tests: update test file names

tests/test_importing.py

@@ -0,0 +1,275 @@
+#!python -m unittest tests.test_utils
+"""This module provides unit tests for alphamap.cli."""
+
+# builtin
+import unittest
+
+import os
+import pandas as pd
+
+# local
+from alphamap.importing import read_file, \
+    extract_rawfile_unique_values, \
+    import_spectronaut_data, \
+    import_maxquant_data, \
+    convert_ap_mq_mod, \
+    import_alphapept_data, \
+    convert_diann_mq_mod, \
+    import_diann_data, \
+    convert_fragpipe_mq_mod, \
+    import_fragpipe_data, \
+    import_data
+
+THIS_FOLDER = os.path.dirname(__file__)
+TEST_FOLDER = os.path.join(
+    f"{os.path.dirname(THIS_FOLDER)}",
+    "nbs",
+    "testdata",
+)
+
+class TestImporting(unittest.TestCase):
+
+    def test_read_file(self,):
+        file_with_missing_col = os.path.join(TEST_FOLDER,'test_not_all_columns_spectronaut.csv')
+        spectronaut_columns = ["PEP.AllOccurringProteinAccessions","EG.ModifiedSequence","R.FileName"]
+
+        try:
+            out = read_file(file_with_missing_col, spectronaut_columns)
+        except ValueError as e:
+            out = e
+        assert str(out) == "The list of specified column names cannot be extracted from the file." 
+
+    def test_extract_rawfile_unique_values(self, ):
+        data_Spectronaut_csv = os.path.join(TEST_FOLDER, 'test_spectronaut_input.csv')
+        data_Spectronaut_tsv = os.path.join(TEST_FOLDER, 'test_spectronaut_input.tsv')
+        assert ['raw_01', 'raw_02'] == extract_rawfile_unique_values(data_Spectronaut_csv)
+        assert extract_rawfile_unique_values(data_Spectronaut_csv) == extract_rawfile_unique_values(data_Spectronaut_tsv)
+
+        data_MQ = os.path.join(TEST_FOLDER, 'test_maxquant_input.txt')
+        assert len(extract_rawfile_unique_values(data_MQ)) == 381
+
+        data_wrong = os.path.join(TEST_FOLDER, 'test_maxquant_imported.csv')
+        try:
+            out = extract_rawfile_unique_values(data_wrong)
+        except ValueError as e:
+            out = e
+        assert str(out) == "A column with the raw file names is not in the file." 
+
+        data_fragpipe_combined = os.path.join(TEST_FOLDER, 'combined_peptide.txt')
+        assert ['Y731F1', 'Y731F2', 'wt1', 'wt2'] == extract_rawfile_unique_values(data_fragpipe_combined)
+
+    def test_import_spectronaut_data(self, ):
+        # test entire input test data
+        data = import_spectronaut_data(os.path.join(TEST_FOLDER, 'test_spectronaut_input.csv'))
+        #print(data.shape[0])
+        assert data.shape[0] == 40
+        data_t = import_spectronaut_data(os.path.join(TEST_FOLDER, 'test_spectronaut_input.tsv'))
+        #print(data_t.shape[0])
+        pd.testing.assert_frame_equal(data, data_t)
+        test = pd.read_csv(os.path.join(TEST_FOLDER, 'test_spectronaut_imported.csv'), sep=',') 
+        #print(test.shape[0])
+        pd.testing.assert_frame_equal(data, test)
+
+        # test single sample
+        data = import_spectronaut_data(os.path.join(TEST_FOLDER, 'test_spectronaut_input.csv'), 
+                                    sample="raw_01")
+        #print(data.shape[0])
+        assert data.shape[0] == 40
+        data = import_spectronaut_data(os.path.join(TEST_FOLDER, 'test_spectronaut_input.csv'), 
+                                    sample="raw_02")
+        #print(data.shape[0])
+        assert data.shape[0] == 20
+
+        # test multiple samples
+        data = import_spectronaut_data(os.path.join(TEST_FOLDER, 'test_spectronaut_input.csv'), 
+                                    sample=["raw_01","raw_02"])
+        #print(data.shape[0])
+        assert data.shape[0] == 40
+
+    def test_import_maxquant_data(self, ):
+        data = import_maxquant_data(os.path.join(TEST_FOLDER, 'test_maxquant_input.txt'))
+        test = pd.read_csv(os.path.join(TEST_FOLDER, 'test_maxquant_imported.csv'), sep=',') 
+        pd.testing.assert_frame_equal(data, test)
+
+        data_s = import_maxquant_data(os.path.join(TEST_FOLDER, 'test_maxquant_input.txt'), 
+                                    sample = "raw_1")
+        assert data_s.shape[0] == 85
+
+        data_s = import_maxquant_data(os.path.join(TEST_FOLDER, 'test_maxquant_input.txt'), 
+                                    sample = "raw_2")
+        assert data_s.shape[0] == 77
+
+        data_s = import_maxquant_data(os.path.join(TEST_FOLDER, 'test_maxquant_input.txt'), 
+                                    sample = ["raw_1", "raw_2"])
+        assert data_s.shape[0] == 136
+
+    def test_convert_ap_mq_mod(self, ):
+        # test oxidation
+        seq1 = 'HAEoxMVHTGLK' 
+        assert "HAEM[Oxidation (M)]VHTGLK" == convert_ap_mq_mod(seq1)
+        seq2 = 'HAEoxPVHTGLK' 
+        assert "HAEP[Oxidation (MP)]VHTGLK" == convert_ap_mq_mod(seq2)
+        # test acetylation
+        seq4 = 'aMDEPSPLAQPLELNQHSR' 
+        assert "[Acetyl (N-term)]MDEPSPLAQPLELNQHSR" == convert_ap_mq_mod(seq4)
+        seq5 = 'MDEPSaKPLA' 
+        assert "MDEPSK[Acetyl (K)]PLA" == convert_ap_mq_mod(seq5)
+        # test amidation
+        seq6 = 'MDEPSKPLamA' 
+        assert "MDEPSKPLA[Amidated (C-term)]" == convert_ap_mq_mod(seq6)
+        # test deamidation
+        seq7 = 'MDEPSdeamNKPLA' 
+        assert "MDEPSN[Deamidation (NQ)]KPLA" == convert_ap_mq_mod(seq7)
+        seq8 = 'MDEPSdeamQKPLA' 
+        assert "MDEPSQ[Deamidation (NQ)]KPLA" == convert_ap_mq_mod(seq8)
+        # test phosporylation
+        seq9 = 'MDEPSpSKPLA' 
+        assert "MDEPSS[Phospho (STY)]KPLA" == convert_ap_mq_mod(seq9)
+        # test pyro-Glu
+        seq10 = 'MDpgEPSNKPLA' 
+        assert "MDE[Glu->pyro-Glu]PSNKPLA" == convert_ap_mq_mod(seq10)
+        seq11 = 'MDpgQPSNKPLA' 
+        assert "MDQ[Gln->pyro-Glu]PSNKPLA" == convert_ap_mq_mod(seq11)
+        # test disylfide bonds
+        seq12 = 'cCVNTTLQIK'
+        assert "C[Cys-Cys]VNTTLQIK" == convert_ap_mq_mod(seq12)
+        seq1_several_dif_mods = 'AcCLDYPVTSVLPPASLoxMK'
+        assert "AC[Cys-Cys]LDYPVTSVLPPASLM[Oxidation (M)]K" == convert_ap_mq_mod(seq1_several_dif_mods)
+        seq2_several_same_mods = 'LFTToxMELoxMR'
+        assert "LFTTM[Oxidation (M)]ELM[Oxidation (M)]R" == convert_ap_mq_mod(seq2_several_same_mods)
+        seq3_several_same_mods = 'LFTToxMELoxMRoxM'
+        assert "LFTTM[Oxidation (M)]ELM[Oxidation (M)]RM[Oxidation (M)]" == convert_ap_mq_mod(seq3_several_same_mods)
+        seq4_several_same_mods = 'LFTTdeamNELdeamNR'
+        assert "LFTTN[Deamidation (NQ)]ELN[Deamidation (NQ)]R" == convert_ap_mq_mod(seq4_several_same_mods)
+        seq_no_mod = 'CVNTTLQIK'
+        assert "CVNTTLQIK" == convert_ap_mq_mod(seq_no_mod)
+
+    def test_import_alphapept_data(self, ):
+        data = import_alphapept_data(os.path.join(TEST_FOLDER, 'test_alphapept_input.csv'))
+        assert data.shape == (4228, 3)
+
+        data_s1 = import_alphapept_data(os.path.join(TEST_FOLDER, 'test_alphapept_input.csv'), 
+                                    sample = "exp_1")
+        assert data_s1.shape[0] == 2127
+
+        data_s2 = import_alphapept_data(os.path.join(TEST_FOLDER, 'test_alphapept_input.csv'), 
+                                    sample = "exp_2")
+        assert data_s2.shape[0] == 2101
+
+        data_s_both = import_alphapept_data(os.path.join(TEST_FOLDER, 'test_alphapept_input.csv'), 
+                                    sample = ["exp_1", "exp_2"])
+        assert data_s_both.shape[0] == 4228
+
+    def test_convert_diann_mq_mod(self, ):
+        seq1 = 'VSHGSSPSLLEALSSDFLAC(UniMod:4)K'
+        assert 'VSHGSSPSLLEALSSDFLAC[Carbamidomethyl (C)]K' == convert_diann_mq_mod(seq1)
+        seq2 = 'VSVINTVDTSHEDMIHDAQM(UniMod:35)DYYGTR'
+        assert 'VSVINTVDTSHEDMIHDAQM[Oxidation (M)]DYYGTR' == convert_diann_mq_mod(seq2)
+        seq3 = 'HAEMPVHTGLK(UniMod:2)' 
+        assert 'HAEMPVHTGLK[Amidated (C-term)]' == convert_diann_mq_mod(seq3)
+        seq4 = 'HAEMPVHTGLKS(UniMod:23)A'
+        assert 'HAEMPVHTGLKS[Dehydrated (ST)]A' == convert_diann_mq_mod(seq4)
+        seq5 = 'HAEMPVHTGLKY(UniMod:23)A' 
+        assert 'HAEMPVHTGLKY[Dehydrated (Y)]A' == convert_diann_mq_mod(seq5)
+
+        seq1_several_dif_mods = '(UniMod:1)VSHGSSPSLLEALSSDFLAC(UniMod:4)K'
+        assert '[Acetyl (N-term)]VSHGSSPSLLEALSSDFLAC[Carbamidomethyl (C)]K' == convert_diann_mq_mod(seq1_several_dif_mods)
+        seq2_several_same_mods = 'CAALVATAEENLC(UniMod:4)C(UniMod:4)EELSSK'
+        assert 'CAALVATAEENLC[Carbamidomethyl (C)]C[Carbamidomethyl (C)]EELSSK' == convert_diann_mq_mod(seq2_several_same_mods)
+        seq_no_mod = 'CVNTTLQIK'
+        assert "CVNTTLQIK" == convert_diann_mq_mod(seq_no_mod)
+
+    def test_import_diann_data(self, ):
+        data = import_diann_data(os.path.join(TEST_FOLDER, 'test_diann_input.tsv'))
+        assert data.shape == (44, 3)
+
+        data_s1 = import_diann_data(os.path.join(TEST_FOLDER, 'test_diann_input.tsv'), 
+                                    sample = "20201218_tims03_Evo03_PS_SA_HeLa_200ng_high_speed_21min_8cm_S2-B2_1_22648")
+        assert data_s1.shape[0] == 39
+
+        data_s_both = import_diann_data(os.path.join(TEST_FOLDER, 'test_diann_input.tsv'), 
+                                        sample = ["20201218_tims03_Evo03_PS_SA_HeLa_200ng_high_speed_21min_8cm_S2-B2_1_22648", 
+                                                  "20201218_tims03_Evo03_PS_SA_HeLa_200ng_high_speed_21min_8cm_S2-A2_1_22636"])
+        assert data_s_both.shape[0] == 42
+
+    def test_convert_fragpipe_mq_mod(self, ):
+        seq1 = 'AAEREPPPLGDGKPTDFEDLEDGEDLFTSTVSTLE'
+        modif1 = 'N-term(42.0106)'
+        assert '[Acetyl (N-term)]AAEREPPPLGDGKPTDFEDLEDGEDLFTSTVSTLE' == convert_fragpipe_mq_mod(seq1, modif1)
+        seq2 = 'AAEVISDARENIQRFFGHGAEDSLADQAANEWGRSGKDPNHFRPAGLPEKY'
+        modif2 = 'C-term(-0.9840)'
+        assert 'AAEVISDARENIQRFFGHGAEDSLADQAANEWGRSGKDPNHFRPAGLPEKY[Amidated (C-term)]' == convert_fragpipe_mq_mod(seq2, modif2)
+        seq3 = 'QESQSEEIDCNDKDLFKA'
+        modif3 = '1Q(-17.0265)'
+        assert 'Q[Gln->pyro-Glu]ESQSEEIDCNDKDLFKA' == convert_fragpipe_mq_mod(seq3, modif3)
+        seq4 = 'EKPLLEKSHCIAEVENDEMPA'
+        modif4 = '1E(-18.0106)'
+        assert 'E[Glu->pyro-Glu]KPLLEKSHCIAEVENDEMPA' == convert_fragpipe_mq_mod(seq4, modif4)
+        seq5 = 'SKPLLEKSHCIAEVENDEMPA'
+        modif5 = '1S(-18.0106)'
+        assert 'S[Dehydrated (ST)]KPLLEKSHCIAEVENDEMPA' == convert_fragpipe_mq_mod(seq5, modif5)
+        seq6 = 'YKPLLEKSHCIAEVENDEMPA'
+        modif6 = '1Y(-18.0106)'
+        assert 'Y[Dehydrated (Y)]KPLLEKSHCIAEVENDEMPA' == convert_fragpipe_mq_mod(seq6, modif6)
+        seq1_several_dif_mods = 'AAAAECDVVMAATEPELLDDQEAK'
+        seq1_several_dif_mods_modifs = '10M(15.9949),6C(57.0215),N-term(42.0106)'
+        assert '[Acetyl (N-term)]AAAAEC[Carbamidomethyl (C)]DVVM[Oxidation (M)]AATEPELLDDQEAK' == convert_fragpipe_mq_mod(
+            seq1_several_dif_mods, seq1_several_dif_mods_modifs)
+        seq2_several_dif_mods = 'PGFSIADKKR'
+        seq2_several_dif_mods_modifs = '8K(114.0429),9K(114.0429)'
+        assert 'PGFSIADK[GlyGly (K)]K[GlyGly (K)]R' == convert_fragpipe_mq_mod(
+            seq2_several_dif_mods, seq2_several_dif_mods_modifs)
+        seq_no_mod = 'CVNTTLQIK'
+        seq_no_mod_modifs = ''
+        assert "CVNTTLQIK" == convert_fragpipe_mq_mod(seq_no_mod, seq_no_mod_modifs)
+
+    def test_import_fragpipe_data(self, ):
+        data = import_fragpipe_data(os.path.join(TEST_FOLDER, 'test_fragpipe_input.tsv'))
+        assert data.shape == (50, 3)
+
+        sample = 'Y731F1'
+        file = os.path.join(TEST_FOLDER, 'combined_peptide.txt')
+        assert import_fragpipe_data(file, sample).shape == (23, 3)
+
+        two_samples = ['Y731F1', 'Y731F2']
+        assert import_fragpipe_data(file, two_samples).shape == (26, 3)
+
+    def test_import_data(self, ):
+        data_MQ = import_data(os.path.join(TEST_FOLDER, 'test_maxquant_input.txt'), verbose=False)
+        test = pd.read_csv(os.path.join(TEST_FOLDER, 'test_maxquant_imported.csv'), sep=',') 
+        pd.testing.assert_frame_equal(data_MQ, test)
+
+        data_S_csv = import_data(os.path.join(TEST_FOLDER, 'test_spectronaut_input.csv'), verbose=False)
+        data_S_tsv = import_data(os.path.join(TEST_FOLDER, 'test_spectronaut_input.tsv'), verbose=False)
+        pd.testing.assert_frame_equal(data_S_csv, data_S_tsv)
+        test = pd.read_csv(os.path.join(TEST_FOLDER, 'test_spectronaut_imported.csv'), sep=',') 
+        pd.testing.assert_frame_equal(data_S_csv, test)
+
+        data_S_sub = import_data(os.path.join(TEST_FOLDER, 'test_spectronaut_input.csv'), 
+                                sample = "raw_01", 
+                                verbose=False)
+        assert data_S_sub.shape[0] == 40
+
+        data_alphapept = import_data(os.path.join(TEST_FOLDER, 'test_alphapept_input.csv'), 
+                                sample = "exp_1", 
+                                verbose=False)
+        assert data_alphapept.shape[0] == 2127
+
+        data_diann = import_data(os.path.join(TEST_FOLDER, 'test_diann_input.tsv'), 
+                                    sample = "20201218_tims03_Evo03_PS_SA_HeLa_200ng_high_speed_21min_8cm_S2-B2_1_22648", 
+                                    verbose=False)
+        assert data_diann.shape[0] == 39
+
+        data_fragpipe = import_data(os.path.join(TEST_FOLDER, 'test_fragpipe_input.tsv'),  
+                                    verbose=False)
+        assert data_fragpipe.shape[0] == 50
+
+        try:
+            out = import_data(os.path.join(TEST_FOLDER, 'test_uniprot_df.csv'))
+        except TypeError as e:
+            out = e
+        assert str(out) == "Input data format for "+os.path.join(TEST_FOLDER, 'test_uniprot_df.csv')+" not known."
+
+
+if __name__ == "__main__":
+    unittest.main()