Another approach would be to use the hash both as a lookup table to filter on relevant entries (as already suggested by others), and to collect the results by $gene_id (which I guess was the idea behind looping through the file multiple times — assuming the data in IN aren't necessarily already sorted by ID).  Something like this: 

while(<INlist>){
    chomp;
    $scGeneids{$_} = "";
}

...

while (<IN>){
    chomp;
    my @columns=split /\t/;
    my $gene_id=$columns[0];
    my $SNP_pos=$columns[2];
    if ( exists $scGeneids{$gene_id} ){
        $scGeneids{$gene_id} .= "$gene_id\t$SNP_pos\n";  # collect by 
+ID
    }
}

for my $key (sort keys %scGeneids) {
    print OUT $scGeneids{$key};
}

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In reply to Re: help with loop by Eliya
in thread help with loop by AWallBuilder

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