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 · Answer

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!

User · 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  gt  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 lt  105 i   print  i   myfile  gt  outfile     If you want to use cut  you need to use the -f option   cut -f100-105 myfile  gt  outfile   If the field delimiter is different from TAB you need to specify it using -d   cut -d    -f100-105 myfile  gt  outfile   Check the man page for more info on the cut command

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

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