Help a perl newbie coding for a bioinfo guy please.
I have a shell script that contains the following code
# $1=sequence_file, $2=input_file, $3=output file, $4=chain.
if [ $# != 4 ]
then
echo "Usage: parse_pdb.sh sequence_file pdb_file output_file chain"
exit
fi
TEMP_FILE=$$;
#basename $2 >> $3
grep ^HELIX $2|sed 's/\ \ */\ /g'|cut -d" " -f1,5,6,9 >$TEMP_FILE
grep ^SHEET $2|sed 's/\ \ */\ /g'|cut -d" " -f1,6,7,10 >>$TEMP_FILE
parse_pdb.pl $1 $TEMP_FILE $3
rm $TEMP_FILE
I have to write a cgi-perl script which takes the same inputs as the
shell script and pass them to the parse_pdb.pl script. For that I have
to replicate the grep command. How can I do that using perl ? Ofcourse I
dont have to use the shell script now.
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