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added unit test for tmt prosit predictions
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@picciama
picciama committed Oct 2, 2023
1 parent 1b4e47c commit a2241a7
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12 changes: 12 additions & 0 deletions .gitignore
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Expand Up @@ -52,6 +52,12 @@ coverage.xml
.hypothesis/
.pytest_cache/

# ignore unit test data folder
tests/unit_tests/data/mokapot/**
!tests/unit_tests/data/mokapot/*.tab
!tests/unit_tests/data/predictions/


# Translations
*.mo
*.pot
Expand All @@ -71,6 +77,7 @@ instance/

# Sphinx documentation
docs/_build/
docs/api/

# PyBuilder
target/
Expand Down Expand Up @@ -139,3 +146,8 @@ dmypy.json

# Used by ProteomicsDB runs to describe the oktoberfest version
hash.file


# output files in tutorials folder
tutorials/
!tutorials/Oktoberfest Tutorial.ipynb
4 changes: 4 additions & 0 deletions tests/unit_tests/data/predictions/library_input.csv
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@@ -0,0 +1,4 @@
,"MODIFIED_SEQUENCE","COLLISION_ENERGY","PRECURSOR_CHARGE","FRAGMENTATION"
0,"[UNIMOD:737]-PEPTIDEK[UNIMOD:737]",30,2,"HCD"
1,"[UNIMOD:737]-PEPTIDE",30,2,"HCD"
2,"[UNIMOD:737]-M[UNIMOD:35]EC[UNIMOD:4]TIDEK[UNIMOD:737]",35,1,"CID"
4 changes: 4 additions & 0 deletions tests/unit_tests/data/predictions/library_output.csv
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,MODIFIED_SEQUENCE,COLLISION_ENERGY,PRECURSOR_CHARGE,FRAGMENTATION,INTENSITY_PRED_Y1+,INTENSITY_PRED_Y1++,INTENSITY_PRED_Y1+++,INTENSITY_PRED_B1+,INTENSITY_PRED_B1++,INTENSITY_PRED_B1+++,INTENSITY_PRED_Y2+,INTENSITY_PRED_Y2++,INTENSITY_PRED_Y2+++,INTENSITY_PRED_B2+,INTENSITY_PRED_B2++,INTENSITY_PRED_B2+++,INTENSITY_PRED_Y3+,INTENSITY_PRED_Y3++,INTENSITY_PRED_Y3+++,INTENSITY_PRED_B3+,INTENSITY_PRED_B3++,INTENSITY_PRED_B3+++,INTENSITY_PRED_Y4+,INTENSITY_PRED_Y4++,INTENSITY_PRED_Y4+++,INTENSITY_PRED_B4+,INTENSITY_PRED_B4++,INTENSITY_PRED_B4+++,INTENSITY_PRED_Y5+,INTENSITY_PRED_Y5++,INTENSITY_PRED_Y5+++,INTENSITY_PRED_B5+,INTENSITY_PRED_B5++,INTENSITY_PRED_B5+++,INTENSITY_PRED_Y6+,INTENSITY_PRED_Y6++,INTENSITY_PRED_Y6+++,INTENSITY_PRED_B6+,INTENSITY_PRED_B6++,INTENSITY_PRED_B6+++,INTENSITY_PRED_Y7+,INTENSITY_PRED_Y7++,INTENSITY_PRED_Y7+++,INTENSITY_PRED_B7+,INTENSITY_PRED_B7++,INTENSITY_PRED_B7+++,INTENSITY_PRED_Y8+,INTENSITY_PRED_Y8++,INTENSITY_PRED_Y8+++,INTENSITY_PRED_B8+,INTENSITY_PRED_B8++,INTENSITY_PRED_B8+++,INTENSITY_PRED_Y9+,INTENSITY_PRED_Y9++,INTENSITY_PRED_Y9+++,INTENSITY_PRED_B9+,INTENSITY_PRED_B9++,INTENSITY_PRED_B9+++,INTENSITY_PRED_Y10+,INTENSITY_PRED_Y10++,INTENSITY_PRED_Y10+++,INTENSITY_PRED_B10+,INTENSITY_PRED_B10++,INTENSITY_PRED_B10+++,INTENSITY_PRED_Y11+,INTENSITY_PRED_Y11++,INTENSITY_PRED_Y11+++,INTENSITY_PRED_B11+,INTENSITY_PRED_B11++,INTENSITY_PRED_B11+++,INTENSITY_PRED_Y12+,INTENSITY_PRED_Y12++,INTENSITY_PRED_Y12+++,INTENSITY_PRED_B12+,INTENSITY_PRED_B12++,INTENSITY_PRED_B12+++,INTENSITY_PRED_Y13+,INTENSITY_PRED_Y13++,INTENSITY_PRED_Y13+++,INTENSITY_PRED_B13+,INTENSITY_PRED_B13++,INTENSITY_PRED_B13+++,INTENSITY_PRED_Y14+,INTENSITY_PRED_Y14++,INTENSITY_PRED_Y14+++,INTENSITY_PRED_B14+,INTENSITY_PRED_B14++,INTENSITY_PRED_B14+++,INTENSITY_PRED_Y15+,INTENSITY_PRED_Y15++,INTENSITY_PRED_Y15+++,INTENSITY_PRED_B15+,INTENSITY_PRED_B15++,INTENSITY_PRED_B15+++,INTENSITY_PRED_Y16+,INTENSITY_PRED_Y16++,INTENSITY_PRED_Y16+++,INTENSITY_PRED_B16+,INTENSITY_PRED_B16++,INTENSITY_PRED_B16+++,INTENSITY_PRED_Y17+,INTENSITY_PRED_Y17++,INTENSITY_PRED_Y17+++,INTENSITY_PRED_B17+,INTENSITY_PRED_B17++,INTENSITY_PRED_B17+++,INTENSITY_PRED_Y18+,INTENSITY_PRED_Y18++,INTENSITY_PRED_Y18+++,INTENSITY_PRED_B18+,INTENSITY_PRED_B18++,INTENSITY_PRED_B18+++,INTENSITY_PRED_Y19+,INTENSITY_PRED_Y19++,INTENSITY_PRED_Y19+++,INTENSITY_PRED_B19+,INTENSITY_PRED_B19++,INTENSITY_PRED_B19+++,INTENSITY_PRED_Y20+,INTENSITY_PRED_Y20++,INTENSITY_PRED_Y20+++,INTENSITY_PRED_B20+,INTENSITY_PRED_B20++,INTENSITY_PRED_B20+++,INTENSITY_PRED_Y21+,INTENSITY_PRED_Y21++,INTENSITY_PRED_Y21+++,INTENSITY_PRED_B21+,INTENSITY_PRED_B21++,INTENSITY_PRED_B21+++,INTENSITY_PRED_Y22+,INTENSITY_PRED_Y22++,INTENSITY_PRED_Y22+++,INTENSITY_PRED_B22+,INTENSITY_PRED_B22++,INTENSITY_PRED_B22+++,INTENSITY_PRED_Y23+,INTENSITY_PRED_Y23++,INTENSITY_PRED_Y23+++,INTENSITY_PRED_B23+,INTENSITY_PRED_B23++,INTENSITY_PRED_B23+++,INTENSITY_PRED_Y24+,INTENSITY_PRED_Y24++,INTENSITY_PRED_Y24+++,INTENSITY_PRED_B24+,INTENSITY_PRED_B24++,INTENSITY_PRED_B24+++,INTENSITY_PRED_Y25+,INTENSITY_PRED_Y25++,INTENSITY_PRED_Y25+++,INTENSITY_PRED_B25+,INTENSITY_PRED_B25++,INTENSITY_PRED_B25+++,INTENSITY_PRED_Y26+,INTENSITY_PRED_Y26++,INTENSITY_PRED_Y26+++,INTENSITY_PRED_B26+,INTENSITY_PRED_B26++,INTENSITY_PRED_B26+++,INTENSITY_PRED_Y27+,INTENSITY_PRED_Y27++,INTENSITY_PRED_Y27+++,INTENSITY_PRED_B27+,INTENSITY_PRED_B27++,INTENSITY_PRED_B27+++,INTENSITY_PRED_Y28+,INTENSITY_PRED_Y28++,INTENSITY_PRED_Y28+++,INTENSITY_PRED_B28+,INTENSITY_PRED_B28++,INTENSITY_PRED_B28+++,INTENSITY_PRED_Y29+,INTENSITY_PRED_Y29++,INTENSITY_PRED_Y29+++,INTENSITY_PRED_B29+,INTENSITY_PRED_B29++,INTENSITY_PRED_B29+++,PREDICTED_IRT
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33 changes: 33 additions & 0 deletions tests/unit_tests/test_predictions.py
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import unittest
from pathlib import Path

import pandas as pd

from oktoberfest.data import Spectra
from oktoberfest.pr import grpc_predict


class TestTMTProsit(unittest.TestCase):
"""Test class for TMT model predictions."""

def test_prosit_tmt(self):
"""Test retrieval of predictions from prosit tmt models via koina."""
library = Spectra.from_csv(Path(__file__).parent / "data" / "predictions" / "library_input.csv")
print(library.spectra_data["COLLISION_ENERGY"])
grpc_predict(
library=library,
url="10.157.98.62:8500",
intensity_model="Prosit_2020_intensity_TMT",
irt_model="Prosit_2020_irt_TMT",
ssl=False,
alignment=False,
job_type="",
)

expected_df = pd.read_csv(Path(__file__).parent / "data" / "predictions" / "library_output.csv")
sparse_cols = [col for col in library.spectra_data.columns if col.startswith("INTENSITY_PRED")]
for sparse_col in sparse_cols:
expected_df[sparse_col] = expected_df[sparse_col].astype(library.spectra_data[sparse_col].dtype)
expected_df["PREDICTED_IRT"] = expected_df["PREDICTED_IRT"].astype(library.spectra_data["PREDICTED_IRT"].dtype)

pd.testing.assert_frame_equal(library.spectra_data, expected_df)

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