Merge pull request #59 from Mesnage-Org/test-ftrs

Add test for ftrs files

make_baseline.py

@@ -1,11 +1,18 @@
 import pgfinder.matching as matching
 
+# Set mass database and modifications
 csv_filepath = "data/masses/e_coli_monomer_masses.csv"
-mq_file_name = "data/maxquant_test_data.txt"
-
-raw_data = matching.maxquant_file_reader(mq_file_name)
 theo_masses = matching.theo_masses_reader(csv_filepath)
 mod_test = ['Sodium','Potassium','Anhydro','DeAc','Deacetyl_Anhydro','Nude','Decay','Amidation','Amidase','Double_Anh','multimers_Glyco']
-results = matching.data_analysis(raw_data, theo_masses, 0.5, mod_test, 10)
 
-results.to_csv("data/baseline_output.csv")
+# Generate maxquant baseline
+mq_file_name = "data/maxquant_test_data.txt"
+raw_data_mq = matching.maxquant_file_reader(mq_file_name)
+results = matching.data_analysis(raw_data_mq, theo_masses, 0.5, mod_test, 10)
+results.to_csv("data/baseline_output_mq.csv")
+
+# Generate ftrs baseline
+ftrs_file_name = "data/ftrs_test_data.ftrs"
+raw_data_ftrs = matching.ftrs_reader(ftrs_file_name)
+results = matching.data_analysis(raw_data_ftrs, theo_masses, 0.5, mod_test, 10)
+results.to_csv("data/baseline_output_ftrs.csv")

readme.md

@@ -49,12 +49,12 @@ To run tests:
 pytest
 ```
 
-The tests check output against an [expected baseline](data/baseline_output.csv). To recreate this (e.g. in response to improvements to the scientific "correctness" of the code ouput), use:
+The tests check output against an expected baseline for [Maxquant](data/baseline_output.csv) or [FTRS](data/baseline_output_ftrs.csv). To recreate this (e.g. in response to improvements to the scientific "correctness" of the code ouput), use:
 
 ```
 python make_baseline.py
 ```
 
-and replace the exisiting file.
+and replace the existing file.
 
 **This software is licensed as specified by the [GPL License](COPYING) and [LGPL License](COPYING.LESSER).**

tests/test_regression.py

@@ -1,23 +1,59 @@
 import pandas as pd
+import pytest
 import pgfinder.matching as matching
 import pgfinder.validation as validation
 
-def test_matching_baseline():
-    '''Test that output of the major function in the module is unchanged.'''
-    masses_file_name = "data/masses/e_coli_monomer_masses.csv"
-    mq_file_name = "data/maxquant_test_data.txt"
+@pytest.fixture
+def masses_file_name():
+    return "data/masses/e_coli_monomer_masses.csv"
+
+@pytest.fixture
+def mod_test():
+    """Modifications used in regression testing."""
+    return ['Sodium','Potassium','Anhydro','DeAc','Deacetyl_Anhydro','Nude','Decay','Amidation','Amidase','Double_Anh','multimers_Glyco']
+
+@pytest.fixture
+def mq_file_name():
+    return "data/maxquant_test_data.txt"
+
+@pytest.fixture
+def mq_baseline_df():
+    return pd.read_csv("data/baseline_output_mq.csv", index_col=0)
+
+@pytest.fixture
+def ftrs_file_name():
+    return "data/ftrs_test_data.ftrs"
 
+@pytest.fixture
+def ftrs_baseline_df():
+    return pd.read_csv("data/baseline_output_ftrs.csv", index_col=0)
+
+def test_matching_mq_baseline(masses_file_name, mq_file_name, mod_test, mq_baseline_df):
+    '''Test that output of the major function in the module is unchanged.'''
+
     raw_data = matching.maxquant_file_reader(mq_file_name)
     validation.validate_raw_data_df(raw_data)
 
     theo_masses = matching.theo_masses_reader(masses_file_name)
     validation.validate_theo_masses_df(theo_masses)
-
-    mod_test = ['Sodium','Potassium','Anhydro','DeAc','Deacetyl_Anhydro','Nude','Decay','Amidation','Amidase','Double_Anh','multimers_Glyco']
+
     validation.validate_enabled_mod_list(mod_test)
 
     output_df = matching.data_analysis(raw_data, theo_masses, 0.5, mod_test, 10)
 
-    baseline_df = pd.read_csv("data/baseline_output.csv", index_col=0)
+    pd.testing.assert_frame_equal(output_df, mq_baseline_df)
 
-    pd.testing.assert_frame_equal(output_df, baseline_df)
+def test_matching_ftrs_baseline(masses_file_name, ftrs_file_name, mod_test, ftrs_baseline_df):
+    """Test that output of the major function in the module is unchanged."""
+
+    raw_data = matching.ftrs_reader(ftrs_file_name)
+    validation.validate_raw_data_df(raw_data)
+
+    theo_masses = matching.theo_masses_reader(masses_file_name)
+    validation.validate_theo_masses_df(theo_masses)
+
+    validation.validate_enabled_mod_list(mod_test)
+
+    output_df = matching.data_analysis(raw_data, theo_masses, 0.5, mod_test, 10)
+
+    pd.testing.assert_frame_equal(output_df, ftrs_baseline_df)