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ed-lau / riana

Quantifies relative isotope abundance from proteomics data
MIT License
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Fail to parse various mzid files #1

Closed JB-MS closed 7 years ago

JB-MS commented 7 years ago

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 readpeptide 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 :)

ed-lau commented 7 years ago

Hi Johannes,

Thanks for your email. The mzid parser works for my own personal purpose (thermo raw, searching against uniprot with crux). I would be interested in picking it up again and developing it to be something that might be useful to others. I can look into the error messages and It would be very helpful if you could send me any mzid files you have. As far as I can tell there are quite a lot of many-to-many relationships among terms (from different search engines and experimental designs) that I should be aware of.

Best wishes, Edward

— Edward Lau, PhD Postdoctoral Fellow Stanford Cardiovascular Institute lau1@stanford.edu

On Mar 27, 2017, at 7:49 AM, Johannes Leufken notifications@github.com wrote:

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 readpeptide 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 :)

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ed-lau commented 7 years ago

New commit should catch most exceptions:

To run directly:

python ./parse_mzid.py external_mzid_test/mzidentml-example.mzid --out=mascot.txt

JB-MS commented 7 years ago

Hi Ed,

thanks a lot for the fixes! It works now fine for my files.

Cheers, Johannes