ed-lau / riana Goto Github PK

Hello,

Thanks for putting together this software. However I'm encountering an issue with multiprocessing.

When I run the following ::

python riana.py test_mzid test_mzml --thread 2 -u -i 0,6 -q 0.01 -r 0.25 -k 1

0%| | 0/694 [00:00<?, ?it/s]multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "C:\Users\User\Anaconda3\envs\riana\lib\multiprocessing\pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "C:\Users\User\Anaconda3\envs\riana\lib\multiprocessing\pool.py", line 44, in mapstar
return list(map(*args))
File "E:\Python Projects\nicole\riana\integrate_peaks.py", line 142, in get_isotopes_from_amrt_wrapper
z=charge
File "E:\Python Projects\nicole\riana\integrate_peaks.py", line 216, in get_isotopes_from_amrt
nearby_scans = [[i, rt] for i, rt in self.rt_idx.items()
File "E:\Python Projects\nicole\riana\integrate_peaks.py", line 217, in
if abs(rt - peptide_rt) <= self.rt_tolerance and self.mslvl_idx[i] == 1]
TypeError: unsupported operand type(s) for -: 'float' and 'NoneType'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "riana.py", line 338, in
args.func(args)
File "riana.py", line 240, in integrate
output_table = peaks.get_isotopes_from_amrt_multiwrapper(num_thread=num_thread)
File "E:\Python Projects\nicole\riana\integrate_peaks.py", line 119, in get_isotopes_from_amrt_multiwrapper
total=max(loop_count)))
File "C:\Users\User\Anaconda3\envs\riana\lib\site-packages\tqdm_tqdm.py", line 1022, in iter
for obj in iterable:
File "C:\Users\User\Anaconda3\envs\riana\lib\multiprocessing\pool.py", line 320, in
return (item for chunk in result for item in chunk)
File "C:\Users\User\Anaconda3\envs\riana\lib\multiprocessing\pool.py", line 731, in next
raise value
TypeError: unsupported operand type(s) for -: 'float' and 'NoneType'

Hi,

I'm trying to run your code but the module readlipid is missing, could you add it please?

Many thanks,
Paola

Dear pzmzml-integrator-Team,

i have just found your repo here and i am very excited about the mzid parser, since i am looking for a lightweight python mzid parser.

I have a very simple script using the Mzid class but unfortunately it crashes with my test files (3 different: msgf+ result file, myrimatch result file and an example file from the PRIDE toolsuite) with different errors.

e.g.
"
Reading mzID file as document object model...
Done. Processing time: 1.6 seconds.
Processing 0 of 191 records (PSM).
Traceback (most recent call last):
File "./simple_mzid_parser.py", line 25, in
main()
File "./simple_mzid_parser.py", line 15, in main
reader = Mzid(sys.argv[1])
File "/Users/joe/Dev/pymzml_integrator/parse_mzid.py", line 46, in init
self.psm_df = self.read_psm()
File "/Users/joe/Dev/pymzml_integrator/parse_mzid.py", line 137, in read_psm
value = cvParam.attributes['value'].value
File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/xml/dom/minidom.py", line 555, in getitem
return self._attrs[attname_or_tuple]
KeyError: 'value'
"

or

"
Traceback (most recent call last):
File "./simple_mzid_parser.py", line 25, in
main()
File "./simple_mzid_parser.py", line 15, in main
reader = Mzid(sys.argv[1])
File "/Users/joe/Dev/pymzml_integrator/parse_mzid.py", line 47, in init
self.peptide_df = self.read_peptide()
File "/Users/joe/Dev/pymzml_integrator/parse_mzid.py", line 246, in read_peptide
newcol[i] = re.sub(' |:', '_', peptide_df[i][0][1])
TypeError: 'NoneType' object is not subscriptable
"

Any help is highly appreciated.

Cheers,
Johannes

PS: Thanks for using pymzML :)