Describe the bug
I was going to learn how to use oktoberfest using your tutorial notebook.
but it has a problem about column names.
i also can't find "peptide" anywhere even i downloaded zip file('https://zenodo.org/record/7613029/files/Oktoberfest_input.zip')
anyway, i checked runner.py and there is the point.
peptides_spectral_library.csv(from zenodo) columns are [modified_sequence, collision_energy, precursor_charge]
there is no peptides! so L304 of runner.py have to occur KeyError
To Reproduce
Steps to reproduce the behavior:
- setup conda environment using script.
- make a new jupyter notebook
- copy & paste each cell from Tutorial
Expected behavior
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
File ~/.conda/envs/oktoberfest/lib/python3.11/site-packages/pandas/core/indexes/base.py:3812, in Index.get_loc(self, key)
3811 try:
-> 3812 return self._engine.get_loc(casted_key)
3813 except KeyError as err:
File pandas/_libs/index.pyx:167, in pandas._libs.index.IndexEngine.get_loc()
File pandas/_libs/index.pyx:196, in pandas._libs.index.IndexEngine.get_loc()
File pandas/_libs/hashtable_class_helper.pxi:7088, in pandas._libs.hashtable.PyObjectHashTable.get_item()
File pandas/_libs/hashtable_class_helper.pxi:7096, in pandas._libs.hashtable.PyObjectHashTable.get_item()
KeyError: 'peptide'
The above exception was the direct cause of the following exception:
KeyError Traceback (most recent call last)
Cell In[54], line 1
----> 1 run_job("spectral_library_config.json")
File ~/.conda/envs/oktoberfest/lib/python3.11/site-packages/oktoberfest/runner.py:1389, in run_job(config_path)
1387 try:
1388 if job_type == "SpectralLibraryGeneration":
-> 1389 generate_spectral_lib(config_path)
1390 elif job_type == "CollisionEnergyCalibration":
1391 run_ce_calibration(config_path)
File ~/.conda/envs/oktoberfest/lib/python3.11/site-packages/oktoberfest/runner.py:423, in generate_spectral_lib(config_path)
420 config.read(config_path)
421 config.check()
--> 423 spec_library = _speclib_from_digestion(config)
425 speclib_written_step = ProcessStep(config.output, "speclib_written")
426 if not speclib_written_step.is_done():
File ~/.conda/envs/oktoberfest/lib/python3.11/site-packages/oktoberfest/runner.py:26, in _speclib_from_digestion(config)
23 from oktoberfest import preprocessing as pp
24 from oktoberfest import rescore as re
---> 26 from .data.spectra import Spectra
27 from .utils import Config, JobPool, ProcessStep, apply_quant, group_iterator
29 logger = logging.getLogger(__name__)
File ~/.conda/envs/oktoberfest/lib/python3.11/site-packages/pandas/core/frame.py:4107, in DataFrame.__getitem__(self, key)
4105 if self.columns.nlevels > 1:
4106 return self._getitem_multilevel(key)
-> 4107 indexer = self.columns.get_loc(key)
4108 if is_integer(indexer):
4109 indexer = [indexer]
File ~/.conda/envs/oktoberfest/lib/python3.11/site-packages/pandas/core/indexes/base.py:3819, in Index.get_loc(self, key)
3814 if isinstance(casted_key, slice) or (
3815 isinstance(casted_key, abc.Iterable)
3816 and any(isinstance(x, slice) for x in casted_key)
3817 ):
3818 raise InvalidIndexError(key)
-> 3819 raise KeyError(key) from err
3820 except TypeError:
3821 # If we have a listlike key, _check_indexing_error will raise
3822 # InvalidIndexError. Otherwise we fall through and re-raise
3823 # the TypeError.
3824 self._check_indexing_error(key)
KeyError: 'peptide'
System [please complete the following information]:
- OS: e.g. [Ubuntu 24]
- Language Version: [Python 3.11]
- Virtual environment: [ Conda]
Additional context
Describe the bug
I was going to learn how to use oktoberfest using your tutorial notebook.
but it has a problem about column names.
i also can't find "peptide" anywhere even i downloaded zip file('https://zenodo.org/record/7613029/files/Oktoberfest_input.zip')
anyway, i checked runner.py and there is the point.
peptides_spectral_library.csv(from zenodo) columns are [modified_sequence, collision_energy, precursor_charge]there is no peptides! so L304 of runner.py have to occur KeyError
To Reproduce
Steps to reproduce the behavior:
Expected behavior
System [please complete the following information]:
Additional context