Convert a space delimited file to comma separated values file in python

replace your first bit with this. it's not super pretty but it will give you a csv format.

with open('coord') as infile, open('coordv', 'w') as outfile:
    for line in infile:
        outfile.write(" ".join(line.split()).replace(' ', ','))
        outfile.write(",") # trailing comma shouldn't matter

if you want the outfile to have everything on different lines you could add outfile.write("\n") at the end of the for loop, but i dont think your code that follows this will work with it like that.

You can use python pandas, I have written your data to data.csv:

import pandas as pd
>>> df = pd.read_csv('data.csv',sep='\s+',header=None)
>>> df
     0  1  2         3         4  5
0    1  C  6  0.000000  1.342650  0
1    2  C  6  0.000000 -1.342650  0
2    3  C  6  2.325539  2.685301  0
3    4  C  6  2.325539 -2.685301  0
4    5  C  6  4.651077  1.342650  0
5    6  C  6  4.651077 -1.342650  0
...

The great thing about this is to access the underlying numpy array you can use df.values:

>>> type(df.values)
<type 'numpy.ndarray'>

To save the data frame with comma delimiters:

>>> df.to_csv('data_out.csv',header=None)

Pandas is a great library for managing large amounts of data, as a bonus it works well with numpy. There is also a very good chance that this will be much faster then using the csv module.

You can use csv:

import csv

with open(ur_infile) as fin, open(ur_outfile, 'w') as fout:
    o=csv.writer(fout)
    for line in fin:
        o.writerow(line.split())