Progenesis-MSe data

[tania...@gmail.com]

Hello,

I am trying to analyze a MSe data following this guidelines: https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-progenesisQI/

I exported the file few times but I just get the same error:

PROGENESIS Traceback (most recent call last): File "/data/ccms-gnps/tools/feature-based-molecular-networking/release_18/scripts/reformat_quantification.py", line 117, in <module> main() File "/data/ccms-gnps/tools/feature-based-molecular-networking/release_18/scripts/reformat_quantification.py", line 101, in main compound_scan_mapping = progenesis_formatter.convert_to_feature_csv(args.quantification_table, args.quantification_table_reformatted) File "/data/ccms-gnps/tools/feature-based-molecular-networking/release_18/scripts/progenesis_formatter.py", line 13, in convert_to_feature_csv input_format = pd.read_csv(input_filename, sep=",", skiprows=2) File "/data/ccms-gnps/tools/anaconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 709, in parser_f return _read(filepath_or_buffer, kwds) File "/data/ccms-gnps/tools/anaconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 455, in _read data = parser.read(nrows) File "/data/ccms-gnps/tools/anaconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 1069, in read ret = self._engine.read(nrows) File "/data/ccms-gnps/tools/anaconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 1839, in read data = self._reader.read(nrows) File "pandas/_libs/parsers.pyx", line 902, in pandas._libs.parsers.TextReader.read File "pandas/_libs/parsers.pyx", line 924, in pandas._libs.parsers.TextReader._read_low_memory File "pandas/_libs/parsers.pyx", line 978, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 965, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 2208, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 17 fields in line 5, saw 42

https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=c84c5a339dc74e6cbeaa22e13a256fc8

Would you have a recommendation about what I could do? 

Best regards

Tania

[tania...@gmail.com]

I also deleted the columns after the raw abundances but also get the error.

Is there anything else to try?

Best wishes

Tania

[Mingxun Wang]

Happy to look at this together at my office hours:

https://ccms-ucsd.github.io/GNPSDocumentation/contact/

Best,

Ming

--
You received this message because you are subscribed to the Google Groups "GNPS Discussion Forum and Bug Reports" group.
To unsubscribe from this group and stop receiving emails from it, send an email to molecular_networking_b...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/molecular_networking_bug_reports/4e7f9b4e-db01-41ae-9a4b-d0ac76929bfan%40googlegroups.com.

[Louis-Félix Nothias]

Hi Tania,

This is a known issue related to regional specificities in the CSV format exported by Progenesis QI.

I have pushed a fix to deal with that, which should be part of next GNPS release. https://github.com/CCMS-UCSD/GNPS_Workflows/pull/784

In the meantime, you can convert your Progenesis QI files with this Binder notebook and the use the output for running FBMN jobs on GNPS.

https://github.com/lfnothias/GNPS_Workflows_test_env

Cheers,

LF

[tania...@gmail.com]

Hi Louis-Félix,

Thank you very much! I end up getting it to work after editing in the excel but your solution is better and faster. I have a new problem though, we used all the samples together to convert for the two files in the progenesis. The information about the different samples is in the .csv file, however, after run in the GNPS, I can't see the information about the different samples. Is there a way to find it? I am using cytoscape and I would like to colour the compounds according to the sampling location. I think the metadata won't work because all of the samples have the same .msp/.mgf

https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=6136fdc1af394d08a6acd7c7c2ccc0c9

Thanks in advance for any advice,

Cheers,

Tania

[Louis-Felix Nothias]

Hi Tania,

 

Awesome !

 

About retrieving sample informations in Cytoscape, you should be able to achieve this by adding a metadata file:

https://ccms-ucsd.github.io/GNPSDocumentation/metadata/

 

Note that for Progenesis QI, the samples headers in the metadata table shouldn’t include the file extenion (like .raw). https://github.com/CCMS-UCSD/GNPS_Workflows/tree/master/feature-based-molecular-networking#progenesis-qi

 

Alternatively, in Cytoscape, you can map the converted table by importing it as a node attribute table.

 

Cheers,

 

LF