for loop only executes on last iteration

Question

In the attached code, the for loop for m in re.finditer(match, query): only executes on the last set of data in my data file.

I'm using Python 3.6.5.

I have placed print statements before, within and after the for loop, and the within also only executes on the last data set.

# Example: Finding a Motif in DNA
# The indexing in this problem starts from 1!
import re

def process_data(dataFile, outFile):
    with open(dataFile) as data:
        line = data.readline()
        numTests = int(line)
        print ("Number of tests: ", numTests)

        while True:
            line = data.readline()
            if not line:
                break

            query = line
            print ("Query: ", query)
            line = data.readline()
            match = line
            print ("Match: ", match)

            print("Before for statement")
            for m in re.finditer(match, query):
                print("In for statement")
                print ("match start = ", m.start()+1)

            print("After for statement")

    data.close()
    return


if __name__ == "__main__":
    dataFile = "./test.txt"

test.txt looks like:

3
GACAACTTCCAACTTCCAACTTCCCGTCCCAACTTCACAACTTCGGCCCAACTTCCATGCAACTTCACCATCAACTTCGCTCGAAGCTGCCTTCCACTCCAACTTCACAACTTCCTCAACTTCCTCACCAACTTCAGCAACTTCTCTAGGGCCAACTTCCAACTTCTCAACTTCTCAACTTCCAACTTCCGACAACTTCTCCTGGCAACTTCCAACTTCCAACTTCAATACAACTTCGCAGACAACTTCCGCAACTTCGAACAACTTCCAACTTCCCCAACTTCCAACTTCCAACTTCGCCAACTTCCAACTTCCAACTTCCCAACTTCAGATAGCAACTTCGATCTTACACAACTTCACGCAACTTCTCCAACTTCCAACTTCTGTGCAACTTCTCTGAACAACTTCCTCAACTTCCAACTTCGCAACTTCCCCAACTTCCTCAACTTCATGCAACTTCGAGGCAACTTCCCAACTTCGCAACTTCCTATTCCCAACTTCTGTGGCAACTTCTCAACTTCTGGACAACTTCTATGCCCAACTTCACAACTTCCCCAACTTCTTTACAACTTCGACAACTTCATCAACTTCTAGTCAACTTCTGGTCCAACTTCCAACTTCCCCAACTTCCAAAGTGCCGCAACTTCGTAACAACTTCACGCGCTCAACTTCAACCAACTTCTTTTCCCGCAACTTCGCAACTTCACAACTTCTAATCAACTTCCAACTTCGGATCAACTTCCAACTTCGCCAACTTCCAACTTCCAACTTCTCCAGGGACAACTTCAAGTACAACTTCCAACTTCGCAACTTCACAACTTCCCAACTTCGCAACTTCTACACGCAACTTCCAACTTCTGGTCCCAACTTCATCAACTTCAGTCAACTTC
CAACTTCCA
GAAAGGATAAAGGATGTCAAAGGATGCAGATATAAAGGATAAAGGATACAAAGGATTAAGTATGTCCGAAAAAGGATAAAGGATTAAAAGGATCGCTGAACCTTACACAAAGGATAGTGAACAAAGGATTCAATAAAAGGATAAAGGATCAAAGGATCAAAAGGATACAAAGGATGCCGATGAAAGGATAAAGGATCTAAAGGATAAAGGATGAGAAAGGATTGGAAAGGATTATGAGATCAAAGGATAAAGGATGGTGTAAAAGCTAAAGGATTCGGCAAAGGATAAAGGATTAAAGGATAAAAAGGATAAAGGATGAAAGGATCCGCAGGGACCAGCAAAAGGATAAAGGATCGAATGGGTAAGAAAGGATCAAAGGATGAAAAAGGATTACTAAAGGATAAAGGATCCTGAAAGGATTACAAAGGATCTTAAAAGGATTCGGAAAGGATCCATAGGAAAAGGATAAAGGATCGCGAAAGGATAAAGGATTAAAGGATAAAGGATAAAAGGATTCAAAGGATAAAGGATAGACAAGGGAGAAAGGATGCAAAGGATGAAAGGATAAAGGATAAAGGATAAAGGATTAGGTTAAAGGATCGAAAGGATCCAAAGAGAGCGAAAAGGATGAGGACGAAAGGATCAAAGGATCCAAAGGATCAAAGGATAAAGGATTGCGATGGAAAGGATGTCAAAGGATCACCAAAGGATAAAGGATAATAAAGGATAAAGGATAAAGGATCAAAGGATTTGAAAAGGATAAAGGATCACGAAAGGATAAAAGGATTGGCAAAGGATGAAAAGGATGAAAGGATAAGCCCTCCAAAGGAT
AAAGGATAA
ATTCAAATACTTCAAATAGTCAAATATCAAATATGCTTCAAATATCAAATATCGGTCAAATAAGTCAAATAAGTCAAATATCAAATATCAAATACTCAAATATCAAATAGTGTCAAATACGAATTGGGTCAAATATCAAATATGTGTTCAAATATTCTTCAAATACTGGACACTCAAATAGGAGTCAAATATCAAATATCAAATACGTGAAGTGCTTGTCAAATATTTCAAATACTTTCAAATATTCAAATACTCAAATATGTTCAAATATCAAATATCAAATATTTCAAATATCAAATATCAAATAGTCCTCAAATAGCAAACCAGTCAAATATCAAATATGTCAAATATGCTCACGGCAACCTCAAATATCAAATATCAAATAGATGTCAAATAAGTTTCAAATATCAAATATCAAATATCAAATATCAAATATTCAAATATCAAATAGCGGGCTCAAATAAGCTCAAATACGTCAAATAGGGGGTCAAATAGATCAAATAGTCAAATATTCAAATACATCAAATAGTCAAATACAAGAACCACCGAGATCTCAAATAATCAAATATCAAATATGGTCAAATAAATATTCAAATAGGTCAAATAAGATCAAATATCAAATAAGTCGTCCATCAAATAGTCAAATAGCTCAAATAACCTCAAATATCAAATATTCAAATACCGGTCATCAAATAGGACAAATCAAATAGTCAAATAAGATCCTCTCAAATAATTCAAATAGCTGTTCAAATACTCAAATATCAAATAGTCAAATATCAAATATTCAAATATCAAATACTTCAAATATGTTCAAATAATCAAATACTCAAATATCAAATAATCAAATAATACTTCAAATATACCAAACGCTCAAATATTAGTTGGATCAAATATCTTCAAATATCAAATAA
TCAAATATC

The resulting output is:

Number of tests:  2
Query:  GACAACTTCCAACTTCCAACTTCCCGTCCCAACTTCACAACTTCGGCCCAACTTCCATGCAACTTCACCATCAACTTCGCTCGAAGCTGCCTTCCACTCCAACTTCACAACTTCCTCAACTTCCTCACCAACTTCAGCAACTTCTCTAGGGCCAACTTCCAACTTCTCAACTTCTCAACTTCCAACTTCCGACAACTTCTCCTGGCAACTTCCAACTTCCAACTTCAATACAACTTCGCAGACAACTTCCGCAACTTCGAACAACTTCCAACTTCCCCAACTTCCAACTTCCAACTTCGCCAACTTCCAACTTCCAACTTCCCAACTTCAGATAGCAACTTCGATCTTACACAACTTCACGCAACTTCTCCAACTTCCAACTTCTGTGCAACTTCTCTGAACAACTTCCTCAACTTCCAACTTCGCAACTTCCCCAACTTCCTCAACTTCATGCAACTTCGAGGCAACTTCCCAACTTCGCAACTTCCTATTCCCAACTTCTGTGGCAACTTCTCAACTTCTGGACAACTTCTATGCCCAACTTCACAACTTCCCCAACTTCTTTACAACTTCGACAACTTCATCAACTTCTAGTCAACTTCTGGTCCAACTTCCAACTTCCCCAACTTCCAAAGTGCCGCAACTTCGTAACAACTTCACGCGCTCAACTTCAACCAACTTCTTTTCCCGCAACTTCGCAACTTCACAACTTCTAATCAACTTCCAACTTCGGATCAACTTCCAACTTCGCCAACTTCCAACTTCCAACTTCTCCAGGGACAACTTCAAGTACAACTTCCAACTTCGCAACTTCACAACTTCCCAACTTCGCAACTTCTACACGCAACTTCCAACTTCTGGTCCCAACTTCATCAACTTCAGTCAACTTC

Match:  CAACTTCCA

Before for statement
After for statement
Query:  GAAAGGATAAAGGATGTCAAAGGATGCAGATATAAAGGATAAAGGATACAAAGGATTAAGTATGTCCGAAAAAGGATAAAGGATTAAAAGGATCGCTGAACCTTACACAAAGGATAGTGAACAAAGGATTCAATAAAAGGATAAAGGATCAAAGGATCAAAAGGATACAAAGGATGCCGATGAAAGGATAAAGGATCTAAAGGATAAAGGATGAGAAAGGATTGGAAAGGATTATGAGATCAAAGGATAAAGGATGGTGTAAAAGCTAAAGGATTCGGCAAAGGATAAAGGATTAAAGGATAAAAAGGATAAAGGATGAAAGGATCCGCAGGGACCAGCAAAAGGATAAAGGATCGAATGGGTAAGAAAGGATCAAAGGATGAAAAAGGATTACTAAAGGATAAAGGATCCTGAAAGGATTACAAAGGATCTTAAAAGGATTCGGAAAGGATCCATAGGAAAAGGATAAAGGATCGCGAAAGGATAAAGGATTAAAGGATAAAGGATAAAAGGATTCAAAGGATAAAGGATAGACAAGGGAGAAAGGATGCAAAGGATGAAAGGATAAAGGATAAAGGATAAAGGATTAGGTTAAAGGATCGAAAGGATCCAAAGAGAGCGAAAAGGATGAGGACGAAAGGATCAAAGGATCCAAAGGATCAAAGGATAAAGGATTGCGATGGAAAGGATGTCAAAGGATCACCAAAGGATAAAGGATAATAAAGGATAAAGGATAAAGGATCAAAGGATTTGAAAAGGATAAAGGATCACGAAAGGATAAAAGGATTGGCAAAGGATGAAAAGGATGAAAGGATAAGCCCTCCAAAGGAT

Match:  AAAGGATAA
Before for statement
In for statement
match start =  2
In for statement
match start =  34
In for statement
match start =  71
In for statement
match start =  136
In for statement
match start =  183
In for statement
match start =  199
In for statement
match start =  242
In for statement
match start =  280
In for statement
match start =  295
In for statement
match start =  304
In for statement
match start =  341
In for statement
match start =  396
In for statement
match start =  461
In for statement
match start =  479
In for statement
match start =  494
In for statement
match start =  518
In for statement
match start =  560
In for statement
match start =  574
In for statement
match start =  662
In for statement
match start =  705
In for statement
match start =  722
In for statement
match start =  755
In for statement
match start =  773
In for statement
match start =  809
After for statement

The first two set of match and query had no output. There are no error messages.

`re.finditer(match, query)` does it return exactly what you think it does? Thanks, Karl for editing the question. — offeltoffel, Feb 05 '19 at 10:23
I formatted your output and file contents as code, because it looks like some line breaks were not being preserved otherwise and it wasn't accurately displaying what you had. That said, there still seems to be a mismatch. Please double-check that your test output corresponds to the file contents; that you've saved and closed the file in any other programs before running your script, etc. — Karl Knechtel, Feb 05 '19 at 10:24

score 1 · Answer 1 · answered Feb 05 '19 at 10:27

1

the for loop "for m in re.finditer(match, query):", only executes on the last set of data in my data file.

On the other lines, it executes - for zero iterations, because re.finditer(match, query) finds zero matches. The reason is that both match and query have a newline at the end, except the last time through (since there is presumably no newline at the end of your file, and thus no newline at the end of the match). This happens because the .readline() method of the file includes the newline character at the end of the read-in line.

You can remove these with e.g. query = query.strip().

answered Feb 05 '19 at 10:27

Karl Knechtel

62,466
11
102
153

See also e.g. https://stackoverflow.com/questions/12330522/reading-a-file-without-newlines – Karl Knechtel Feb 05 '19 at 10:29
That was it, I needed to strip both the query and the match. Thank you so very, very, very much. – Jam One Feb 05 '19 at 15:16

for loop only executes on last iteration

1 Answers1