从txt文件中删除列

Question

I'm a beginner in Python and I'm a bit stuck on a trivial problem. I would like to remove some columns and strings from a text file. It is tab separated. The first file is called A.txt

chr1_1792868_SNP    Bcin01g04980    NON_SYNONYMOUS  NON_SYNONYMOUS[T](gene:Bcin01g04980|transcript:Bcin01g04980.1|P->S:225) C   T   C/C C/C C/C C/C C/C C/T 234 233 232 219 233 221 234 233 232 219 233 23  0   0   0   0   0   198

And the output file (let's call it B.txt) should be like :

1   1792868 Bcin01g04980    C   T   C/C C/C C/C C/C C/C C/T 234 233 232 219 233 221 234 233 232 219 233 23  0   0   0   0   0   198

So it would be to perform different operations:

• Remove the "chr" and "_" strings of the first column
• Split the 1 after "chr" and the number after in 2 different columns
• Remove all the columns 3 and 4

I tried so far to do :

with  open ('A.txt', 'r') as mutmut_mutants:
        dble_mut = csv.reader(mutmut_mutants, delimiter='\t')
        with open('B.txt', 'w+') as mutants_coo:
            mut_coo= csv.writer(mutants_coo)
            for i in dble_mut:
                del i[2]
                del i[3]
                mut_coov.writerow( i )

But, big surprise, it's not working. And I'm not splitting the first string in 2 columns. Anyone has an idea on how to proceed?

Thanks a lot!

Answer 1

You can try this:

f = open('data.txt').readlines()

f = [i.strip('\n').split() for i in f]

new_data = []

for i in f:
    data1 = i[0].split("_")
    new = data1[0][-1]+" "+data1[1]+" "

    new += i[1]+" "

    new += ' '.join(i[4:])

    new_data.append(new)
print new_data[0]

Output:

'1 1792868 Bcin01g04980 C T C/C C/C C/C C/C C/C C/T 234 233 232 219 233 221 234 233 232 219 233 23 0 0 0 0 0 198'

Answer 2

Possible solution:

with open('A.txt', 'r') as f:
    data=f.read()

columns = data.split('\t')
result = []

temp = columns[0].split('_')
result.append(temp[0][-1])
result.append(temp[1])

result.extend(columns[4:])

print result

Answer 3

So thanks to the code provided above (thank @Ajax1234 and @doctorlove ), I managed to have what I want in a list. I have some trouble saving it properly into a file. I want it to be tab delimited and with each element of the list as a new line. The code is

f = open('mutmut_mutants.txt').readlines()

f = [i.strip('\n').split() for i in f]

new_data = []

for i in f:
    data1 = i[0].split("_")
    new = data1[0][-1]+" "+data1[1]+" "

    new += i[1]+" "

    new += ' '.join(i[4:])

    new_data.append(new)
print new_data

outfile = open("test.txt", "w")
print >> outfile, "\t".join(str(i) for i in new_data)
outfile.close()

My new_data list looks like that :

['1 1792868 Bcin01g04980 CTC/CC/CC/CC/CC/CC/T 234 233 232 219 233 221 234 233 232 219 233 23 0 0 0 0 0 198', '1 1792869 Bcin01g04980 CTC/CC/TC/TC/TC/TC/T 240 236 233 220 232 220 240 96 66 80 30 25 0 140 166 140 202 194', '2 19718 Bcin02g00005 CAC/AC/AC/AC/AC/AC/A 86 51 78 84 87 108 63 38 58 60 63 86 22 13 20 24 24 22','....','....','...']

And the output in the text file looks ok except that there's not new line at the end of each element of the list :

1 1792868 Bcin01g04980 CTC/CC/CC/CC/CC/CC/T 234 233 232 219 233 221 234 233 232 219 233 23 0 0 0 0 0 198 1 1792869 Bcin01g04980 ...

Thanks for your help!