Merge pull request #21 from bigbio/dev

Dev
bigbio · Aug 13, 2024 · 1e24138 · 1e24138
2 parents b2ffe2c + f2751fb
commit 1e24138
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diff --git a/quantmsutils/features/snr.py b/quantmsutils/features/snr.py
@@ -55,6 +55,7 @@ def spectrum2feature(ctx, ms_path: str, idxml: str, output: str) -> None:
     peptide_ids = []
     oms.IdXMLFile().load(idxml, protein_ids, peptide_ids)
 
+    result_peptides = []
     for peptide in peptide_ids:
         spectrum_reference = peptide.getMetaValue("spectrum_reference")
         scan_number = int(
@@ -88,6 +89,13 @@ def spectrum2feature(ctx, ms_path: str, idxml: str, output: str) -> None:
                 hit.setMetaValue("quantms:SpectralEntropy", str(spectral_entropy))
                 hit.setMetaValue("quantms:FracTICinTop10Peaks", str(fraction_tic_top_10))
                 hit.setMetaValue("quantms:WeightedStdMz", str(weighted_std_mz))
+
+                # update hit in peptidehits list
+                peptide.setHits([hit])
+            ## update peptide in peptide_ids list
+            result_peptides.append(peptide)
+
+
         except IndexError:
             message = "scan_number" + str(scan_number) + "not found in file: " + ms_path
             print(message)

diff --git a/tests/test_commands.py b/tests/test_commands.py
@@ -113,6 +113,22 @@ def test_spectrum2fature_file():
 
     assert result.exit_code == 0
 
+def test_diann2mztab_example():
+    runner = CliRunner()
+    result = runner.invoke(
+        cli, [
+            "diann2mztab",
+            "--folder", "tests/test_data/diann2mztab/",
+            "--exp_design", "tests/test_data/diann2mztab/PXD026600.sdrf_openms_design.tsv",
+            "--diann_version", "tests/test_data/diann2mztab/versions.yml",
+            "--dia_params", "20.0;ppm;10.0;ppm;Trypsin;Carbamidomethyl (C);Oxidation (M)",
+            "--charge", "3",
+            "--missed_cleavages", "1",
+            "--qvalue_threshold", "0.01"
+            ],
+    )
+    assert result.exit_code == 0
+
 
 # test for the convert_psm command in cli
 def test_convert_psm_help():

diff --git a/tests/test_data/diann2mztab/RD139_Narrow_UPS1_0_1fmol_inj1_ms_info.parquet b/tests/test_data/diann2mztab/RD139_Narrow_UPS1_0_1fmol_inj1_ms_info.parquet
diff --git a/tests/test_data/diann2mztab/RD139_Narrow_UPS1_0_1fmol_inj2_ms_info.parquet b/tests/test_data/diann2mztab/RD139_Narrow_UPS1_0_1fmol_inj2_ms_info.parquet
diff --git a/tests/test_data/diann2mztab/RD139_Narrow_UPS1_0_25fmol_inj1_ms_info.parquet b/tests/test_data/diann2mztab/RD139_Narrow_UPS1_0_25fmol_inj1_ms_info.parquet
diff --git a/tests/test_data/diann2mztab/RD139_Narrow_UPS1_0_25fmol_inj2_ms_info.parquet b/tests/test_data/diann2mztab/RD139_Narrow_UPS1_0_25fmol_inj2_ms_info.parquet
diff --git a/tests/test_data/diann2mztab/REF_EColi_K12_UPS1_combined.fasta b/tests/test_data/diann2mztab/REF_EColi_K12_UPS1_combined.fasta
diff --git a/tests/test_data/diann2mztab/versions.yml b/tests/test_data/diann2mztab/versions.yml
@@ -0,0 +1,2 @@
+"NFCORE_QUANTMS:QUANTMS:DIA:DIANNSUMMARY":
+    DIA-NN: 1.8.1