Syntax error: Python for loop and if statement

Question

Novice here!!

I am trying to search through a FASTA for a specific DNA sequence, but I keep getting a sytax error. The if statements work outside of the for loop, so I think it is how I have put them in, can anybody see the syntax error here, I can't work it out:

#!/bin/python

#My Mimp_finder

import re

from Bio import SeqIO


for seq in SeqIO.parse("Focub_mimp12rm_Chang_mimps.faa", "fasta"):
    print(seq.id)
    print(len(seq)                               
    if re.search(r"CAGTGGG..GCAA[TA]AA", seq):
        result_start = re.search(r"CAGTGGG..GCAA[TA]AA", seq)
        match_1_start = result_start.start()
    elif re.search(r"TT[TA]TTGC..CCCACTG", seq):
        result_end = re.search(r"TT[TA]TTGC..CCCACTG", seq)
        match_2_end = result_end.end()

        mimp_lenth = match_2_end - match_1_start

    print('---------------------------\n\n')
    if mimp_lenth < 400 :
    print('Mimp found at postion ' + str(match_1_start) + ' and ' + str(match_2_end) + ' in the sequence: \n\n' + seq + '. \n\nThe $
    print('\n\n---------------------------\n\n')

Returned:

File "./My_mimp_finder.py", line 16
    if re.search(r"CAGTGGG..GCAA[TA]AA", seq):
                                             ^
SyntaxError: invalid syntax

Python version 3.8.3

Could you please reduce your code to minimum needed to reproduce the issue? — Corentin Pane
– Corentin Pane, Commented Aug 7, 2020 at 16:46

Prateek Dewan · Accepted Answer · 2020-08-07 16:51:58Z

3

Parenthesis missing in the second print statement

print(len(seq)

should be

print(len(seq))

answered Aug 7, 2020 at 16:51

Prateek Dewan

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Comments

AKHacks · Accepted Answer · 2020-08-07 16:57:10Z

1

There are two issues in your code. One is already pointed out by @I like coding above.

The reason for your error is in line above the line 16 where error is reported . You are missing closing braces for print statement.

print(len(seq) -- > print(len(seq))

answered Aug 7, 2020 at 16:57

AKHacks

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Comments

RVACode · Accepted Answer · 2020-08-07 16:57:05Z

0

Side Note, there is also an issue with indentation.

After your "if" statement:

if mimp_lenth < 400 :

There needs to be an indentation otherwise you'll get an indentation error.

#!/bin/python

#My Mimp_finder

import re

from Bio import SeqIO


for seq in SeqIO.parse("Focub_mimp12rm_Chang_mimps.faa", "fasta"):
    print(seq.id)
    print(len(seq)                               
    if re.search(r"CAGTGGG..GCAA[TA]AA", seq):
        result_start = re.search(r"CAGTGGG..GCAA[TA]AA", seq)
        match_1_start = result_start.start()
    elif re.search(r"TT[TA]TTGC..CCCACTG", seq):
        result_end = re.search(r"TT[TA]TTGC..CCCACTG", seq)
        match_2_end = result_end.end()

        mimp_lenth = match_2_end - match_1_start

    print('---------------------------\n\n')
    if mimp_lenth < 400 :
         print('Mimp found at postion ' + str(match_1_start) + ' and ' + str(match_2_end) + ' in the sequence: \n\n' + seq + '. \n\nThe $


    print('\n\n---------------------------\n\n')

edited Aug 7, 2020 at 16:57

answered Aug 7, 2020 at 16:48

RVACode

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2 Comments

Michael Butscher Over a year ago

No, indentation errors produce an IndentationError (or semantic errors).

RVACode Over a year ago

@MichaelButscher Oh good point, my fault. I will edit my answer once I figure out the syntax error, but there is an indentation error as well.

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