]*ATOM'
 ATOM 1 N GLN A 1 45.346 45.040 5.004 1.00 90.15 N  
 ATOM 2 CA GLN A 1 45.068 43.614 4.669 1.00 89.25 C  
 ATOM 3 C GLN A 1 45.626 42.698 5.751 1.00 89.26 C  
 ATOM 4 O GLN A 1 46.326 43.158 6.652 1.00 89.60 O  
 ATOM 5 CB GLN A 1 45.662 43.254 3.302 0.20 89.81 C  
 ATOM 6 CG GLN A 1 45.062 44.027 2.134 0.20 89.99 C  
 ATOM 7 CD GLN A 1 43.546 43.995 2.137 0.20 89.88 C  
 ATOM 8 OE1 GLN A 1 42.909 44.738 2.883 0.20 89.97 O  
 ATOM 920 OG SER A 125 44.804 18.922 -1.607 1.00 91.77 O  
 ATOM 921 OXT SER A 125 43.350 14.761 -1.403 1.00 94.70 O  
 ATOM 923 N GLN B 1 11.868 35.655 8.087 1.00 91.68 N  
 ATOM 924 CA GLN B 1 13.224 35.969 8.625 1.00 90.25 C  
 ATOM 925 C GLN B 1 13.335 37.449 8.982 1.00 89.59 C  
 ATOM 926 O GLN B 1 12.346 38.180 8.909 1.00 89.38 O  
 ATOM 927 CB GLN B 1 14.309 35.585 7.611 0.20 91.63 C  
 ATOM 928 CG GLN B 1 15.059 34.291 7.944 0.20 89.78 C

Edit: Probably a cleaner way to do this using just awk, but I never do things that way, so not sure on the exact changes you'd need to make.
Last edited by Vryali; 07-18-2012 at 02:13 PM.. Reason: Cleaned a bit.
This User Gave Thanks to Vryali For This Post:
AshwaniSharma09
 

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