python error with --coverage

[mikeyweigand]

In attempting to use '--coverage' I encounter the following python error, which I have been unable to correct. Admittedly, I am not a skilled python user.

Traceback (most recent call last):
File "/home/yrh8/Tools/stringMLST/stringMLST.py", line 1613, in
getCoverage(results)
File "/home/yrh8/Tools/stringMLST/stringMLST.py", line 790, in getCoverage
allele = gene+'_'+re.sub("*", "", str(results[sample][gene]))
File "/usr/lib/python2.7/re.py", line 151, in sub
return _compile(pattern, flags).sub(repl, string, count)
File "/usr/lib/python2.7/re.py", line 244, in _compile
raise error, v # invalid expression
sre_constants.error: nothing to repeat

[ar0ch]

Hi Mike,

There's is an oddball bug in Python in early version of Python 2.7 (2.7.x < 2.7.5 if memory serves). What version of Python 2.7 are you running (python --version will tell you)?

[mikeyweigand]

Thanks. I get this error with Python 2.7.6; and a similar error with Python 3.4.3.

[ar0ch]

I'll take a look this week

[ar0ch]

I haven't forgotten about this issue Mike, just haven't had the time to look at it yet. I'm sorry for the wait! 😞

[garfinjm]

Hello,

I am encountering the same issue with python 2.7.12 and 3.5.2, working in a docker container based on ubuntu:xenial. I get the same error with the Neisseria test dataset and a Salmonella enterica dataset.

I am using the suggested samtools/bedtools/bwa versions.

For Neisseria I tried:

stringMLST.py --predict -1 tests/fastqs/ERR026529_1.fastq.gz -2 tests/fastqs/ERR026529_2.fastq.gz --prefix Nm -k 35 --coverage --config datasets/Neisseria_spp/neisseria_config.txt -o testingout

and my error looks like:

Traceback (most recent call last):
  File "/stringMLST/stringMLST.py", line 1613, in <module>
    getCoverage(results)
  File "/stringMLST/stringMLST.py", line 790, in getCoverage
    allele = gene+'_'+re.sub("*", "", str(results[sample][gene]))
  File "/usr/lib/python2.7/re.py", line 155, in sub
    return _compile(pattern, flags).sub(repl, string, count)
  File "/usr/lib/python2.7/re.py", line 251, in _compile
    raise error, v # invalid expression
sre_constants.error: nothing to repeat

Let me know if there is anything you want me to try. Thanks!

[ar0ch]

Alright...I'll carve out some time during the begining of January to finally squash this bug. It's been around long enough and I should really fix it.

[ar0ch]

Alrighty, this bug should be fixed now. I missed escaping the "*" in the re.sub statement on line 790 while refactoring code .

python2 --version;python2 ./stringMLST.py --predict -d tests/fastqs -P neisseria/nmb --coverage --config neisseria/nmb_config.txt; python3 --version; python3 ./stringMLST.py --predict -d tests/fastqs -P neisseria/nmb --coverage --config neisseria/nmb_config.txt

Python 2.7.11
Sample  abcZ    adk     aroE    fumC    gdh     pdhC    pgm  ST
ERR027250       581 (100.00)    408 (99.35)     655 (91.63)  602 (92.47)        633 (99.60)     612 (100.00)    632 (97.33)     10252
ERR026529       231 (100.00)    180 (100.00)    306 (100.00) 612 (100.00)       269 (100.00)    277 (100.00)    260 (99.78)     10174
ERR036104       2 (100.00)      3 (100.00)      4 (100.00)   3 (100.00) 8 (100.00)      4 (100.00)      6 (100.00)      11

Python 3.6.3 :: Anaconda custom (64-bit)
Sample  abcZ    adk     aroE    fumC    gdh     pdhC    pgm  ST
ERR026529       231 (100.00)    180 (100.00)    306 (100.00) 612 (100.00)       269 (100.00)    277 (100.00)    260 (99.78)     10174
ERR027250       581 (100.00)    408 (99.35)     655 (91.63)  602 (92.47)        633 (99.60)     612 (100.00)    632 (97.33)     10252
ERR036104       2 (100.00)      3 (100.00)      4 (100.00)   3 (100.00) 8 (100.00)      4 (100.00)      6 (100.00)      11

And this also has made me realize why #36 is happening... So hopefully I'll get that fixed today as well

[ar0ch]

@mikeyweigand @garfinjm Does the update from last week (you can update via pip if you want) solve this for you?

[garfinjm]

Works perfect for me with the Neisseria test dataset.

Thanks for the fix!

[ar0ch]

Great! 😄

[garfinjm]

Sorry to reopen this one, could you do 0.5.2 release on github? For validation purposes, I would like to have a static release to put in my dockerfile, but I am getting an error with pip3:

root@3510db9e948f:/stringMLST-0.5.2# pip3 install stringMLST
Collecting stringMLST
  Using cached https://files.pythonhosted.org/packages/c0/15/beb76e4fcbc196862812c4ad08f86ca1ace2d67424eeb02d257309deaa37/stringMLST-0.5.2.tar.gz
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-u7exvti2/stringMLST/setup.py", line 9, in <module>
        with open("README.md", "r") as fh:
    FileNotFoundError: [Errno 2] No such file or directory: 'README.md'

Thanks again for all your help with this, let me know if you want any more debugging info from my attempts with pip.

[ar0ch]

Done! https://github.com/jordanlab/stringMLST/releases/tag/0.5.2

I'll track down that pip error and put out a new pip bundle

[garfinjm]

Working perfect now. Thanks for your help!