Python file renaming syntax error

Question

I need to rename many files with the following format:

509938_OPS001_ACTCGCTA-TCGACTAG_L001_R1_001.fastq.gz

I've tested my regex:

\d+\w([OPS]+\d+)[_]\w+-\w+[_](\d+)(\.fastq\.gz)

I've tried many versions of the following script, but each throws a syntax error following re.sub.

import glob, re, os

for filename in glob.glob('some/dir/*.fastq.gz'):
    new_name = re.sub(\d+\w([OPS]+\d+)[_]\w+-\w+[_](\d+)(\.fastq\.gz), r'\1_\2\3', filename)
    os.rename(filename, new_name)

$python fastq_rename.py
  File "fastq_rename.py", line 6
    new_name = re.sub(\d+\w([OPS]+\d+)[_]\w+-\w+[_](\d+)(\.fastq\.gz)), r'\1_\2\3', filename)
                                                                                            ^
SyntaxError: unexpected character after line continuation character

Presuming this has to do with an unescaped backslash, I've enclosed the regex with r' ', and this avoids the error, but does not change filenames.

vks · Accepted Answer · 2015-09-15 03:17:16Z

1

new_name = re.sub(r'\d+\w([OPS]+\d+)[_]\w+-\w+[_](\d+)(\.fastq\.gz)', r'\1_\2\3', filename)
new_name="some/dir/"+newname

Enclose regex in r.Also the newname parameter to os.rename should include filepath or else it will rename file to the directory from where script if being called.

edited Sep 15, 2015 at 3:17

answered Sep 15, 2015 at 3:06

vks

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1 Comment

Vaughn Cooper Over a year ago

Thank you, the filepath was key!

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