I have a file I'm working with where each row begins with a SNP ID and is followed by 510 mean genotypes.
These are space delimited like so:
Chr1_25 0 0 0 0.1
Chr1_33 0.2 0 0 1
Chr5_44 1.2 2 0 2
Chr7_87 0 0 0 0
I want to convert each row into tab delimited columns like so:
Chr1_25 Chr1_33 ....
0 0.2
0 0
0 0
0.1 1
•
written
by
selplat21 •
I was able to solve this with the following:
conda install bioconda -c csvtk
grep -w -f candidate.snps Test.bimbam | csvtk transpose | sed -e '2,3d' >> candidate.list
candidate.snps is a list of snp_ids (rs......). This provides a transposed matrix with snpID as the header and dosages for all individuals as the rows.
•
written
by
selplat21 •
You're looking to transpose your file. This is straight forward to do in R using t() and likely easy in Python but if you want to do it by command line it's probably a little more convuluted. Here's a stack overflow link that goes through how to do it using awk https://stackoverflow.com/questions/1729824/an-efficient-way-to-transpose-a-file-in-bash
So I was able to locate posts like this, but I consistently get the output as a single vector:
Chr1_25
0
0
0
0.1
Chr1_33
0.2
0
0
1
while read i; do grep -w $i Test.bimbam | cut -d, --output-delimiter $'\t' -f1,4- \
| awk '
{
for (i=1; i<=NF; i++) {
a[NR,i] = $i
}
}
NF>p { p = NF }
END {
for(j=1; j<=p; j++) {
str=a[1,j]
for(i=2; i<=NR; i++){
str=str" "a[i,j];
}
print str
}
}' ; done < candidate.snps
I have tried transposing with R but am getting the same solution:
I made an Rscript transpose.R
#!/usr/bin/env Rscript
input <- file("stdin", "r")
x <- readLines(input)
x <- as.data.frame(x)
x1 <- t(x)
write(x1, "")
I then do the following to my bimbam file:
while read i; do grep -w $i Test.bimbam | cut -d, --output-delimiter $'\t' -f1,4- | transpose.R ; done < candidate.snps
I am getting the same solution:
Chr1_25
0
0
0
0.1
Chr1_33
...
...
...
The original bimbam is in this format
Chr1_25,A,T,0,0,0,0.1
Chr1_33,C,G,......
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