Recode alphabet into numbers


 
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# 1  
Old 08-09-2012
Recode alphabet into numbers

I have a genotype.bim file where it contains information about SNPs and genotype. As a hypothetical example, let's say

genotype.bim

Code:
snp1 ... A G
snp2 ... G T
snp3 ... G T
snp4 ... G A
...
snpN ... C G

where first column identifies each SNP and 5th and 6th column has genotype information.
First step is todesignate the first allele of each SNP from the bim file and recode it as 0, then recode the second allele as 1.
So for the snp1, A=0, G=1, for snp2, G=0,T=1, for snp3, G=0,T=1, so forth.
Then we apply these designations to genotype.ped file.

genotype.ped

Code:
id1 id1 A A G T T G G A C C
id2 id2 A G T T G T G A G C
..
idN idN A A T T G T G A G G

first two columns are id numbers (they are identical).
suceeding two columns (3rd,4th) correpond to snp1, (5th,6th) correpond to snp2, etc; each snp contains two columns of genotype information in the ped file.
now I want to recode the allele in the same way it was done for the bim file.
so for snp1, A=0, G=1, so the 3rd,4th column of the first row will be 0 0 (A A)
and 5th,6th column will be 0 1 (G T) because for snp2, G=0,T=1,

then the desirable ouput will look like

Code:
id1 id1 0 0 0 1 1 0 0 1 0 0
id2 id2  0 1 1 1 0 1 0 1 1 0
..
idn idn 0 0 1 1 0 1 0 1 1 1

If you can contribute your idea as to how to write a generalized script for this problem (I have thousands of Snps and individuals), your help will be really appreciated.
Thanks in advance!
Moderator's Comments:
Mod Comment
Please use code tags when posting data and code samples!

Last edited by vgersh99; 08-09-2012 at 12:07 PM.. Reason: code tags, please!
# 2  
Old 08-09-2012
If there are N rows in genotype.bim, there are 2N+2 columns in each row of genotype.ped?

Also, how large are these files? If they are humongous, it would help to know in advance, lest time is wasted on an unsuitable approach. If the files are very large, it would help to know something about the hardware (available ram, free storage, etc).

Regards,
Alister
# 3  
Old 08-09-2012
Yes, ifthere are N rows in genotype.bim, there are 2N+2 columns in each row of genotype.ped

and the file is 2.5GB, pretty big file. As long as it does the job, i think it will be okay

Thanks
# 4  
Old 08-10-2012
Tested on your sample data:
Code:
awk '
FNR==NR { a[NR,$5]=0; a[NR,$6]=1; next }
{ for (i=3; i<=NF; i++) $i=a[int((i-3)/2+1),$i]; print }
' genotype.bim genotype.ped

Regards,
Alister
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