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Hello,
I have a file that contains 64,235 columns and over 1000 rows and looks similar to this:

ID dad mom 1 2 3 4 5.... 64232
1234 5678 6789 AA BB CC DD EE....ZZ
1342 5786 6897 BB CC...

Here is the original file:
ID 1 2 3 4 5 6 7 8
83845676 0 0 0 0 CC -1 CC CC
83846900 -1 -1 1 GG CC 0 CC 1
83847041 -1 . 0 0 . 0 0 0...

Here is the original file formatted by Sdanner:
Code:
ID 1 2 3 4 5 6 7 883845676 0 0 0 0 CC -1 CC CC83846900 -1 -1 1 GG CC 0 CC 183847041 -1 . 0 ...

Hello Sdanner and Steadyonabix,
I have tried to come up with an easier way to describe what I need to do with my file. If you recall I have a file that looks like this:
ID 1 2 3 4 5...

Yes so far you are correct on the GG assignments. So to answer your questions I think it may help more if I answer them out of order:

c) are you garuanteed to have at least one 1 or -1 in each...

I have a file that has been partially recoded so that data points that were formerly letter combinations are now -1, 0, or 1. I need to finish recoding the GG and CC data points. The file looks like...

Ok great. Thank you so much! Now the problem with the GG and CC is that in either case they can be a -1 or a 1, depending on what has already been recoded. If a GG is in a column that already...

Hello again,
Again, I apologize for the confsion. I made a mistake in the first post, the letters should be recoded to -1, 0, 1. This is the tricky part. I need to recode the letters on a per...

I apologize for the confusion! I understand where I need to go with this but I have no clue how to tell the computer to do it so it is hard for me to explain it to others as well...let me try...

Hello all,
I have a data file that needs some serious work...I have no idea how to implement the changes that are needed!

The file is a genotypic file with >64,000 columns representing genetic...

Hello all,
I have a text file that is arranged:

name 3 7 2 9 5
jim a d e g k
max d g u x g
rob f w v k o

This is just an example as my real file has >1000 individuals and >64,000...

Thanks cfajohnson!!!

Hello!
I am very new to Linux and I do not know where to begin...

I have a column with >64,000 elements (that are not in numberical order) like this:

name
2
5
9
.
.
.
64,000

I...