Dear perlmonkers, Could you point out what's wrong with my code? I want to get for each gene, the maximum value of the associated frequency printed in the 3rd column, but it gives wrong result (e.g. MUC2), see output below 

Frequency  GENE
20      SEMA4G
80      CTBP2
80      CTBP2
80      CTBP2
100     SPRN
40      SVIL
80      TIMM23
80      MINPP1
80      BTAF1
20      MUC2
60      MUC2
80      MUC2
100     MUC2
60      OR10G9
60      C11orf91
80      OR4S1
40      OR4C3
40      OR4C3
20      OR4C3
40      OR4C45
60      OR4C45

[download]
$file1 = $ARGV[0];

%hashfreq = ();
$freq = 0;
$geneold = "NA";
open(INPUTR,"<$file1") || die "Can't open \$file1 for reading.\n";
while($line=<INPUTR>){
    chomp $line;
    @toks = split(/\t/, $line);
    $gene = $toks[1];
    if ($gene =~ /^$geneold$/){
        if ($toks[0] >= $numold){
            $freq = $toks[0];
            print $toks[0]."\t".$numold."\t".$freq."\t".$gene."\n";
        } else {
            $freq = $numold;
        }
        $hashfreq{$toks[0]} = $freq;
    } else {
        $hashfreq{$toks[1]} = $toks[0];
    }
    $numold = $toks[0];
    $geneold = $toks[1];
}
close(INPUTR);

open(OUTD1,">output.txt");
open(INPUTR,"<$file1") || die "Can't open \$file1 for reading.\n";
while($line=<INPUTR>){
    chomp $line;
    @toks = split(/\t/, $line);
    $idgene = $toks[1];
    if (exists $hashfreq{$idgene}){
        print OUTD1 $line."\t".$hashfreq{$idgene}."\n";
        print $line."\t".$hashfreq{$idgene}."\n";
    }
}

[download]
Frequency  GENE     MAX
20      SEMA4G  20
80      CTBP2   80
80      CTBP2   80
80      CTBP2   80
100     SPRN    100
40      SVIL    40
80      TIMM23  80
80      MINPP1  80
80      BTAF1   80
20      MUC2    20
60      MUC2    20
80      MUC2    20
100     MUC2    20
60      OR10G9  60
60      C11orf91        60
80      OR4S1   80
40      OR4C3   40
40      OR4C3   40
20      OR4C3   40
40      OR4C45  40
60      OR4C45  40

[download]

In reply to Error in Code: Need help by angerusso

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