perl - incorrect syntax when closing if statement - perl

Question

I'm trying to write a script that searches the BLAST output against a previously-generated file that gives the genomic positions of each GI number. However, I get three syntax errors related to closing IF statements. Being a novice at Perl, I am at a loss as to how to fix this. Can anyone help me? I have copied the code and labeled the offending closing braces. I did do a quick check to make sure all delimiters are balanced.
#!/usr/bin/perl -w
#decided to have input file entered in command line
#call program followed by genome name.
#the program assumes that a file with the extensions ptt and faa exist in the same dirctory.
#####INPUT Name of multiple seq file containing ORF of genome, open file and assign IN filehandle #############
unless(#ARGV==2) {die "usage: perl nucnums.pl BLAST_output_filename query.ref subject.ref\n\nSubject is the database you made with FormatDB or MakeBlastDB.\n\nQuery is the other file";}
$blastname=$ARGV[0];
$queryname=$ARGV[1];
$subjectname=$ARGV[2];
#nameparts=split(/\./, $blastname);
$ofilename="$blastname[0]"."pos";
open(INBLAST, "< $blastname") or die "cannot open $blastname:$!";
open(OUT, "> $ofilename") or die "cannot open $ofilename:$!";
$line=<INBLAST>;
print OUT $line;
while (defined ($line=<INBLAST>)){ # read through rest of table line by line
if ($line=/^g/){
#parts=split/\t/,$line;
#girefq=split/\|/,$parts[0];
$ginumq = ($girefq[1]);
$postartq = $parts[6];
#girefs=split/|/,$parts[1];
$ginums = ($girefs[1]);
$postarts = $parts[8];
open(INQUER, "< $queryname") or die "cannot open $queryname:$!";
open(INSUBJ, "< $subjectname") or die "cannot open $subjectname:$!";
SCOOP: while (defined ($locq=<INQUER>)){
#locsq=split/\t/,$locq
if $locsq[0] = $ginumq{
$posq = $locsq[1] + $postartq - 1;
} # <- Syntax error
}
close(INQUER);
SLOOP: while (defined ($locs=<INSUBJ>)){
#locsq=split/\t/,$locs
if $locss[0] = $ginums {
$poss = $locss[1] + $postarts - 1;
} # <- Syntax error
}
close(INSUBJ);
print "$ginumq at position $posq matches with $ginums at position $poss \n" or die "Failed to find a match, try changing the order of the REF files";
print OUT "$ginumq\t$posq\t$ginums\t$poss\t$parts[2]\t$parts[3]\t$parts[4]\t$parts[5]\t$parts[6]\t$parts[7]\t$parts[8]\t$parts[9]\t$parts[10]\t$parts[11]\t$parts[12]\n";
} # <- Syntax error
}
close(OUT);
close(INBLAST);

Answer 1

You need to change:
#locsq=split/\t/,$locs
if $locss[0] = $ginums {
to something like:
#locsq=split/\t/,$locs;
if ($locss[0] == $ginums) {
Same goes for $locsq[0]. If you are comparing strings instead of numbers, use eq instead of ==.
UPDATE: Thanks to Zaid for pointing out the missing semicolons.

Answer 2

#locsq=split/\t/,$locs
if $locss[0] = $ginums {
$poss = $locss[1] + $postarts - 1;
} # <- Syntax error
You get a misleading error message here because the first part of that is syntactically valid, though not what you intend. The missing semicolon on the first line means that the first part of the above is parsed as a postfix if (since the condition in a postfix if doesn't require parentheses):
#locsq=split/\t/,$locs if $locss[0] = $ginums
More than that, the part starting with $ginums{ is parsed as a reference to an element of a hash. (There's no %ginums hash, but that error would be reported after any syntax errors):
#locsq=split/\t/,$locs if $locss[0] = $ginums{$poss = $locss[1] + $postarts - 1;}
where $poss = $locss[1] + $postarts - 1; is taken as the hash key.
You only got a syntax error message because of the semicolon preceding the }. If you had omitted that semicolon, you probably would have gotten a complaint about %ginums being nonexistent (assumimg you have use strict; use warnings;; without that you might not get a warning at all).
This is one of those cases where a typo can transform a piece of code into something that's valid (or, in this case almost valid) but that doesn't mean anything like what you intended.
Add a semicolon to the end of the first line, and parenthesize the if condition.

Answer 3

It looks like you have written the entire program before doing any testing on it. That isn't the way to go. You should write small sections and test that they work in isolation before adding to them or assembling them into the complete program.
use warnings is preferable to putting -w on the #! line.
There are also a number of errors in this program that would have been highlighted if you had added use strict at the top of your program and declared all your variables using my. For instance, you write
$ofilename = "$blastname[0]" . "pos";
but there is no #blastname array. $ofilename will end up always containing just pos, but use strict wouldn't have let you run the program in this condition.
You also write (what I presume is supposed to be)
my #locsq = split /\t/, $locs;
if ($locss[0] = $ginums) {
$poss = $locss[1] + $postarts - 1;
}
and, again, there is no #locss array, so this if will never be executed unless $ginums is an empty string.
I recommend you at least take a look at this rewrite of your program, which uses commonly-accepted good practice, and I hope you will agree is more readable.
There is a problem with your final print statement, as print to the console always returns true so the die will never get executed, but I don't understand enough about what you are doing to fix it.
use strict;
use warnings;
unless (#ARGV == 2) {
die <<END;
usage: perl nucnums.pl BLAST_output_filename query.ref subject.ref
Subject is the database you made with FormatDB or MakeBlastDB.
Query is the other file
END
}
my ($blastname, $queryname, $subjectname) = #ARGV;
my #nameparts = split /\./, $blastname;
my $ofilename = "${blastname}pos";
open my $inblast, '<', $blastname or die "cannot open $blastname: $!";
open my $out, '>', $ofilename or die "cannot open $ofilename: $!";
print $out scalar <$inblast>;
while (my $line = <$inblast>) {
next unless $line =~ /^g/;
my #parts = split /\t/, $line;
my #girefq = split /\|/, $parts[0];
my $ginumq = $girefq[1];
my $postartq = $parts[6];
my #girefs = split /|/, $parts[1];
my $ginums = $girefs[1];
my $postarts = $parts[8];
my ($posq, $poss);
open my $inquer, '<', $queryname or die "cannot open $queryname: $!";
while (my $locq = <$inquer>) {
my #locsq = split /\t/, $locq;
if ($locsq[0] = $ginumq) {
$posq = $locsq[1] + $postartq - 1;
}
}
close($inquer);
open my $insubj, '<', $subjectname or die "cannot open $subjectname: $!";
while (my $locs = <$insubj>) {
my #locss = split /\t/, $locs;
if ($locss[0] = $ginums) {
$poss = $locss[1] + $postarts - 1;
}
}
close($insubj);
print "$ginumq at position $posq matches with $ginums at position $poss \n"
or die "Failed to find a match, try changing the order of the REF files";
print $out join("\t", $ginumq, $posq, $ginums, $poss, #parts[2..12]), "\n";
}
close $inblast;
close $out or die $!;