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.

Related: [Compare two files and write to a new file but only output a few lines?](http://stackoverflow.com/questions/18514979/compare-two-files-and-write-to-a-new-file-but-only-output-a-few-lines) — Ashwini Chaudhary, Sep 01 '13 at 07:58

score 40 · Accepted Answer · answered Sep 01 '13 at 07:57

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.

eisoku9618 · Answer 2 · 2013-09-01T09:36:56.410

You need to parse the numeric strings to their corresponding integer values.

You can use int('hoge') as follows.

import sys

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

with open(filename1) as file1:
    for x in file1:
        with open(filename2) as file2:
            col = x.strip().split()
            for y in file2:
                col2 = y.strip().split()
                if col[1] == col2[1] and int(col[3]) < int(col2[2]):
                    print x

how to break out of only one nested loop

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