Extracting columns from text file with different delimiters in Linux

Question

I have very large genotype files that are basically impossible to open in R, so I am trying to extract the rows and columns of interest using linux command line. Rows are st

Answer 1

You can use cut with a delimiter like this:

with space delim:

cut -d " " -f1-100,1000-1005 infile.csv > outfile.csv

with tab delim:

cut -d$'\t' -f1-100,1000-1005 infile.csv > outfile.csv

I gave you the version of cut in which you can extract a list of intervals...

Hope it helps!

Answer 2

If the command should work with both tabs and spaces as the delimiter I would use awk:

awk '{print $100,$101,$102,$103,$104,$105}' myfile > outfile

As long as you just need to specify 5 fields it is imo ok to just type them, for longer ranges you can use a for loop:

awk '{for(i=100;i<=105;i++)print $i}' myfile > outfile

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If you want to use cut, you need to use the -f option:

cut -f100-105 myfile > outfile

If the field delimiter is different from TAB you need to specify it using -d:

cut -d' ' -f100-105 myfile > outfile

Check the man page for more info on the cut command.