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Old 07-12-2013, 02:06 AM   #1
genetist
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Registered: Jul 2013
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how to find match between two rows of column in same file using PERL


Hi to all my data looks like this

Code pedigree A B C D E F A B C D E F
X X1 -/- -/- -/- C/C A/A -/- eq eq eq ne eq eq
Y Y1 C/C C/C A/A A/A A/A A/A
1 X1/Y1 C/C C/C A/A A/A Z/Z A/A
2 X1/Y1 C/C -/- A/A A/A A/A A/A
3 X1/Y1 -/- C/C A/A A/A A/A A/A
4 X1/Y1 Z/Z C/C A/A A/A A/A A/A
5 X1/Y1 C/C C/C A/A A/A A/A A/A
First I would like to count total number of different coulmns within a pair of X1 and Y1 across from cloumn A to F, If data is missing (-/-) or unscorable (Z) from cloumns A to F for any one of X1 or Y1 with in a pair of X1Y1 then that column is same between X1 and Y1 else that column is different. I tried folowwing code to do that but not succeed,

#!/usr/bin/perl
print("enter file name to read:\n");
$data=<stdin>;
chop($data);
for($column = 1 ; $column <= 8 ; $column++)
{
for($row = 1 ; $row <= 2 ; $row++)
{
if($row1 eq $row2)
{
$result = "EQ";
}
else
{
$result="NQ";
}
print $result;
}
print "\n";
}
any help would be appreciated
thanks
 
Old 07-12-2013, 06:54 PM   #2
jpollard
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Registered: Dec 2012
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Well... one way is to load the file into a series of hash tables. One indexed by record number, the others by the column value, with an array of record indexes for the value(that way you also know if two or more rows have the same value, and a list of which records they were). The purpose of the first (indexed by record number) is so that you can look at the entire record where something interesting occurs.
 
Old 07-13-2013, 10:40 AM   #3
chrism01
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Location: Sydney
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1. use
Code:
#!/usr/bin/perl
use strict;
2. Perl counts arrays from zero

3, you don't use 'data' after loading it

4. please use code tags

5. data should be an array
 
Old 07-13-2013, 12:17 PM   #4
jpollard
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I would use hash tables so that I don't need to hunt through an array.
 
  


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