Python Script To Split Dna Strings Into New Lines

Question

[Studentguy]

I have this string:

'ACC': 2, 'ACACAGTTTGCGCGCGCGGGG': 1, 'ACCGTA': 3, 'GCTTTAAAAAGGCAA': 1, 'ACCGTAACCTTG': 2

I want it to print out like this:

'ACC': 2,

'ACACAGTTTGCGCGCGCGGGG': 1,

'ACCGTA': 3,

'GCTTTAAAAAGGCAA': 1,

'ACCGTAACCTTG': 2

I know im supposed to use split() or splitlines() to get it to break after every comma but I am dumbfounded right now and it seems like i am missing something simple

[Istvan Albert]

Note that by accident it seems that you included the same output in for both input and output, please edit your question and change that.

Answer 1

[Giovanni M Dall'Olio]

In case your input is a string, you just have to use the string's .split method to split it into a list:

>>> original_string = "'ACC': 2, 'ACACAGTTTGCGCGCGCGGGG': 1, 'ACCGTA': 3, 'GCTTTAAAAAGGCAA': 1, 'ACCGTAACCTTG': 2"
>>> splitted = original_string.split(', ')
>>> splitted
["'ACC': 2",
 "'ACACAGTTTGCGCGCGCGGGG': 1",
 "'ACCGTA': 3",
 "'GCTTTAAAAAGGCAA': 1",
 "'ACCGTAACCTTG': 2"]
>>> for el in splitted: 
        print el + ','
'ACC': 2,
'ACACAGTTTGCGCGCGCGGGG': 1,
'ACCGTA': 3,
'GCTTTAAAAAGGCAA': 1,
'ACCGTAACCTTG': 2,

However, I suspect that you just want to print the contents of a dictionary in order to see them more clearly. If that is the case, have a look at the pprint function:

>>> import pprint
>>> mydict = {'ACC': 2, 'ACACAGTTTGCGCGCGCGGGG': 1, 'ACCGTA': 3, 'GCTTTAAAAAGGCAA': 1, 'ACCGTAACCTTG': 2}
>>> pprint.pprint(mydict)            
{'ACACAGTTTGCGCGCGCGGGG': 1,
 'ACC': 2,
 'ACCGTA': 3,
 'ACCGTAACCTTG': 2,
 'GCTTTAAAAAGGCAA': 1}

Also, consider using ipython instead of the standard python interpreter, which has many features and pretty-prints dictionaries by default.

Answer 2

[Eric Normandeau]

Hi,

In the case where you really have a string to work with (like in your question), try this:

my_string = "'ACC': 2, 'ACACAGTTTGCGCGCGCGGGG': 1, \
            'ACCGTA': 3, 'GCTTTAAAAAGGCAA': 1, 'ACCGTAACCTTG': 2"

my_list = [x.strip() for x in my_string.split(",")]
for i in my_list:
    print i + "," # Added the comma as is is present in the form asked by the OP

As Istvan pointed out, you seem to have a dictionary, but this might provide an example of splitting and 'listifying' a string :)

Cheers

[Niek De Klein]

Am I missing something or can you just do my_list = my_string.split(",")?

[Eric Normandeau]

You could either use my_string.split(", ") #Note the space after the comma, or the form I used. Both will get rid of the trailing space. Cheers

Answer 3

[Istvan Albert]

The string that you seem to have is a dictionary printed out directly on screen. The second output could be generated by something like:

mydict = {'ACC': 2, 'ACACAGTTTGCGCGCGCGGGG': 1, 'ACCGTA': 3, 'GCTTTAAAAAGGCAA': 1, 'ACCGTAACCTTG': 2}

print mydict

print '-----'

for key, value in mydict.items():
   print '%s:%s,' % (key, value)

this will print:

{'ACC': 2, 'ACACAGTTTGCGCGCGCGGGG': 1, 'ACCGTAACCTTG': 2, 'ACCGTA': 3, 'GCTTTAAAAAGGCAA': 1}
-----
ACC:2,
ACACAGTTTGCGCGCGCGGGG:1,
ACCGTAACCTTG:2,
ACCGTA:3,
GCTTTAAAAAGGCAA:1,

Answer 4

[Sai Liu]

>>>a=''''ACC': 2, 'ACACAGTTTGCGCGCGCGGGG': 1, 'ACCGTA': 3, 'GCTTTAAAAAGGCAA': 1
, 'ACCGTAACCTTG': 2'''

>>> a.replace(',',',\n')
"'ACC': 2,\n 'ACACAGTTTGCGCGCGCGGGG': 1,\n 'ACCGTA': 3,\n 'GCTTTAAAAAGGCAA': 1,\n 'ACCGTAACCTTG': 2"

>>> print a.replace(',',',\n')
'ACC': 2,
'ACACAGTTTGCGCGCGCGGGG': 1,
'ACCGTA': 3,
'GCTTTAAAAAGGCAA': 1,
'ACCGTAACCTTG': 2