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Add a small system test for sage2lib #9

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Add a small system test for sage2lib #9

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6 changes: 5 additions & 1 deletion petasus/scripts/sage2lib.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,11 @@ def read_peptides(peptides, qvalue):
polars.DataFrame
The parsed and filtered peptides.
"""
peptide_df = pl.read_csv(peptides, separator="\t")
try:
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Request: Could we add an error/warning message saying the fallback is occurring?

peptide_df = pl.read_parquet(peptides)
except pl.exceptions.ComputeError:
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R: Can we add a check of the error to make sure the compute error comes from the parsing and not anywhere else?

peptide_df = pl.read_csv(peptides, separator="\t")

peptide_df.columns = [c.lower() for c in peptide_df.columns]
if "mokapot q-value" in peptide_df.columns:
qval_col = "mokapot q-value"
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2 changes: 2 additions & 0 deletions tests/data/results.sage.csv
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@@ -0,0 +1,2 @@
filename scannr peptide stripped_peptide proteins num_proteins rank is_decoy expmass calcmass charge peptide_len missed_cleavages isotope_error precursor_ppm fragment_ppm hyperscore delta_next delta_best rt aligned_rt predicted_rt delta_rt_model matched_peaks longest_b longest_y longest_y_pct matched_intensity_pct scored_candidates poisson sage_discriminant_score posterior_error spectrum_q peptide_q protein_q
LQSRPAAPPAPGPGQLTLR.mzML controllerType=0 controllerNumber=1 scan=30069 LQSRPAAPPAPGPGQLTLR LQSRPAAPPAPGPGQLTLR sp|Q99536|VAT1_HUMAN 1 1 false 1926.0815 1926.08 3 19 0 0.0 0.8239083 0.503857 72.265915 72.265915 0.0 108.2854 0.993444 0.0 0.993444 22 9 12 0.6315789 64.770966 1 -1.9562812 1.2944585 1.0 1.0 1.0 1.0
29 changes: 29 additions & 0 deletions tests/system_tests/test_sage2lib.py
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"""Test building a dlib"""
import sqlite3
import subprocess

import pytest


@pytest.mark.parametrize("ftype", ["parquet", "csv"])
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Note: Since the whole XZ situation ive become a bit more paranoid ... we whould make a PR so the .parquet is generated from a .csv ... just to have no binaries in source control.

def test_simpole_speclib_generation(data_path, tmp_path, ftype):
"""Test spectral library generation"""
psms = data_path / f"results.sage.{ftype}"
mzml = data_path / "LQSRPAAPPAPGPGQLTLR.mzML"
outfile = tmp_path / "results.sage.dlib"
cmd = [
"petasus",
"sage2lib",
"--qvalue",
"1",
f"{psms}",
f"{mzml}",
]

subprocess.run(cmd, check=True)

con = sqlite3.Connection(str(outfile))
cur = con.cursor()
res = cur.execute("select PeptideModSeq from entries;")
res = [x[0] for x in res.fetchall()]
assert len(res)
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