I have the following conditional code as part of my script and I keep getting a syntax error for only the last open
call. Suggestions?
if ($contig_string =~ /($pattern)/) {
print "$ERR_number \n";
print "Found forward pattern.\n";
print "Pattern found is: $1 \n";
$position = index($contig_string,$1);
print "Index returned: $position \n";
$substr_forward = substr($contig_string, $position, -2000);
print "$substr_forward \n";
open (REPORT, ">>", spacer_contigs) or die "Could not open";
print REPORT ">$ERR_number \n";
print REPORT "$substr_forward \n";
}
elsif ($contig_string =~ /($pattern_reverse)/) {
print "$ERR_number \n";
print "Found reverse pattern.\n";
print "Pattern found is: $1 \n";
$position_reverse = index($contig_string,$1);
print "Index returned: $position_reverse \n";
$substr_reverse = substr($contig_string, $position_reverse, 2000);
print "$substr_reverse \n";
open (REPORT, ">>", spacer_contigs) or die "Could not open";
print REPORT ">$ERR_number \n" or die "Could not append";
print REPORT "$substr_reverse \n";
}
elsif ($contig_string !~ /$pattern_forward/) {
print "$ERR_number \n";
print "Did not find pattern. \n"
open (NOMATCH, ">>", no_match) or die "Could not open"; # SYNTAX ERROR
print NOMATCH ">$ERR_number \n" or die "Could not append";
}
You're missing a semicolon on the
print
before theopen
that is causing trouble.Also, there's seldom a need to output blanks before newlines. You have numerous strings such as:
that would be better written as: