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Full Discussion: Duplication | awk | result
Top Forums UNIX for Beginners Questions & Answers Duplication | awk | result Post 303035759 by Aurimas on Sunday 2nd of June 2019 10:19:28 AM
Old 06-02-2019
When I run your proposed code

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 HS_*.pdb
          do  cat $i | voronota get-balls-from-atoms-file --annotated | \
                  awk -F"[<>]" -vSRCH="$AAA" '$0 ~ SRCH && !OCC[$4]++ {CNT++ } END {print CNT+0}' $i 
          done
  else  echo exit 1
fi

on MAC OS Mojave terminal I get this error:
Code:
awk: invalid -v option


Last edited by Scrutinizer; 06-06-2019 at 12:37 PM.. Reason: quote tags -> code tags
 

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BFBTESTER(1)						      General Commands Manual						      BFBTESTER(1)

NAME
bfbtester - Brute Force Binary Tester SYNOPSIS
bfbtester [-htv] [-d level] [-r rejects] [-o out-file] [-x max-execs] -a|[-sme] files ... DESCRIPTION
BFBTester is great for doing quick, proactive, security checks of binary programs. BFBTester will perform checks of single and multiple argument command line overflows as well as environment variable overflows. BFBTester can also watch for tempfile creation activity to alert the user of any programs using unsafe tempfile names. While BFBTester can not test all overflows in software, it is useful for detecting initial mistakes that can red flag dangerous software. OPTIONS
You must specify one or more of the following tests: -s Single Argument Test. -m Multiple Argument Test. -e Environment Variable Test. -a Selects all tests Other options: -h Print help. -t Enable tempfile monitoring. -v Print version string. -d level Set debug level (default = 0, max = 2). -r rejects Comma separated list of binaries to skip. -o out-file Output to out-file rather than stdout. -x max-execs Set maximum executables to run in parallel (default = 250). file Specific binary or a directory of binaries to test. OVERVIEW
You must specify at least one test to run and you must specify either a binary or a directory. Executable selection is now done in one of several ways: If the executable filename is specified with a leading slash (an absolute path), no selection is used and the supplied absolute filename is used. If there is no leading slash in the filename the selection is made in one of two ways (in this order): 1) Prepend file name with $PWD and test accesiblity 2) Search through $PATH and find first accessible executable The first one to succeed is the executable choosen. If the filename found is a directory, we walk the directory (one level deep) looking for executable binaries. Symbolic links are followed. You can specify binaries to skip (useful when loading a whole directory) by using the -r option. The following is a crash report: *** Crash </usr/bin/patch> *** args: -D [05120] envs: (null) Signal: 11 ( Segmentation fault ) Core? Yes This means "/usr/bin/patch" crashed when fed with an "-D" and a word 5,120 characters long: $ /usr/bin/patch -D AAA...5,120 characters...AAA (Numbers in brackets mean replace with a word that many characters long) BFBTester is very CPU intensive, and will open many files, so you probably don't want to run it on a production machine during it's busiest period. Just a warning... EXAMPLES
bfbtester -s /usr/bin Run the single argument test on all binaries in folder /usr/bin. bfbtester -ta patch traceroute Run all tests against patch and traceroute and run the tempfile monitor. bfbtester -a ./bfbtester Tests bfbtester (provided it's in the same directory). bfbtester -r kill /usr/bin/kill Does nothing. AUTHOR
This manual page was written by Karl Soderstrom <ks@debian.org>, for the Debian GNU/Linux system (but may be used by others). januari 23, 2001 BFBTESTER(1)
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