use strict;
use warnings;

my %scGeneids; # gene ids for marker genes 
my $key;

open(INlist,"scCOGwSNPs_geneids.txt");
while(<INlist>){
chomp;
$scGeneids{$_}=1;
}
close(INlist);

open(IN,"snps.position.txt") or die "can't open infile";
open(OUT,">markerGen_allSNPPos.txt");


foreach $key (keys %scGeneids){
        print "searching for $key \n";
        while (<IN>){
        chomp;
        my @columns=split("\t",$_);
        my $gene_id=$columns[0];
        my $SNP_pos=$columns[2];
        if ($key eq $gene_id){
                print OUT join("\t",$key,$SNP_pos),"\n"; }


}
}

close(IN);