Hello perlMonks! I am turning to the internet for what I am sure is a very benign issue with my perl script. I am trying to convert a file from one format to the other but continue to get these errors that read this: syntax error at ./impute2chromopainter_ng.pl line 56, near ") {" syntax error at ./impute2chromopainter_ng.pl line 59, near "else" syntax error at ./impute2chromopainter_ng.pl line 64, near "}" Execution of ./impute2chromopainter_ng.pl aborted due to compilation errors. I am not sure how to modify the code in a way that will allow it to run. I did not write this script it was written by authors who designed fineStructure! Please, any guidance or advice would be immensely appreciated! Thank you! The code is below

#!/usr/bin/perl
## CONVERTS PHASED IMPUTE2 OUTPUT TO CHROMOPAINTER-STYLE INPUT FILES

sub help {
print("CONVERTS PHASED SHAPEIT/IMPUTE2 OUTPUT TO CHROMOPAINTER-STYLE I
+NPUT FILES\n");

print("usage:   perl impute2chromopainter.pl <options> impute_output_f
+ile.haps output_filename_prefix\n");

print("where:\n");
print("        (i) impute_output_file.haps = filename of IMPUTE2 outpu
+t file with suffix \".haps\" that contains phased haplotypes\n");
print("        (ii) output_filename_prefix = filename prefix for chrom
+opainter input file(s). The suffix \".phase\" is added\n\n");
print("The output, by default, is in CHROMOPAINTER v2 input format.\n"
+);

print("<options>:\n");
print("-J:                 Jitter (add 1) snp locations if snps are no
+t strictly ascending. Otherwise an error is produced.\n");

print("<further options>   NOTE: YOU ONLY NEED THESE OPTIONS FOR BACKW
+ARDS COMPATABILITY!\n");
print("-v1:                Produce output compatible with CHROMOPAINTE
+R v1, i.e. include the line of \"S\" for each SNP. \n");
print("-f:                 By default, this script produces PHASE-styl
+e output, which differs from \n");
print("               ChromoPainter input which requires an additional
+ first line.  This option creates the correct\n");
print("                   first line for standard fineSTRUCTURE usage 
+(i.e. the first line is \"0\", all other lines are appended)\n\n");

print("NOTE: TO USE IN CHROMOPAINTER: You also need a recombination ma
+p. Create this with the \"convertrecfile.pl\" or \"makeuniformrecfile
+.pl\" scripts provided.\n\n");
print(" !!! WARNING:  THIS PROGRAM DOES NOT SUFFICIENTLY CHECK FOR MIS
+SPECIFIED FILES. WE ARE NOT ACCOUNTABLE FOR THIS RUNNING INCORRECTLY 
+!!!\n");
die "\n";
}

 use feature "switch";


###############################
## INPUT:

$numindsmaxsize=500;     ## ONLY READ IN THIS NUMBER OF IMPUTE2 INDS A
+T A TIME (TO MINIMIZE RAM REQUIREMENTS -- MAKES PROGRAM RUN A FACTOR 
+OF (N/$numindsmaxsize) SLOWER THAN IF YOU SET $numindsmaxsize=N, wher
+e N is the total number of individuals in your ".haps" IMPUTE2 output
+ file, but also uses a factor of (N/$numindsmaxsize) less RAM

###############################
## ARGUMENT PROCESSING

$v1=0; ## version 1 mode
$fsmode=0; ## finestructure mode (i.e. start with an additional line c
+ontaining 0)
$jitter=0; ## whether we jitter snp locations

$Mb = 1000000.0;
$IMPUTEinfile="";
$outfilePRE="";

$argon=0;
for (my $i = 0; $i < scalar(@ARGV); ++$i){
    if(@ARGV[$i] eq "-f"){
        $fsmode=1;
    }elsif(@ARGV[$i] eq "-v1"){
        $v1=1;
    }elsif(@ARGV[$i] eq "-J"){
        $jitter=1;
    }else{
        switch($argon) {
        my $case = 0; {$IMPUTEinfile="$ARGV[$i]";}
        my $case = 1; {$outfilePRE="$ARGV[$i]";}
        else {
            help();
        }
        }
        $argon++;
    }
}

if($outfilePRE eq "" || $argon != 2) {help();}
$outfilePRE =~ s/.phase$//;

##############################
## PROGRAM:


## (II) GET NUMBER OF SITES AND INDS: 
open(IN,"$IMPUTEinfile");
$line=<IN>;
@linearray=split(/\s+/,$line);
$totalINDS=(@linearray-5)/2;
$totalhaps=@linearray-5;
$numsplits=int($totalINDS/$numindsmaxsize);
if (($numsplits*$numindsmaxsize)<$totalINDS)
{
    $numsplits=$numsplits+1;
}
$nsites=1;
while(<IN>)
{
    $line=$_;
    $nsites=$nsites+1;
}
#print "$numsplits $nsitesFULL $totalINDS\n";

              ## (III) READ IN IMPUTE2 HAPLOTYPES AND MAKE CHROMOPAINT
+ER HAPLOTYPE INPUT FILE:
open(OUT,">${outfilePRE}.phase");
if($fsmode==1) {
    print OUT "0\n";
}
for ($a=0; $a < $numsplits; $a+=1)
{
    $startIND=$a*$numindsmaxsize;
    $endIND=($a+1)*$numindsmaxsize;
    if ($endIND > $totalINDS)
    {
    $endIND=$totalINDS;
    }

                              ## read in:
    open(IN,"$IMPUTEinfile");
    @rsvec=();
    @posvec=();
    @genomat=();
    $snpcount=0;
    while(<IN>)
    {
    $line=$_;
    @linearray=split(/\s+/,$line);
    push(@rsvec,$linearray[1]);
#    print("BEFORE: SNP location $linearray[2] lup $lastuniquesnp\n");
    if(scalar(@posvec)>0 &&($linearray[2] <= $posvec[-1]) && $linearra
+y[2]>=0){
        if(!$jitter){
        die("ERROR: SNPs are not strictly ascending, exiting. Rerun wi
+th -J to jitter the SNP locations.\n");
        }
#        print("Duplication found: setting $linearray[2] to $posvec[-1
+]+1\n");
        $linearray[2]=$posvec[-1]+1;
    }
#    print("AFTER:  SNP location $linearray[2] lup $lastuniquesnp\n");
    if( $linearray[2] == $posvec[-1] ){
        die("Strange error due to jittering?\n");
    }
    push(@posvec,$linearray[2]);
    # shift(@linearray);
    # shift(@linearray);
    # shift(@linearray);
    # shift(@linearray);
    # shift(@linearray);

    for ($i=$startIND; $i < $endIND; $i+=1)
    {
        $genomat[(($i-$startIND)*2)][$snpcount]=$linearray[(2*$i)+5];
        $genomat[(($i-$startIND)*2+1)][$snpcount]=$linearray[(2*$i+1)+
+5];
    }

    $snpcount=$snpcount+1;
    }

                                ## print out:    
    if ($a==0)
    {
    if($v1){
        print OUT "$totalINDS\n";
    }else {
        print OUT "$totalhaps\n";
    }
    print OUT "$nsites\n";
    print OUT "P @posvec\n";
    if($v1){
        for ($j=0; $j < $nsites; $j+=1)
        {
        print OUT "S";
        }
        print OUT "\n";
    }
    }
    for ($i=0; $i < (2*($endIND-$startIND)); $i+=1)
    {
    for ($j=0; $j < $nsites; $j+=1)
    {
        print OUT "$genomat[$i][$j]";
    }
    print OUT "\n";
    }
}
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