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Full Discussion: Use shell variable in perl command line
Top Forums Shell Programming and Scripting Use shell variable in perl command line Post 302864441 by jdilts on Wednesday 16th of October 2013 02:06:33 PM
Old 10-16-2013
Use shell variable in perl command line
Hi,

I would like to use a shell variable
Code:
$amp

in my perl command line.

Code:
	for fa in $WORKSPACE/*.fa; do
	
		amp=`grep ">.*" $fa | sed -e's#>\(.*\)#\1#g'`
		ampsam="$WORKSPACE/$base/$base.$amp.sam"
		sqheader=`grep "^@SQ.*SN:$amp.*" $sam`

		printf "$sqheader\n" >> $ampsam
		
		#lines=`grep ".*\:.*\:.*$amp.*" $sam` # | sed 's/%/%%/'` #this also includes the @SQ line.
		
		perl -n -e 'if($_=~/.*\:.*\:.*$amp/){print "$_";}' $sam >> $ampsam

	done

Is there a way to do this?
 

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LEARN ABOUT BSD

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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