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Proteobench / ProteoBench

ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to allow a continuous, easy, and controlled comparison of proteomics data analysis workflows.
https://proteobench.readthedocs.io
Apache License 2.0
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:sparkles: parse parameters from i2masschroq #279

Closed enryH closed 1 month ago

enryH commented 2 months ago

Add support for i2masschroq parameter parsing.

enryH commented 2 months ago

With the latest format the configuration has to be still updated:

toml file with config:

[mapper]
"sequence" = "Sequence"
"rawfile" = "Raw file"
"proteins" = "Proteins"
"ProForma" = "Modified sequence"
"charge" = "Charge"
"area" = "Intensity"  # changed

Then I run into a new error...

File "C:\Users\kzl465\Documents\repos\ProteoBench\webinterface\pages\DDA_Quant_ion.py", line 238, in _run_proteobench
    result_performance, all_datapoints, input_df = self.ionmodule.benchmarking(
File "C:\Users\kzl465\Documents\repos\ProteoBench\proteobench\modules\dda_quant_ion\module.py", line 42, in benchmarking
    self.precursor_name, parse_settings.species_expected_ratio(), parse_settings.species_dict()
TypeError: 'dict' object is not callable

Which is probably due to an attribute and the corresponding method having the same name:

https://github.com/Proteobench/ProteoBench/blob/8284e9c5f8764cbf8ea0e66e40c1bb10e28eba0b/proteobench/io/parsing/parse_settings_ion.py#L43-L63

enryH commented 2 months ago

First PR: https://github.com/Proteobot/Results_quant_ion_DDA/pull/187

enryH commented 2 months ago

Now it works without errors. Closing #229 and ready to merge. Associated submission with this PR is https://github.com/Proteobot/Results_quant_ion_DDA/pull/188

In general we might need to work on showing the PR link the moment it is created - even if error are occuring later. Otherwise it is confusing (as @brvpuyve and @mlocardpaulet ) experienced.