Hi, all.
I have the following dataset and need to calculate a P/A ratio for each
replicates in the dataset. In this case, treatment 1 has 4 replicats and
treatment2 has 3 replicates. The P/A = [((#of P)*2) + (# of M)]/# of
replicates. The output should be two columns of P/A ratios for two
treatments.
Dataset:
Replicates 1 1 1 1 2 2 2
AFFX-BioB-5_at P P P P P P P
AFFX-BioB-M_at P P P P P P P
AFFX-BioB-3_at P P P A A P P
AFFX-BioC-5_at P P P P P P P
AFFX-BioC-3_at P P P P P P P
AFFX-BioDn-5_at P P M P P P P
AFFX-BioDn-3_at P P P P P P P
AFFX-CreX-5_at P P P P P P P
AFFX-CreX-3_at P P P P P P P
AFFX-DapX-5_at A A P A A P A
AFFX-DapX-M_at A A A A A A A
AFFX-DapX-3_at A A A A A A A
AFFX-LysX-5_at A A A P A A A
AFFX-LysX-M_at A A A A A A A
AFFX-LysX-3_at A A A A P M A
AFFX-PheX-5_at A A A A A A A
AFFX-PheX-M_at A A A A A A A
AFFX-PheX-3_at A A A A A A A
Use strict;
Use warning;
My @split;
My @replicate = ( 4, 3);
My @ratio;
My $p=0, $m=0, $a=0, $rep=0, $i;
Open (IN, "C:\replicate.txt") or die "can not open file\n";
While (<IN>) {
@split = split (/\t/, $_);
foreach $rep (@replicate)
{
for(my $i=0; $i<$rep; $i++)
{
foreach $item (@split);
{
if ($item == "P")
{
$p = $p +1;
}
elseif ($item == "M")
{
$m = $m +1;
}
else ($item == "A")
{
$a = $a +1;
}
@ratio = (($p*2)+$m)/$a;
print push (@ratio, $ratio);
}
}
}
}
I have not been able to make this work yet. I would be appreciative of any
suggestions or help.
Thx in advance,
Aiguo Li
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