Hi to all PERL programmers,

I have data like this with 6 columns

```
LINES XY1 XY2 XY3 XY4 XY5
P1 Z/Z T/T -/- T/T T/T
P2 A/A A/A G/G Z/Z T/T
1 G/G T/T G/G T/T G/G
2 T/T A/A C/C C/C T/T
3 T/T G/G T/T G/G T/T
4 A/A C/C A/A A/A A/A
5 A/A A/A T/T T/T A/A
```

First I want to find how many columns (from XY1 to XY5) are different for P1 and P2 ,

Eq means:

Both P1 and P2 should contain same same letters (alleles) or if any one of P1 or P2 contains Z/Z or -/- I should consider them as eq only.`2. I will compare lines column values from 1 with P2 for all columns (from XY1 to XY5) in horizontal way and continue for remaining lines from 2 to 5. if they match I would like to give 1 else 0`

- I will make sum for lines 1 to 5 across all the columns from columns XY1 to XY5 but I will include only columns showing different for P1 and P2 in my sum count.
- I will calculate percentage of matching lines 1 to 5 with P2 by dividing sum with number of different markers between P1 and P2.

I am expecting like this

I am expecting like this

```
LINES XY1 XY2 XY3 XY4 XY5
```

P1 eq nq eq eq eq SUM %

P2 1

1 0 0 1 0 0 0 0

2 0 1 0 0 1 1 100

3 0 0 0 0 1 0 0

4 1 0 0 0 0 0 0

5 1 1 0 0 0 1 100

Like this I have data in more than 5000 rows and at present I am doing in excel 2010 with different formulas but it is taking lot of my energy.

I would like to do this PERL and I am newbie in PERL, I am succeeded in file reading onto screen.

I really need help in solving this in PERL with code. Any help would be appreciated