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RalfGRalfG
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Merge branch 'main' of https://github.com/compomics/psm_utils into ATPs/main
2 parents 92e02e9 + 247471b commit f001857

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‎.github/workflows/publish.yml‎

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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.9"
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python-version: "3.10"
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- name: Install dependencies
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run: |

‎.github/workflows/test.yml‎

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steps:
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- uses: actions/checkout@v4
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- name: Set up Python 3.9
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.9"
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python-version: "3.10"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install ruff
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- name: Lint with Ruff
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uses: astral-sh/ruff-action@v3
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with:
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args: check --exclude docs,tests
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- name: Check with Ruff
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run: ruff check --output-format=github .
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- name: Check formatting with Ruff
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uses: astral-sh/ruff-action@v3
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with:
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args: format --check --diff --exclude docs,tests
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- name: Install package and its dependencies
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run: pip install --editable .[dev,idxml]
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run: pip install --editable .[dev,io]
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- name: Static type checking with mypy
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run: mypy --non-interactive
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- name: Test with pytest and codecov
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run: |
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pytest --cov=psm_utils --cov-report=xml tests/
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pytest --cov=psm_utils --cov-report=xml tests/
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- name: Upload coverage reports to Codecov
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uses: codecov/codecov-action@v3
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
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python-version: ["3.10", "3.11", "3.12", "3.13"]
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steps:
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- uses: actions/checkout@v4
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- name: Install optional dependencies that might not be available
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continue-on-error: true
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run: pip install .[idxml]
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run: pip install .[io]
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- name: Test imports
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run: python -c "import psm_utils"

‎README.rst‎

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File format psm_utils tag Read support Write support Comments
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===================================================================================================================== ======================== =============== =============== ==========
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`AlphaDIA precursors TSV <https://alphadia.readthedocs.io/en/latest/quickstart.html#output-files>`_ ``alphadia`` ✅ ❌
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`CBOR <https://psm-utils.readthedocs.io/en/stable/api/psm_utils.io#module-psm_utils.io.cbor>`_ ``cbor`` ✅ ✅
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`DIA-NN TSV <https://github.com/vdemichev/DiaNN#output>`_ ``diann`` ✅ ❌
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`FlashLFQ generic TSV <https://github.com/smith-chem-wisc/FlashLFQ/wiki/Identification-Input-Formats>`_ ``flashlfq`` ✅ ✅
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`FragPipe PSM TSV <https://fragpipe.nesvilab.org/docs/tutorial_fragpipe_outputs.html#psmtsv/>`_ ``fragpipe`` ✅ ❌
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`ionbot CSV <https://ionbot.cloud/>`_ ``ionbot`` ✅ ❌
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`JSON <https://psm-utils.readthedocs.io/en/stable/api/psm_utils.io#module-psm_utils.io.json>`_ ``json`` ✅ ✅
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`OpenMS idXML <https://www.openms.de/>`_ ``idxml`` ✅ ✅ Requires the optional ``openms`` dependency (``pip install psm-utils[idxml]``)
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`MaxQuant msms.txt <https://www.maxquant.org/>`_ ``msms`` ✅ ❌
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`MS Amanda CSV <https://ms.imp.ac.at/?goto=msamanda>`_ ``msamanda`` ✅ ❌

‎docs/source/api/psm_utils.io.rst‎

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psm_utils.io.alphapept
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##################
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psm_utils.io.alphadia
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#####################
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.. automodule:: psm_utils.io.alphapept
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.. automodule:: psm_utils.io.alphadia
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:members:
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:inherited-members:
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psm_utils.io.cbor
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#################
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.. automodule:: psm_utils.io.cbor
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:members:
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:inherited-members:
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psm_utils.io.fragpipe
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##################
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#####################
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.. automodule:: psm_utils.io.fragpipe
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:members:
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psm_utils.io.json
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#################
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.. automodule:: psm_utils.io.json
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:members:
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:inherited-members:
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psm_utils.io.maxquant
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#####################
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‎example_files/example.psm_utils.cbor‎

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‎example_files/example.psm_utils.json‎

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[
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{
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"peptidoform": "SSYGSSSNDDSYGSSNNDDSYGSSNK/3",
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"spectrum_id": "71876",
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"run": "LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01",
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"spectrum": "71876",
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"is_decoy": false,
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"score": 136.160126,
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"qvalue": 0.0,
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"pep": 0.0,
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"precursor_mz": 894.33783,
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"retention_time": 2800.518555,
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"ion_mobility": 1e-06,
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"protein_list": [
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"P18899"
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],
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"rank": 1,
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"source": "AlphaDIA",
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"provenance_data": {
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"alphadia_filename": "C:\\Users\\ralfg\\git\\psm_utils\\example_files\\alphadia.precursors.tsv"
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},
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"metadata": {},
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"rescoring_features": {
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"rt_observed": 2800.518555,
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"mobility_observed": 1e-06,
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"mz_observed": 894.33783,
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"charge": 3.0,
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"delta_rt": 452.909424
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}
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},
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{
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"peptidoform": "SSQGSSSSTQSAPSETASASK/2",
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"spectrum_id": "41978",
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"run": "LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01",
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"spectrum": "41978",
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"is_decoy": false,
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"score": 122.27832,
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"qvalue": 0.0,
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"pep": 0.0,
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"precursor_mz": 986.440491,
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"retention_time": 1647.208252,
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"ion_mobility": 1e-06,
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"protein_list": [
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"Q9ULU4"
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],
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"rank": 1,
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"source": "AlphaDIA",
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"provenance_data": {
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"alphadia_filename": "C:\\Users\\ralfg\\git\\psm_utils\\example_files\\alphadia.precursors.tsv"
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},
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"metadata": {},
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"rescoring_features": {
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"rt_observed": 1647.208252,
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"mobility_observed": 1e-06,
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"mz_observed": 986.440491,
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"charge": 2.0,
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"delta_rt": -23.25415
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}
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},
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{
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"peptidoform": "SSQTSGTNEQSSAIVSAR/2",
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"spectrum_id": "68554",
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"run": "LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01",
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"spectrum": "68554",
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"is_decoy": false,
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"score": 152.012512,
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"qvalue": 0.0,
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"pep": 0.0,
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"precursor_mz": 905.432312,
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"retention_time": 2678.317139,
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"ion_mobility": 1e-06,
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"protein_list": [
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"O60763"
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],
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"rank": 1,
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"source": "AlphaDIA",
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"provenance_data": {
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"alphadia_filename": "C:\\Users\\ralfg\\git\\psm_utils\\example_files\\alphadia.precursors.tsv"
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},
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"metadata": {},
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"rescoring_features": {
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"rt_observed": 2678.317139,
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"mobility_observed": 1e-06,
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"mz_observed": 905.432312,
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"charge": 2.0,
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"delta_rt": 31.525879
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}
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}
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]

‎example_files/example.psm_utils.tsv‎

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peptidoform spectrum_id run collection is_decoy score qvalue pep precursor_mz retention_time ion_mobility protein_list rank source provenance:alphadia_filename rescoring:rt_observed rescoring:mobility_observed rescoring:mz_observed rescoring:charge rescoring:delta_rt
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SSYGSSSNDDSYGSSNNDDSYGSSNK/3 71876 LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01 False 136.160126 0.0 0.0 894.33783 2800.518555 1e-06 ['P18899'] 1 AlphaDIA C:\Users\ralfg\git\psm_utils\example_files\alphadia.precursors.tsv 2800.518555 1e-06 894.33783 3.0 452.909424
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SSQGSSSSTQSAPSETASASK/2 41978 LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01 False 122.27832 0.0 0.0 986.440491 1647.208252 1e-06 ['Q9ULU4'] 1 AlphaDIA C:\Users\ralfg\git\psm_utils\example_files\alphadia.precursors.tsv 1647.208252 1e-06 986.440491 2.0 -23.25415
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SSQTSGTNEQSSAIVSAR/2 68554 LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01 False 152.012512 0.0 0.0 905.432312 2678.317139 1e-06 ['O60763'] 1 AlphaDIA C:\Users\ralfg\git\psm_utils\example_files\alphadia.precursors.tsv 2678.317139 1e-06 905.432312 2.0 31.525879

‎online/Home.py‎

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class StreamlitPageHome(StreamlitPage):
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"""Streamlit page for the home section."""
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def _main_page(self):
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pass
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‎online/_utils.py‎

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----------
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Observations
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"""
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def fdr_plot(psm_df, fdr_threshold):
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"""Plot number of identifications in function of FDR threshold."""
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df = (
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target_psm_df = (
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psm_df[~psm_df["is_decoy"]]
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.reset_index(drop=True)
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.sort_values("qvalue", ascending=True)
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target_psm_df["count"] = (~target_psm_df["is_decoy"]).cumsum()
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‎psm_utils/__main__.py‎

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"""Command line interface for psm_utils."""
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