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 straightforward enough using head tail  but I m having difficulty figuring out how to handle the columns   If I attempt to extract  say  the 100-105th tab or space delimited column using    cut -c100-105 myfile  gt outfile   this obviously won t work if there are strings of multiple characters in each column  Is there some way to modify cut with appropriate arguments so that it extracts the entire string within a column  where columns are defined as space or tab  or any other character  delimited

User · Accepted Answer

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

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.

User · Answer

You can use cut with a delimiter like this   with space delim   cut -d     -f1-100 1000-1005 infile csv  gt  outfile csv   with tab delim   cut -d   t  -f1-100 1000-1005 infile csv  gt  outfile csv   I gave you the version of cut in which you can extract a list of intervals     Hope it helps

[linux] Extracting columns from text file with different delimiters in Linux

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