add tests for xi

.github/workflows/python-app-xi.yml

@@ -0,0 +1,49 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# Reference workflow provided by (c) GitHub
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: msannika_spectral_library_xi
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Copy scripts and data to "/tests"
+      run: |
+        rm -f config.py
+        cp data/config_xi.py .
+        mv config_xi.py config.py
+        cp create_spectral_library.py tests
+        cp config.py tests
+        cp data/XLpeplib_Beveridge_QEx-HFX_DSS_R1.mgf .
+        cp data/example_CSM_xiFDR2.2.1.csv .
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest tests/tests-xi.py

tests/tests-xi.py

@@ -0,0 +1,239 @@
+#!/usr/bin/env python3
+
+# MS ANNIKA SPECTRAL LIBRARY EXPORTER - TESTS XI
+# 2023 (c) Micha Johannes Birklbauer
+# https://github.com/michabirklbauer/
+# micha.birklbauer@gmail.com
+
+# check converted csm file
+def test1_converter():
+
+    import pandas as pd
+    from create_spectral_library import main
+    from config import CSMS_FILE as CSMS_FILE
+
+    sl = main()
+    csms = pd.read_csv(CSMS_FILE + ".converted.csv")
+
+    assert csms.shape[0] == 2
+    assert csms.shape[1] == 17
+
+    assert str(csms.loc[0, "Sequence A"]) == "KIECFDSVEISGVEDR"
+    assert str(csms.loc[0, "Modifications A"]) == "C4(Carbamidomethyl);K1(BS3)"
+    assert str(csms.loc[0, "Sequence B"]) == "KIECFDSVEISGVEDR"
+    assert str(csms.loc[0, "Modifications B"]) == "C4(Carbamidomethyl);K1(BS3)"
+    assert str(csms.loc[0, "First Scan"]) == "19140"
+    assert str(csms.loc[0, "Spectrum File"]) == "XLpeplib_Beveridge_QEx-HFX_DSS_R1.mgf"
+    assert str(csms.loc[0, "A in protein"]) == "574"
+    assert str(csms.loc[0, "B in protein"]) == "574"
+    assert str(csms.loc[0, "Crosslinker Position A"]) == "1"
+    assert str(csms.loc[0, "Crosslinker Position B"]) == "1"
+    assert str(csms.loc[0, "Accession A"]) == "Cas9"
+    assert str(csms.loc[0, "Accession B"]) == "Cas9"
+    assert str(csms.loc[0, "Charge"]) == "4"
+    assert str(int(csms.loc[0, "m/z [Da]"])) == "976"
+    assert str(csms.loc[0, "Crosslink Strategy"]) == "xi"
+    assert str(int(csms.loc[0, "RT [min]"])) == "85"
+    assert str(int(csms.loc[0, "Compensation Voltage"])) == "0"
+
+    assert str(csms.loc[1, "Sequence A"]) == "MIAKSEQEIGK"
+    assert str(csms.loc[1, "Modifications A"]) == "K4(BS3)"
+    assert str(csms.loc[1, "Sequence B"]) == "DFQFYKVR"
+    assert str(csms.loc[1, "Modifications B"]) == "K6(BS3)"
+    assert str(csms.loc[1, "First Scan"]) == "15867"
+    assert str(csms.loc[1, "Spectrum File"]) == "XLpeplib_Beveridge_QEx-HFX_DSS_R1.mgf"
+    assert str(csms.loc[1, "A in protein"]) == "1024"
+    assert str(csms.loc[1, "B in protein"]) == "972"
+    assert str(csms.loc[1, "Crosslinker Position A"]) == "4"
+    assert str(csms.loc[1, "Crosslinker Position B"]) == "6"
+    assert str(csms.loc[1, "Accession A"]) == "Cas9"
+    assert str(csms.loc[1, "Accession B"]) == "Cas9"
+    assert str(csms.loc[1, "Charge"]) == "3"
+    assert str(int(csms.loc[1, "m/z [Da]"])) == "825"
+    assert str(csms.loc[1, "Crosslink Strategy"]) == "xi"
+    assert str(int(csms.loc[1, "RT [min]"])) == "72"
+    assert str(int(csms.loc[1, "Compensation Voltage"])) == "0"
+
+# check output shape target
+def test1_spectral_library_exporter():
+
+    from create_spectral_library import main
+
+    sl = main()
+    sl = sl["TargetLib"]
+
+    assert sl.shape[0] == 55 and sl.shape[1] == 30
+
+# check values target
+def test2_spectral_library_exporter():
+
+    from create_spectral_library import main
+
+    sl = main()
+    sl = sl["TargetLib"]
+
+    assert str(sl.loc[0, "ModifiedPeptide"]) == "KIEC[Carbamidomethyl]FDSVEISGVEDR_KIEC[Carbamidomethyl]FDSVEISGVEDR"
+    assert str(sl.loc[0, "FragmentCharge"]) == "1"
+    assert str(sl.loc[0, "FragmentType"]) == "y"
+    assert str(sl.loc[0, "FragmentNumber"]) == "1"
+    assert str(sl.loc[0, "FragmentPepId"]) == "0"
+    assert str(sl.loc[0, "CLContainingFragment"]) == "False"
+    assert str(sl.loc[0, "IsDecoy"]) == "False"
+    assert str(sl.loc[0, "DecoyType"]) == "TT"
+
+    assert str(sl.loc[54, "ModifiedPeptide"]) == "MIAKSEQEIGK_DFQFYKVR"
+    assert str(sl.loc[54, "FragmentCharge"]) == "1"
+    assert str(sl.loc[54, "FragmentType"]) == "b"
+    assert str(sl.loc[54, "FragmentNumber"]) == "5"
+    assert str(sl.loc[54, "FragmentPepId"]) == "1"
+    assert str(sl.loc[54, "CLContainingFragment"]) == "False"
+    assert str(sl.loc[54, "IsDecoy"]) == "False"
+    assert str(sl.loc[54, "DecoyType"]) == "TT"
+
+# check output shape decoy dd
+def test3_spectral_library_exporter():
+
+    from create_spectral_library import main
+
+    sl = main()
+    sl = sl["DecoyLib"]
+
+    assert sl.shape[0] == 54 and sl.shape[1] == 30
+
+# check values decoy dd
+def test4_spectral_library_exporter():
+
+    from create_spectral_library import main
+
+    sl = main()
+    sl = sl["DecoyLib"]
+
+    assert str(sl.loc[0, "ModifiedPeptide"]) == "DEVGSIEVSDFC[Carbamidomethyl]EIKR_DEVGSIEVSDFC[Carbamidomethyl]EIKR"
+    assert str(sl.loc[0, "FragmentCharge"]) == "1"
+    assert str(sl.loc[0, "FragmentType"]) == "y"
+    assert str(sl.loc[0, "FragmentNumber"]) == "1"
+    assert str(sl.loc[0, "FragmentPepId"]) == "0"
+    assert str(sl.loc[0, "CLContainingFragment"]) == "False"
+    assert str(sl.loc[0, "IsDecoy"]) == "True"
+    assert str(sl.loc[0, "DecoyType"]) == "DD"
+
+    assert str(sl.loc[53, "ModifiedPeptide"]) == "GIEQESKAIMK_VKYFQFDR"
+    assert str(sl.loc[53, "FragmentCharge"]) == "1"
+    assert str(sl.loc[53, "FragmentType"]) == "b"
+    assert str(sl.loc[53, "FragmentNumber"]) == "5"
+    assert str(sl.loc[53, "FragmentPepId"]) == "1"
+    assert str(sl.loc[53, "CLContainingFragment"]) == "True"
+    assert str(sl.loc[53, "IsDecoy"]) == "True"
+    assert str(sl.loc[53, "DecoyType"]) == "DD"
+
+# check output shape decoy dt
+def test5_spectral_library_exporter():
+
+    from create_spectral_library import main
+
+    sl = main()
+    sl = sl["DecoyLib_DT"]
+
+    assert sl.shape[0] == 54 and sl.shape[1] == 30
+
+# check values decoy dt
+def test6_spectral_library_exporter():
+
+    from create_spectral_library import main
+
+    sl = main()
+    sl = sl["DecoyLib_DT"]
+
+    assert str(sl.loc[0, "ModifiedPeptide"]) == "DEVGSIEVSDFC[Carbamidomethyl]EIKR_KIEC[Carbamidomethyl]FDSVEISGVEDR"
+    assert str(sl.loc[0, "FragmentCharge"]) == "1"
+    assert str(sl.loc[0, "FragmentType"]) == "y"
+    assert str(sl.loc[0, "FragmentNumber"]) == "1"
+    assert str(sl.loc[0, "FragmentPepId"]) == "0"
+    assert str(sl.loc[0, "CLContainingFragment"]) == "False"
+    assert str(sl.loc[0, "IsDecoy"]) == "True"
+    assert str(sl.loc[0, "DecoyType"]) == "DT"
+
+    assert str(sl.loc[53, "ModifiedPeptide"]) == "GIEQESKAIMK_DFQFYKVR"
+    assert str(sl.loc[53, "FragmentCharge"]) == "1"
+    assert str(sl.loc[53, "FragmentType"]) == "b"
+    assert str(sl.loc[53, "FragmentNumber"]) == "5"
+    assert str(sl.loc[53, "FragmentPepId"]) == "1"
+    assert str(sl.loc[53, "CLContainingFragment"]) == "False"
+    assert str(sl.loc[53, "IsDecoy"]) == "True"
+    assert str(sl.loc[53, "DecoyType"]) == "DT"
+
+# check output shape decoy td
+def test7_spectral_library_exporter():
+
+    from create_spectral_library import main
+
+    sl = main()
+    sl = sl["DecoyLib_TD"]
+
+    assert sl.shape[0] == 55 and sl.shape[1] == 30
+
+# check values decoy td
+def test8_spectral_library_exporter():
+
+    from create_spectral_library import main
+
+    sl = main()
+    sl = sl["DecoyLib_TD"]
+
+    assert str(sl.loc[0, "ModifiedPeptide"]) == "KIEC[Carbamidomethyl]FDSVEISGVEDR_DEVGSIEVSDFC[Carbamidomethyl]EIKR"
+    assert str(sl.loc[0, "FragmentCharge"]) == "1"
+    assert str(sl.loc[0, "FragmentType"]) == "y"
+    assert str(sl.loc[0, "FragmentNumber"]) == "1"
+    assert str(sl.loc[0, "FragmentPepId"]) == "0"
+    assert str(sl.loc[0, "CLContainingFragment"]) == "False"
+    assert str(sl.loc[0, "IsDecoy"]) == "True"
+    assert str(sl.loc[0, "DecoyType"]) == "TD"
+
+    assert str(sl.loc[54, "ModifiedPeptide"]) == "MIAKSEQEIGK_VKYFQFDR"
+    assert str(sl.loc[54, "FragmentCharge"]) == "1"
+    assert str(sl.loc[54, "FragmentType"]) == "b"
+    assert str(sl.loc[54, "FragmentNumber"]) == "5"
+    assert str(sl.loc[54, "FragmentPepId"]) == "1"
+    assert str(sl.loc[54, "CLContainingFragment"]) == "True"
+    assert str(sl.loc[54, "IsDecoy"]) == "True"
+    assert str(sl.loc[54, "DecoyType"]) == "TD"
+
+# check output shape full
+def test9_spectral_library_exporter():
+
+    from create_spectral_library import main
+
+    sl = main()
+    sl = sl["FullLib"]
+
+    assert sl.shape[0] == 218 and sl.shape[1] == 30
+    assert sl["DecoyType"].value_counts()["TT"] == 55
+    assert sl["DecoyType"].value_counts()["TD"] == 55
+    assert sl["DecoyType"].value_counts()["DD"] == 54
+    assert sl["DecoyType"].value_counts()["DT"] == 54
+
+# check values full
+def test10_spectral_library_exporter():
+
+    from create_spectral_library import main
+
+    sl = main()
+    sl = sl["FullLib"]
+
+    assert str(sl.loc[0, "ModifiedPeptide"]) == "KIEC[Carbamidomethyl]FDSVEISGVEDR_KIEC[Carbamidomethyl]FDSVEISGVEDR"
+    assert str(sl.loc[0, "FragmentCharge"]) == "1"
+    assert str(sl.loc[0, "FragmentType"]) == "y"
+    assert str(sl.loc[0, "FragmentNumber"]) == "1"
+    assert str(sl.loc[0, "FragmentPepId"]) == "0"
+    assert str(sl.loc[0, "CLContainingFragment"]) == "False"
+    assert str(sl.loc[0, "IsDecoy"]) == "False"
+    assert str(sl.loc[0, "DecoyType"]) == "TT"
+
+    assert str(sl.loc[217, "ModifiedPeptide"]) == "MIAKSEQEIGK_VKYFQFDR"
+    assert str(sl.loc[217, "FragmentCharge"]) == "1"
+    assert str(sl.loc[217, "FragmentType"]) == "b"
+    assert str(sl.loc[217, "FragmentNumber"]) == "5"
+    assert str(sl.loc[217, "FragmentPepId"]) == "1"
+    assert str(sl.loc[217, "CLContainingFragment"]) == "True"
+    assert str(sl.loc[217, "IsDecoy"]) == "True"
+    assert str(sl.loc[217, "DecoyType"]) == "TD"