Writing into text file as tab separated columns in Python

Question

I have two lists

A = ["ATTTGTA", "ATTTGTA", "ATTTGTA", "ATTTGTA"]

A_modified = ["ATTGTA", "AAAT", "TTTA"]

I want an output tab separated txt file looking like

ATTTGTA ATTGTA
ATTTGTA AAAT
ATTTGTA TTTA

I tried the following piece of code but it does not write o/p in two columns, just as new rows each time

with open ('processed_seq.txt','a') as proc_seqf:
          proc_seqf.write(A)
          proc_seqf.write("\t")
          proc_seqf.write(A_modified)

This is the output I get

ATTTGTA
    ATTGTA
ATTTGTA
    AAAT
ATTTGTA
    TTTA

proc_seqf.write("%s\t%s" % (A, A_modified)) might also work as a replacement for all of your write() lines, but using zip is probably the best way to get it organized in a meaningful way first, then follow mihai's answer — TehTris
– TehTris, Commented Oct 28, 2014 at 16:19
I realised this is happening due to the following problem: each of the lists look like A = ["ATTTGTA\n", "ATTTGTA\n",..] and that is why the new line gets added. Can you tell me how to get rid of the \n at the end. thanks — Ssank
– Ssank, Commented Oct 28, 2014 at 17:35
Just found using str.strip on the strings after reading them from the text file and before creating the string solved all my problems.Thanks — Ssank
– Ssank, Commented Oct 28, 2014 at 17:47

Mihai Maruseac · Accepted Answer · 2014-10-28 15:57:45Z

10

You just need to pair the elements in the two list. You can do that using the zip function:

with open ('processed_seq.txt','a') as proc_seqf:
    for a, am in zip(A, A_modified):
        proc_seqf.write("{}\t{}".format(a, am))

I have also used format (see specs) to format the string to get everything in a single line.

answered Oct 28, 2014 at 15:57

Mihai Maruseac

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gmas80 · Accepted Answer · 2014-10-28 16:13:30Z

What about something like this? It provides you with some flexibility in input and output..

lines = [
    ['a', 'e', '7', '3'],
    ['b', 'f', '1', '5'],
    ['c', 'g', '2', '10'],
    ['d', 'h', '1', '14'],
    ]

def my_print( lns, spacing = 3 ):
    widths = [max(len(value) for value in column) + spacing
              for column in zip(*lines)]
    proc_seqf = open('processed_seq.txt','a')
    for line in lns:
       pretty = ''.join('%-*s' % item for item in zip(widths, line))
       print(pretty) # debugging print
       proc_seqf.write(pretty + '\n')
    return

my_print( lines )

I added the option that the user can decide the size of the spacing..

To match with your example data:

A = ["ATTTGTA", "ATTTGTA", "ATTTGTA", "ATTTGTA"]

A_modified = ["ATTGTA", "AAAT", "TTTA"]

lines = [ A, A_modified ]

Anzel · Accepted Answer · 2014-10-28 16:14:15Z

1

Apart from other great answers, as an alternative with try/except it will write all remaining elements in the list if their lengths are different (at least in your sample):

with open ('processed_seq.txt','w') as proc_seqf:
    for each in range(max(len(A), len(A_modified))):
        try:
            proc_seqf.write("{}\t{}\n".format(A[each], A_modified[each]))
        except IndexError:
            if len(A) > len(A_modified):
                proc_seqf.write("{}\t\n".format(A[each]))
            else:
                proc_seqf.write("\t{}\n".format(A_modified[each]))

cat processed_seq.txt
ATTTGTA ATTGTA
ATTTGTA AAAT
ATTTGTA TTTA
ATTTGTA

answered Oct 28, 2014 at 16:14

Anzel

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Comments

Kasravnd · Accepted Answer · 2014-10-28 16:29:05Z

1

If your lists are huge ,i suggest use itertools.cycle() :

import itertools
ac=itertools.cycle(A)
a_mc=itertools.cycle(A_modified)
with open ('processed_seq.txt','a') as proc_seqf:
    for i in A_modified:
      proc_seqf.write("{}\t{}".format(ac.next(), a_mc.next()))

edited Oct 28, 2014 at 16:29

answered Oct 28, 2014 at 16:08

Kasravnd

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