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Hi I am working on a program that reads a file with multiple columns and was curious how to specify the columns to be manipulated in the command line.
For example the file may look something like:
...

Okay I now have a new specification that I would like to add to my program.
Given this is the original file and corresponding program:

Non-ref "A" "A1" "A2" ....... (column6)
A ...

Sorry I was not more clear. I meant to say that I want the output of the first part of the program to be the input for the second part. So basically I would like to count the number of each type of...

Hi I am now facing two current issues when trying to expand this program. Ddreggors you have been wonderful so far and I am hoping you can help me with these issues.

The first is that for some of...

That program appears to be running but no output is given when it is written as above. Do you know what could have happened?
thanks

Thank you so much that is working great for me and I really appreciate the help.
Hopefully one my last questions but I now have a similar situation but the data and reference are both in the same...

This is what it currently is:

#!/usr/bin/perl


use strict;
use warnings;
my ($idx, $tmp, $geno, @ref, @data);
open(FILE1,"<","file1.txt") or die $!;
while (<FILE1>) {
chomp;
...

when I make the change to '=~' i get the following errors:


Use of uninitialized value $1 in concatenation (.) or string at ddreggors.pl line 26, <FILE2> line 5.
Use of uninitialized value $1...

Thank you so much its running flawlessly for me.
Is there any quick alteration that could be made so that instead of reporting back the cases in which neither letter is the same as the reference, it...

Okay I'll start over and try to be more exact.
I am looking at a file that has about 3 million rows and about 100 columns. The row number is given by the index number, in the 1st column, as...

Yes but the numbers continue into the millions so itd be easier to set the reference as the entire filename instead I believe.

I still don't believe I am explaining it correctly:
The index number for the given data must match that of the reference.
Data:
Index Chr Genotype Mutation Type
1 Chr1 ...

Thank you ddreggors for your help. It is similar to that but the reference is not the same for each index. For example, for index 1, 'T' is the reference and thus the genotype, 'TT', for that index...

Yes sorry for not specifying more.
Say the given reference was:

Index
1)T
2)A
3)C
4)G
5)C


and that the matix in my first post remains the same, indexes 3 and 4 would not have an...

Hi I have a multi-step project I am working on and have been finding it difficult to come up with the correct approach.
The data I have been given resembles:


Index Chr Genotype ...