Duplication | awk | result Post: 303035785

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Top Forums UNIX for Beginners Questions & Answers Duplication | awk | result Post 303035785 by Aurimas on Monday 3rd of June 2019 07:48:48 AM

06-03-2019

Registered User

Thank you it works and I edited my previous post. I also have a similar question for this code then:

Code:

#!/bin/bash
read -p "amino acid: " AAA
if [[ "ALA ARG ASN ASP CYS GLN GLY GLU HIS ILE \
	   LEU LYS MET PHE PRO SER THR TRP TYR VAL" =~ $AAA ]]
then 
	for i in qac_"$AAA"_HS_*.pdb.txt; 
		do
			cat $i | grep -o -i $AAA | wc -l | awk '{print $1}'
    	       done
else
	exit 1
fi

.pdb.txt file looks like this:

Code:

c<A>r<134>R<ALA> c<C>r<7>R<DC> 12.9516 3.80289 . .
c<A>r<134>R<ALA> c<C>r<8>R<DG> 5.92777 4.58004 . .
c<A>r<138>R<ALA> c<C>r<7>R<DC> 2.65391 4.55194 . .
c<A>r<248>R<ALA> c<C>r<10>R<DG> 9.10674 3.59363 . .
c<A>r<248>R<ALA> c<C>r<11>R<DT> 0.0228499 5.34781 . .
c<A>r<248>R<ALA> c<W>r<4>R<DC> 21.2356 2.61229 . .
c<A>r<260>R<ALA> c<C>r<5>R<DC> 6.66863 5.26436 . .

You have 7 lines of r<x> where x is a number from 1 to 100 and 7 occurrences of ALA. However, how I could change grep to awk in the code so it would count 4 ALA instead of 7?

Last edited by Scrutinizer; 06-06-2019 at 12:23 PM.. Reason: quote tags -> code tags

Aurimas

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zegrep

ZGREP(1)                                                      General Commands Manual                                                     ZGREP(1)

NAME

       zgrep - search possibly compressed files for a regular expression

SYNOPSIS

       zgrep [ grep_options ] [ -e ] pattern filename...

DESCRIPTION

       Zgrep  invokes  grep  on  compressed  or  gzipped  files.   These  grep  options  will  cause  zgrep  to  terminate  with  an  error  code:
       (-[drRzZ]|--di*|--exc*|--inc*|--rec*|--nu*).  All other options specified are passed directly to grep.  If no file is specified,  then  the
       standard input is decompressed if necessary and fed to grep.  Otherwise the given files are uncompressed if necessary and fed to grep.

       If the GREP environment variable is set, zgrep uses it as the grep program to be invoked.

EXIT CODE

       2 - An option that is not supported was specified.

AUTHOR

       Charles Levert (charles@comm.polymtl.ca)

SEE ALSO

       grep(1), gzexe(1), gzip(1), zdiff(1), zforce(1), zmore(1), znew(1)

                                                                                                                                          ZGREP(1)

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