CODEWITHSUNDEEP
python
mary
mary

Reputation: 59

How to re-order cloumn in txt file?

I have a large txt file sample.txt with over 54000 columns. They are ordered like this:

1011001 1 1001164 981328 1 -9 A G G G G G C C A . . . .    
1011002 1 1001164 981328 1 -9 A G G G G G A C A . . . .

I need to re-order the columns as follows:

1 1011001 1001164 981328 1 -9 A G G G G G C C A . . . .
1 1011002 1001164 981328 1 -9 A G G G G G A C A . . . .

I.e I want the second column be the first one.

Is there some way for me to do this with Python?

Upvotes: 0

Views: 172

Answers (3)

U13-Forward
U13-Forward

Reputation: 71620

List comprehension:

with open(filename,'r') as f:
   l=[' '.join([i.split()[1],i.split()[0],i.split()[2]])+'\n' for i in f.readlines()]
with open(filename,'w') as f:
   f.writelines(l)

Or in this case maybe:

with open(filename,'r') as f:
   l=[' '.join([i.split()[1],i.split()[0],i.split()[2:]])+'\n' for i in f.readlines()]
with open(filename,'w') as f:
   f.writelines(l)

Upvotes: 2

Andrej Kesely
Andrej Kesely

Reputation: 195623

With 54000 columns I would use regular expression, which is fast:

import re

with open('sample.txt', 'r') as f_in, open('sample_out.txt', 'w', newline='') as f_out:
    for line in f_in.readlines():
        g = re.findall(r'[^\s]+', line)
        if g:
            f_out.write(' '.join([g[1], g[0]] + g[2:]) + '\n')

Upvotes: 2

whackamadoodle3000
whackamadoodle3000

Reputation: 6748

Try this:

elements=[]
with open(filename,"r") as f:
    for e in f.readlines():
        line = e.split(" ")
        line0 = line[0]
        line[0] = line[1]
        line[1] = line0
        elements.append(" ".join(line))
with open(filename,"w") as f:
    f.write("\n".join(elements))

Alternatively, if the above code crashes due to file size, you can do everything at once like this:

with open(filename,"r") as f:
    with open(filename2,"w") as f2:
        for e in f.readlines():
            line = e.split(" ")
            line0 = line[0]
            line[0] = line[1]
            line[1] = line0
            f2.write(" ".join(line) + "\n")

... where filename2 is some other filename. Once you run the code, replace filename with filename2, and you are done.

Upvotes: 2

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