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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 302674069 by AshwaniSharma09 on Thursday 19th of July 2012 10:27:57 AM
Old 07-19-2012
Thank you very much Corona688, you made my day Smilie.
This script is working fine when I put it in a shell script like this:
Code:
cat temp.sh 
awk -F":" '(!RGX) && /CYTOCHROME C/ && (NF==2) {
        getline
        gsub(/[;, ]*/, "");
        RGX="[" $2 "]"
        FS=" ";
} RGX && ($5 ~ RGX) && /^ATOM/' 1A3R.pdb

But I don't know how to run it on command line directly or by saving it in an AWK script like temp.awk although I use AWK a little bit. Once again thank you very much for the helpSmilie.

Quote:
Originally Posted by Corona688
Whenever you have sed | awk | grep | kitchen | sink, it can probably be done all in one awk. It's a lot more than a glorified 'cut'.

1) Search for a line containing CYTOCHROME C where there's two fields (as delimited by : )
2) Get the next line, clean it up with gsub(strip out " " ";" ","), turn the second field into a regex like [AB]
3) Set field separator to space.
4) For every line thereafter, if the line contains ATOM and the fifth field matches the regex, print the line.

Code:
awk -F":" '(!RGX) && /CYTOCHROME C/ && (NF==2) {
        getline
        gsub(/[;, ]*/, "");
        RGX="[" $2 "]"
        FS=" ";
} RGX && ($5 ~ RGX) && /ATOM/' inputfile

---------- Post updated at 11:24 AM ---------- Previous update was at 11:21 AM ----------

Thanks Vryali for your reply Smilie.

---------- Post updated at 07:57 PM ---------- Previous update was at 11:24 AM ----------

On running the script, some files are giving error. These are few top most lines of 2 files and their respective errors:


Code:
  	 	 	 	 	 	   cat 132L.pdb
 

 HEADER    HYDROLASE(O-GLYCOSYL)                   02-JUN-93   132L 
 TITLE     STRUCTURAL CONSEQUENCES OF REDUCTIVE METHYLATION OF LYSINE 
 TITLE    2 RESIDUES IN HEN EGG WHITE LYSOZYME: AN X-RAY ANALYSIS AT 
 TITLE    3 1.8 ANGSTROMS RESOLUTION 
 COMPND    MOL_ID: 1; 
 COMPND   2 MOLECULE: HEN EGG WHITE LYSOZYME; 
 COMPND   3 CHAIN: A; 
 COMPND   4 EC: 3.2.1.17; 
 COMPND   5 ENGINEERED: YES 
 SOURCE    MOL_ID: 1; 
 SOURCE   2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; 
 SOURCE   3 ORGANISM_COMMON: CHICKEN; 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 

 cat 1G7H.pdb  
 

 HEADER    HYDROLASE INHIBITOR/HYDROLASE           10-NOV-00   1G7H 
 TITLE     CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED 
 TITLE    2 WITH THE MUTANT ANTI-HEL MONOCLONAL ANTIBODY D1.3(VLW92A) 
 COMPND    MOL_ID: 1; 
 COMPND   2 MOLECULE: ANTI-HEN EGG WHITE LYSOZYME MONOCLONAL ANTIBODY 
 COMPND   3 D1.3; 
 COMPND   4 CHAIN: A; 
 COMPND   5 FRAGMENT: LIGHT CHAIN; 
 COMPND   6 ENGINEERED: YES; 
 COMPND   7 MUTATION: YES; 
 COMPND   8 MOL_ID: 2; 
 COMPND   9 MOLECULE: ANTI-HEN EGG WHITE LYSOZYME MONOCLONAL ANTIBODY 
 COMPND  10 D1.3; 
 COMPND  11 CHAIN: B; 
 COMPND  12 FRAGMENT: HEAVY CHAIN; 
 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 

 errors:
 

 awk: cmd. line:6: (FILENAME=132L.pdb FNR=4) fatal: Unmatched [ or [^: /[]/ 
 

 awk: cmd. line:6: (FILENAME=1G7H.pdb FNR=6) fatal: Unmatched [ or [^: /[]/

Is it something with gsub function or following expression? Thanks & Regards
 

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