Question

I’ve just started programming, therefore I’m kinda noob.

I’m trying to use python to remove a column from a .txt table. All columns are separated by tabs.
This is an example line:

100226.SCO0401  1   440 COG0001 glutamate-1-semialdehyde 2,1-aminomutase

I want to remove all text in the line after the fourth tab (the “glutamate-1-semialdehyde 2,1-aminomutase” part).

I’ve seen some people importing csv to work around this issue, but I was thinking of something simple like:

def remove(infilename, outfilename):
    # Open original file and output file
    infile = open(infilename, 'rt')
    outfile = open(outfilename, 'wt')

    # Read lines and remove annotation
    for line in infile:
        outfile.write(line['**everything-until-the-fourth-tab**']

    # Close files
    infile.close()
    outfile.close()

The bold part is my issue right now. Any suggestions?
Thanks in advance.

Answer 1

Use .split('\t') to split the entries in the row into an array. You can then slice the array with [:4], keeping only the first 4 elements. Finally, join it back up again with '\t'.join:

for line in infile:
     columns = line.split('\t')
     columns = columns[:4]
     outfile.write('\t'.join(columns))

As a one-liner:

for line in infile:
     outfile.write('\t'.join(line.split('\t')[:4]))