Question

I would like to join two lines in file, based on whether or not they start with the same element.
I could turn the first element of each line into a list, and use the elements in this list to search each line, but that hardly seems the most efficient way?

I have the following file

1,AF534061.1,T,A  
1,K02718.1,T,A  
16,AF534061.1,G,-  
16,K02718.1,G,-  
17,AF534061.1,T,-  
17,K02718.1,T,-  
18,AF534061.1,A,-  
18,K02718.1,A,-  
19,AF534061.1,T,-  
19,K02718.1,T,-  
20,AF534061.1,A,-  
20,K02718.1,A,-  
21,AF534061.1,A,-   
21,K02718.1,A,-  
24,AF534061.1,C,T   

I would like to join lines if the first item is shared between the lines. So I would like to get the following output

1,AF534061.1,T,A,1,K02718.1,T,A
16,AF534061.1,G,-,16,K02718.1,G,-
17,AF534061.1,T,-,17,K02718.1,T,-
18,AF534061.1,A,-,18,K02718.1,A,-
19,AF534061.1,T,-,19,K02718.1,T,-
20,AF534061.1,A,-,20,K02718.1,A,-
21,AF534061.1,A,-,21,K02718.1,A,-
24,AF534061.1,C,T

In this example, it looks like I might just be able to join every-other line, but I want (need) to make the code more general!

I do not think this is hard, but I cannot seem to figure it out!
thanks for the help

Answer 1

The Python standard library is full of tools. For this job, use itertools.groupby.

import itertools

lines = '''1,AF534061.1,T,A
1,K02718.1,T,A
16,AF534061.1,G,-
16,K02718.1,G,-
17,AF534061.1,T,-
17,K02718.1,T,-
18,AF534061.1,A,-
18,K02718.1,A,-
19,AF534061.1,T,-
19,K02718.1,T,-
20,AF534061.1,A,-
20,K02718.1,A,-
21,AF534061.1,A,-
21,K02718.1,A,-
24,AF534061.1,C,T'''.split('\n')

for key, group in itertools.groupby(lines, lambda line: line.partition(',')[0]):
    print ','.join(group)