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Full Discussion: Problem with multiple grep in bash loop
Top Forums UNIX for Dummies Questions & Answers Problem with multiple grep in bash loop Post 302771879 by spacebar on Thursday 21st of February 2013 11:43:37 PM
Old 02-22-2013
If I understand what you want to do, You can do something like the below:

Code:
$ cat t
Sample1 Gene1   ##      Gene2   ##
Sample2 Gene2   ##      Gene4   ##
Sample3 Gene3   ##      Gene6   ##

$ cat test.sh
s="Sample1"
g1="Gene1"
g2="Gene2"
grep -q "$s[[:cntrl:]]$g1\|$s[[:cntrl:]][[:alnum:]]*[[:cntrl:]]##[[:cntrl:]]$g1" t
if [ $? = 0 ]; then
  echo "Found First" 
else
  echo "Not Found First"
fi
grep -q "$s[[:cntrl:]]$g2\|$s[[:cntrl:]][[:alnum:]]*[[:cntrl:]]##[[:cntrl:]]$g2" t
if [ $? = 0 ]; then
  echo "Found second"
else
  echo "Not Found second"
fi

$ test.sh
Found First
Found second

 

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LEARN ABOUT POSIX

zgrep

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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