Hi all
I have two txt file (file1: genotype.txt and file2: 6first coloum of ped), I used them to make ped with paste file1.txt file2.txt which use it for make a ped. the problem is that when I run plink with :
Options in effect:
--ped scottsheep.ped
--map scottisheep.map
--noweb
it give me this error:
52857 (of 52857) markers to be included from [ scottisheep.map ]
ERROR:
A problem with line 1 in [ scottsheep.ped ]
Expecting 6 + 2 * 52857 = 105720 columns, but found 52864
when I chek the ped file I found that I have successfully added all of the required information columns and just need to split all of my SNP columns which are currently in the following format ("AA") into two separate columns per SNP ("A" "A"). I search it and I know it could be solve in R, But I am new in use R. dose any command for txt file in bash which can split a colom to two coloum .
I am tired to search for this and not found any slouction.
dose any one has any suggestion for me?
5 answers
A python solution:
python -c "for line in open('test.txt'): print(' '.join(list(line.strip().replace(' ', ''))))"
Adapt test.txt to suit your input file.
This all requires that there are only normal SNPs in there, no funky alleles etc.
I think that Python may have the same issue - not sure.
Could you take a look here to see about installing gawk on Ubuntu 12.04? - https://askubuntu.com/questions/244268/installing-gawk-4-0-on-ubuntu-12-04
Edit: Wouter has helpfully added a Python solution for you to test. Here is a sed only solution, too:
sed 's/ \+//g' test.txt | sed 's/\(.\{1\}\)/\1 /g'
A A G G T G C C
A A G G T G C C
Good work!
$ echo "AA GG TG CC" | sed 's/\([^ ]\)\([^ ]\)/\1 \2/g'
A A G G T G C C
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Can you confirm exactly what you want to get?
Your data is currently in this format:
You need to get it to this format for input to PLINK:
From where did you obtain your data?
Grazie mille.
Hi Kevin I downloaded the data from https://datadryad.org, and yes I need to do what you wrote. I can do it on R but I want to know can I do it on bash
Are you using Mac or linux?
This works on linux:
I cannot see your exact input, though.
Hi , I use above command but I get this error
awk: program limit exceeded: maximum number of fields size=32767 FILENAME="-" FNR=1 NR=1
I try to install and use gawk , but I use Ubuntu 12.04 I think the package I am looking for doesn't existand. so I am looking Python script to do that dose any body have sloution?
thanks a lot every body, all of them worked
Which solution worked?
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