Merge pull request #1 from michabirklbauer/develop

Develop

.github/workflows/python-app.yml

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+# This workflow will lint with Python 3.10
+# e.g. check for syntax errors and undefined names
+# 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: peptide_matching_game
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        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

LICENSE

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+MIT License
+
+Copyright (c) 2022 Micha Birklbauer, FH OOE Campus Hagenberg BIN Research Group
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,2 +1,33 @@
-# peptide-matching-game
-Peptide Matching Game Solution Browser
+# Peptide Matching Game
+
+A simple game to illustrate how peptide identification in mass spectra works
+using database search engines like [MS Amanda](https://pubs.acs.org/doi/full/10.1021/pr500202e).
+
+## Usage
+
+**How the game works:**
+- Read through the [game instructions](https://github.com/michabirklbauer/peptide_matching_game/blob/master/Game_Rules.pdf).
+
+**Setting up the game:**
+- Print the [game poster](https://github.com/michabirklbauer/peptide_matching_game/blob/master/Game_Poster.pdf).
+- Print at least one copy of each spectrum in `spectrum_cards`.
+- Print the [game instructions](https://github.com/michabirklbauer/peptide_matching_game/blob/master/Game_Rules.pdf) for people to understand the game.
+- [Optional] Set up your own game solution browser or use [https://michabirklbauer.github.io/peptide_matching_game/](https://michabirklbauer.github.io/peptide_matching_game/) so people are able to check their solutions.
+
+**Setting up the game solution browser:**
+- Install requirements: `pip install -r requirements.txt`
+- Run streamlit app: `streamlit run streamlit_app.py`
+- Alternatively pull and run the docker container: `docker run -p 8501:8501 michabirklbauer/peptidematchinggame:latest`
+- Open your browser and navigate to `localhost:8501`.
+
+## References
+
+- PDB structure [3RFM](https://www.rcsb.org/structure/3RFM) by [Dore et al.](http://dx.doi.org/10.1016/j.str.2011.06.014) is shown on the poster.
+
+## License
+
+- [MIT](https://github.com/michabirklbauer/peptide_matching_game/blob/master/LICENSE)
+
+## Contact
+
+- [[email protected]](mailto:[email protected])

resources/createSpectra.py

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+#!/usr/bin/env python3
+
+from matplotlib import pyplot as plt
+import ms2pip.single_prediction
+import spectrum_utils.spectrum as spectrum
+import spectrum_utils.plot as spectrum_plot
+
+## 5 x 4 matrix
+
+peptide_1 = "PLPGER"
+peptide_2 = "FIYAYR"
+peptide_3 = "GEQVSLR"
+peptide_4 = "DRYIAIR"
+peptide_5 = "ARSTLQK"
+
+# a 3 - easy
+# y4 matches only 3
+peptides_1 = ["PLFGER", "PLHGER", "PLPGER", "PLGGER"]
+# b 2 - medium
+# b3 is only correct in 2
+peptides_2 = ["FIFAYR", "FIYAYR", "FIHAYR", "FIKAYR"]
+# c 3 - medium
+# b3 intensity only matches 3
+peptides_3 = ["GEQASLR", "GEQTSLR", "GEQVSLR", "GEQSSLR"]
+# d 1 - hard
+# b3 and y4 only correct in 1
+peptides_4 = ["DRYIAIR", "DRYFAIR", "DRYWAIR", "DRYPAIR"]
+# e 4 - hard
+# b4 and b5 of 1, 2 are too intense, b4 of 3 is off by ~15 Da
+peptides_5 = ["ARSILQK", "ARSLLQK", "ARSSLQK", "ARSTLQK"]
+
+gridlines = False
+
+
+all_peptides = [peptides_1,
+                peptides_2,
+                peptides_3,
+                peptides_4,
+                peptides_5]
+
+def get_spectrum(peptide_sequence, charge = 1):
+
+    model = ms2pip.single_prediction.SinglePrediction()
+    mz, intensity, annotation = model.predict(peptide_sequence, "-", charge, model = "HCD2021")
+    identifier = f"{peptide_sequence}/{charge}/-"
+    precursor_mz = model.mod_info.calc_precursor_mz(peptide_sequence, "-", charge)
+    mod_dict = model._modifications_to_dict("-")
+    spectrum_annotation = model._get_sus_annotation(mz, annotation)
+
+    s = spectrum.MsmsSpectrum(identifier,
+                              precursor_mz,
+                              charge,
+                              mz,
+                              intensity,
+                              annotation = spectrum_annotation,
+                              peptide = peptide_sequence,
+                              modifications = mod_dict)
+
+    return s
+
+def main():
+    fig, axs = plt.subplots(5,4, figsize = (25,20), dpi = 300, tight_layout = True)
+    i = 0
+    rows = ["A", "B", "C", "D", "E"]
+    for peptide_group in all_peptides:
+        j = 0
+        for peptide in peptide_group:
+            s = get_spectrum(peptide)
+            spectrum_plot.spectrum(s, ax = axs[i, j])
+            axs[i, j].set_title(rows[i] + str(j + 1) + " - " + peptide)
+            axs[i, j].set_xlim([0, 900])
+            axs[i, j].grid(visible = gridlines, which = "both")
+            j += 1
+        i += 1
+
+    plt.savefig("result.svg")
+
+def main2():
+    rows = ["A", "B", "C", "D", "E"]
+    for i, peptide in enumerate([peptide_1, peptide_2, peptide_3, peptide_4, peptide_5]):
+        s = get_spectrum(peptide)
+        fig = plt.figure(figsize = (8,4.5))
+        plt.title("Peptide Group " + rows[i])
+        spectrum_plot.spectrum(s)
+        plt.xlim([0, 900])
+        plt.grid(visible = gridlines, which = "both")
+        plt.savefig(rows[i] + ".svg")
+
+
+if __name__ == "__main__":
+    main()
+    main2()