how to break out of only one nested loop

Question

I have two tab-delimited files, and I need to test every row in the first file against all the rows in the other file. For instance,

file1:

row1    c1    36    345   A
row2    c3    36    9949  B
row3    c4    36    858   C

file2:

row1    c1    3455  3800
row2    c3    6784  7843
row3    c3    10564 99302
row4    c5    1405  1563

let's say I would like to output all the rows in (file1) for which col[3] of file1 is smaller than any (not every) col[2] of file2, given that col[1] are the same.

Expected output:

row1    c1    36    345   A
row2    c3    36    9949  B

Since I am working in Ubuntu, I would like the input command to look like this:
python code.py [file1] [file2] > [output]

I wrote the following code:

import sys

filename1 = sys.argv[1]
filename2 = sys.argv[2]

file1 = open(filename1, 'r')
file2 = open(filename2, 'r')

done = False

for x in file1.readlines():
    col = x.strip().split()
    for y in file2.readlines():
        col2 = y.strip().split()
        if col[1] == col2[1] and col[3] < col2[2]:
            done = True
            break
        else: continue
print x

However, the output looks like this:

row2    c3    36    9949  B

This is evident for larger datasets, but basically I always get only the last row for which the condition in the nested loop was true. I am suspecting that "break" is breaking me out of both loops. I would like to know (1) how to break out of only one of the for loops, and (2) if this is the only problem I've got here.

Answer 1

break and continue apply to the innermost loop.

The issue is that you open the second file only once, and therefore it's only read once. When you execute for y in file2.readlines(): for the second time, file2.readlines() returns an empty iterable.

Either move file2 = open(filename2, 'r') into the outer loop, or use seek() to rewind to the beginning of file2.