Calculation


 
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# 1  
Old 08-16-2013
Calculation

Hi, i have a large file like this:
Code:
Contig1 1  5
Contig1 2  4
Contig1 3  3
Contig1 4  5
Contig1 5 3
Contig1 6 4
Contig2 1  3
Contig2 2  7
Contig2 3  2
Contig2 4  9
Contig2 5 10
Contig2 6 3
Contig2 7 7
Contig2 8 2
Contig2 9 7
Contig2 10 5
contig1 2  4
contig1 3  3
contig1 4  5
contig1 5 3
contig1 6 4
contig1 7 5
contig1 8 6
contig1 9 3
contig1 10 4
contig1 11 5
contig1 12 6

...

I want to calculate the mean value of each contig from column 3.
For example: Contig1: (5+4+3+5+3+4)/6=24/6=4
Contig2: (3+7+2+..+2+7+5)/10=?
contig1: =?

btw, it also needs to distinguish big C(Contig1) and little c(contig1)..

Thanks a lot!!

Last edited by Scrutinizer; 08-16-2013 at 04:36 AM.. Reason: code tags
# 2  
Old 08-16-2013
So, where are you stuck with the code?

--ahamed
# 3  
Old 08-16-2013
Here is the piece of PERL script you can use to implement your requirement.

Code:
 
foreach (@lines) {
 chomp;
 my @Cols = split(/ /, $_);
 $HashVal{$Cols[0]}->{CNT}++;
 $HashVal{$Cols[0]}->{TOTAL} += $Cols[2];
 $HashVal{$Cols[0]}->{AVER} = $HashVal{$Cols[0]}->{TOTAL}/$HashVal{$Cols[0]}->{CNT};
}
foreach my $Key (keys(%HashVal)) {
 print $Key." = ".$HashVal{$Key}->{AVER};
}

# 4  
Old 08-16-2013
Code:
awk '{a[$1]+=$3;b[$1]++} END{for(i in a) print i, a[i]/b[i]}'  filename

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