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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 302673811 by AshwaniSharma09 on Wednesday 18th of July 2012 12:17:58 PM
Old 07-18-2012
Search for a pattern,extract value(s) from next line, extract lines having those extracted value(s)
I have hundreds of files to process. In each file
  1. I need to look for a pattern then
  2. extract value(s) from next line and then
  3. search for value(s) selected from point (2) in the same file at a specific position.



Code:
 HEADER ELECTRON TRANSPORT 18-MAR-98 1A7V  
 TITLE CYTOCHROME C' FROM RHODOPSEUDOMONAS PALUSTRIS  
 COMPND MOL_ID: 1;  
 COMPND 2 MOLECULE: CYTOCHROME C';  
 COMPND 3 CHAIN: A, B  
 SOURCE MOL_ID: 1;  
 SOURCE 2 ORGANISM_SCIENTIFIC: RHODOPSEUDOMONAS PALUSTRIS;  
 SOURCE 3 ORGANISM_TAXID: 1076  
 KEYWDS ELECTRON TRANSPORT  
 EXPDTA X-RAY DIFFRACTION  
 AUTHOR N.SHIBATA,S.IBA,S.MISAKI,T.E.MEYER,R.G.BARTSCH,  
 AUTHOR 2 M.A.CUSANOVICH,Y.HIGUCHI,N.YASUOKA  
 REVDAT 2 24-FEB-09 1A7V 1 VERSN  
 REVDAT 1 17-JUN-98 1A7V 0  
 ...........................................................................
 Many lines in between
 ..........................................................................
 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  
 TER 922 SER A 125
 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  
 ..........................................................................................................................
 ..........................................................................................................................

In this example,
  1. I need to look for CYTOCHROME C
  2. extract a and b from just next line
  3. print all lines having a and b at field number 5.


So the output should be:

Code:
 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  
 .............................................................................................................................
 .............................................................................................................................

Now the problem is, the search pattern can be in many ways, like:
Code:
  
 COMPND 2 MOLECULE: CYTOCHROME C';  
 COMPND 3 CHAIN: A;
 

 OR
 

 COMPND 2 MOLECULE: CYTOCHROME C';  
 COMPND 3 CHAIN: A, B  
 

 OR
 

 COMPND 2 MOLECULE: CYTOCHROME C';  
 COMPND 3 CHAIN: A, B , C, D;
 

 OR
 

 COMPND 2 MOLECULE: CYTOCHROME C;  
 COMPND 3 CHAIN: A;  
 COMPND 4 SYNONYM: SOXA;  
 COMPND 5 MOL_ID: 2;  
 COMPND 6 MOLECULE: CYTOCHROME C;  
 COMPND 7 CHAIN: B;


Sorry for sounding complicated. Any help is highly appreciated. I respect your time.



Thanks and Regards,
Ashwani
 

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