Use shell variable in perl command line

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# 1  
Old 10-16-2013
Use shell variable in perl command line


I would like to use a shell variable

in my perl command line.

	for fa in $WORKSPACE/*.fa; do
		amp=`grep ">.*" $fa | sed -e's#>\(.*\)#\1#g'`
		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


Is there a way to do this?
# 2  
Old 10-16-2013
There are few ways actually. I think this is the most elegant:
perl -s -n -e 'if($_=~/.*\:.*\:.*$amp/){print "$_";}' -- -amp="$amp" $sam >> $ampsam

This User Gave Thanks to bartus11 For This Post:
# 3  
Old 10-16-2013
Worked like a charm. Is there any decent documentation on using command line perl? Every time I google 'command line' and 'perl' together I get hits for passing arguments to a perl script.
# 4  
Old 10-16-2013
This User Gave Thanks to bartus11 For This Post:
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