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pyXLMS 0.0.1__tar.gz

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pyxlms-0.0.1/LICENSE +21 -0
pyxlms-0.0.1/PKG-INFO +94 -0
pyxlms-0.0.1/README.md +52 -0
pyxlms-0.0.1/pyproject.toml +36 -0
pyxlms-0.0.1/setup.cfg +4 -0
pyxlms-0.0.1/src/pyXLMS/__init__.py +0 -0
pyxlms-0.0.1/src/pyXLMS/data.py +126 -0
pyxlms-0.0.1/src/pyXLMS.egg-info/PKG-INFO +94 -0
pyxlms-0.0.1/src/pyXLMS.egg-info/SOURCES.txt +11 -0
pyxlms-0.0.1/src/pyXLMS.egg-info/dependency_links.txt +1 -0
pyxlms-0.0.1/src/pyXLMS.egg-info/requires.txt +4 -0
pyxlms-0.0.1/src/pyXLMS.egg-info/top_level.txt +1 -0
pyxlms-0.0.1/tests/tests.py +103 -0

pyxlms-0.0.1/LICENSE ADDED Viewed

@@ -0,0 +1,21 @@
+MIT License
+Copyright (c) 2024 Micha Johannes Birklbauer
+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.

pyxlms-0.0.1/PKG-INFO ADDED Viewed

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+Metadata-Version: 2.1
+Name: pyXLMS
+Version: 0.0.1
+Summary: A python package to process protein cross-linking data.
+Author-email: Micha Johannes Birklbauer <micha.birklbauer@fh-hagenberg.at>
+Maintainer-email: Micha Johannes Birklbauer <micha.birklbauer@fh-hagenberg.at>
+License: MIT License
+        Copyright (c) 2024 Micha Johannes Birklbauer
+        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.
+Project-URL: Homepage, https://github.com/hgb-bin-proteomics/pyXLMS
+Project-URL: Documentation, https://hgb-bin-proteomics.github.io/pyXLMS
+Project-URL: Issues, https://github.com/hgb-bin-proteomics/pyXLMS/issues
+Keywords: crosslink,crosslinker,crosslinking,mass spectrometry,proteomics
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas
+Provides-Extra: gui
+Requires-Dist: streamlit; extra == "gui"
+# pyXLMS
+Supported search engines:
+- MS Annika
+- xiSearch / xiFDR
+- MaxLynx
+- ?
+General interface with csv input
+Packages to include:
+- Export to xiNET
+  - Req:
+  - fasta file
+  - Crosslink:
+    - Sequence
+    - XL position in peptide
+    - protein accession
+    - XL position in protein
+    - Score
+- Export to xiVIEW
+  - Req: cover by xiNET Req
+- Export to xiFDR
+  - Req:
+  - CSM:
+    - Spectrum File
+    - Scan Nr
+    - Sequence
+    - XL position in peptide
+    - Precursor charge
+    - Score CSM
+    - Score peptide
+    - protein accession
+    - position of peptide in protein
+    - decoy peptide
+- Export to pyXlinkViewer
+  - Req: all covered
+- Export to XMAS
+  - Req: all covered
+- Export to Spectral Library
+  - Req:
+  - MGF
+  - CSM:
+    - Modification
+    - RT
+    - Ion Mobility / Compensation Voltage
+- MS Annika FDR
+  - Req: all covered
+- MS Annika Combine Results
+  - Req: all covered
+- CSM Annotation
+  - Req: this is probably MS Annika only, as it requires doublet information

pyxlms-0.0.1/README.md ADDED Viewed

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+# pyXLMS
+Supported search engines:
+- MS Annika
+- xiSearch / xiFDR
+- MaxLynx
+- ?
+General interface with csv input
+Packages to include:
+- Export to xiNET
+  - Req:
+  - fasta file
+  - Crosslink:
+    - Sequence
+    - XL position in peptide
+    - protein accession
+    - XL position in protein
+    - Score
+- Export to xiVIEW
+  - Req: cover by xiNET Req
+- Export to xiFDR
+  - Req:
+  - CSM:
+    - Spectrum File
+    - Scan Nr
+    - Sequence
+    - XL position in peptide
+    - Precursor charge
+    - Score CSM
+    - Score peptide
+    - protein accession
+    - position of peptide in protein
+    - decoy peptide
+- Export to pyXlinkViewer
+  - Req: all covered
+- Export to XMAS
+  - Req: all covered
+- Export to Spectral Library
+  - Req:
+  - MGF
+  - CSM:
+    - Modification
+    - RT
+    - Ion Mobility / Compensation Voltage
+- MS Annika FDR
+  - Req: all covered
+- MS Annika Combine Results
+  - Req: all covered
+- CSM Annotation
+  - Req: this is probably MS Annika only, as it requires doublet information

pyxlms-0.0.1/pyproject.toml ADDED Viewed

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+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+[project]
+name = "pyXLMS"
+version = "0.0.1"
+authors = [
+  { name="Micha Johannes Birklbauer", email="micha.birklbauer@fh-hagenberg.at" },
+]
+maintainers = [
+  { name="Micha Johannes Birklbauer", email="micha.birklbauer@fh-hagenberg.at" },
+]
+readme = "README.md"
+license = {file = "LICENSE"}
+description = "A python package to process protein cross-linking data."
+keywords = ["crosslink", "crosslinker", "crosslinking", "mass spectrometry", "proteomics"]
+requires-python = ">=3.7"
+classifiers = [
+  "Programming Language :: Python :: 3",
+  "License :: OSI Approved :: MIT License",
+  "Operating System :: OS Independent",
+]
+dependencies = [
+  "pandas"
+]
+[project.optional-dependencies]
+gui = [
+  "streamlit"
+]
+[project.urls]
+Homepage = "https://github.com/hgb-bin-proteomics/pyXLMS"
+Documentation = "https://hgb-bin-proteomics.github.io/pyXLMS"
+Issues = "https://github.com/hgb-bin-proteomics/pyXLMS/issues"

pyxlms-0.0.1/setup.cfg ADDED Viewed

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+[egg_info]
+tag_build =
+tag_date = 0

pyxlms-0.0.1/src/pyXLMS/__init__.py ADDED Viewed

File without changes

pyxlms-0.0.1/src/pyXLMS/data.py ADDED Viewed

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+#!/usr/bin/env python3
+# 2024 (c) Micha Johannes Birklbauer
+# https://github.com/michabirklbauer/
+# micha.birklbauer@gmail.com
+from typing import List
+from typing import Dict
+from typing import Any
+def check_input(parameter: Any,
+                parameter_name: str,
+                supported_class: Any,
+                supported_subclass: Any = None) -> bool:
+    """Checks if the given parameter is of the specified type.
+    Parameters
+    ----------
+    parameter : any
+        Parameter to check class of.
+    parameter_name : str
+        Name of the parameter.
+    supported_class : any
+        Class the parameter has to be of.
+    supported_subclass : any
+        Class of the values in case the parameter is a list.
+    Returns
+    -------
+    bool
+        If the given input is okay.
+    Raises
+    ------
+    TypeError
+        If the parameter is not of the given class.
+    """
+    if type(parameter) != supported_class:
+        raise TypeError(f"{parameter_name} must be {supported_class}!")
+    if type(parameter) == list and supported_subclass is not None:
+        for value in parameter:
+            if type(value) != supported_subclass:
+                raise TypeError(f"List values of {parameter_name} must be {supported_subclass}")
+    return True
+def create_crosslink(peptide_a: str,
+                     xl_position_peptide_a: int,
+                     proteins_a: List[str],
+                     xl_position_proteins_a: List[int],
+                     peptide_b: str,
+                     xl_position_peptide_b: int,
+                     proteins_b: List[str],
+                     xl_position_proteins_b: List[int],
+                     score: float) -> Dict[str, Any]:
+    """Returns a crosslink dictionary.
+    Parameters
+    ----------
+    peptide_a : str
+        The unmodified amino acid sequence of the first peptide.
+    xl_position_peptide_a : int
+        The position of the crosslinker in the sequence of the first peptide (1-based).
+    proteins_a: list of str
+        The accessions of proteins that the first peptide is associated with.
+    xl_position_proteins_a: list of int
+        Positions of the crosslink in the proteins of the first peptide (1-based).
+    peptide_b : str
+        The unmodified amino acid sequence of the second peptide.
+    xl_position_peptide_b : int
+        The position of the crosslinker in the sequence of the second peptide (1-based).
+    proteins_b: list of str
+        The accessions of proteins that the second peptide is associated with.
+    xl_position_proteins_b: list of int
+        Positions of the crosslink in the proteins of the second peptide (1-based).
+    score: float
+        Score of the crosslink.
+    Returns
+    -------
+    dict
+        The dictionary representing the crosslink with keys data_type, alpha_peptide, alpha_peptide_crosslink_position,
+        alpha_proteins, alpha_proteins_crosslink_positions, beta_peptide, beta_peptide_crosslink_position, beta_proteins,
+        beta_proteins_crosslink_positions, and score.
+        Alpha and beta are assigned based on peptide sequence, the peptide that alphabetically comes first is assigned to alpha.
+    """
+    ## input checks
+    check_input(peptide_a, "peptide_a", str)
+    check_input(peptide_b, "peptide_b", str)
+    check_input(xl_position_peptide_a, "xl_position_peptide_a", int)
+    check_input(xl_position_peptide_b, "xl_position_peptide_b", int)
+    check_input(proteins_a, "proteins_a", list, str)
+    check_input(proteins_b, "proteins_b", list, str)
+    check_input(xl_position_proteins_a, "xl_position_proteins_a", list, int)
+    check_input(xl_position_proteins_b, "xl_position_proteins_b", list, int)
+    check_input(score, "score", float)
+    if len(proteins_a) != len(xl_position_proteins_a):
+        raise ValueError("Crosslink position has to be given for every protein! Length of proteins_a and xl_position_proteins_a has to match!")
+    if len(proteins_b) != len(xl_position_proteins_b):
+        raise ValueError("Crosslink position has to be given for every protein! Length of proteins_b and xl_position_proteins_b has to match!")
+    ## processing
+    crosslink = {f"{peptide_a.strip()}{xl_position_peptide_a}":
+                    {
+                        "peptide": peptide_a,
+                        "xl_position_peptide": xl_position_peptide_a,
+                        "proteins": proteins_a,
+                        "xl_position_proteins": xl_position_proteins_a
+                    },
+                 f"{peptide_b.strip()}{xl_position_peptide_b}":
+                    {
+                        "peptide": peptide_b,
+                        "xl_position_peptide": xl_position_peptide_b,
+                        "proteins": proteins_b,
+                        "xl_position_proteins": xl_position_proteins_b
+                    }
+                }
+    keys = sorted(list(crosslink.keys()))
+    return {"data_type": "crosslink",
+            "alpha_peptide": crosslink[keys[0]]["peptide"].strip(),
+            "alpha_peptide_crosslink_position": crosslink[keys[0]]["xl_position_peptide"],
+            "alpha_proteins": [protein.strip() for protein in crosslink[keys[0]]["proteins"]],
+            "alpha_proteins_crosslink_positions": crosslink[keys[0]]["xl_position_proteins"],
+            "beta_peptide": crosslink[keys[1]]["peptide"].strip(),
+            "beta_peptide_crosslink_position": crosslink[keys[1]]["xl_position_peptide"],
+            "beta_proteins": [protein.strip() for protein in crosslink[keys[1]]["proteins"]],
+            "beta_proteins_crosslink_positions": crosslink[keys[1]]["xl_position_proteins"],
+            "score": score}

pyxlms-0.0.1/src/pyXLMS.egg-info/PKG-INFO ADDED Viewed

@@ -0,0 +1,94 @@
+Metadata-Version: 2.1
+Name: pyXLMS
+Version: 0.0.1
+Summary: A python package to process protein cross-linking data.
+Author-email: Micha Johannes Birklbauer <micha.birklbauer@fh-hagenberg.at>
+Maintainer-email: Micha Johannes Birklbauer <micha.birklbauer@fh-hagenberg.at>
+License: MIT License
+        Copyright (c) 2024 Micha Johannes Birklbauer
+        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.
+Project-URL: Homepage, https://github.com/hgb-bin-proteomics/pyXLMS
+Project-URL: Documentation, https://hgb-bin-proteomics.github.io/pyXLMS
+Project-URL: Issues, https://github.com/hgb-bin-proteomics/pyXLMS/issues
+Keywords: crosslink,crosslinker,crosslinking,mass spectrometry,proteomics
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas
+Provides-Extra: gui
+Requires-Dist: streamlit; extra == "gui"
+# pyXLMS
+Supported search engines:
+- MS Annika
+- xiSearch / xiFDR
+- MaxLynx
+- ?
+General interface with csv input
+Packages to include:
+- Export to xiNET
+  - Req:
+  - fasta file
+  - Crosslink:
+    - Sequence
+    - XL position in peptide
+    - protein accession
+    - XL position in protein
+    - Score
+- Export to xiVIEW
+  - Req: cover by xiNET Req
+- Export to xiFDR
+  - Req:
+  - CSM:
+    - Spectrum File
+    - Scan Nr
+    - Sequence
+    - XL position in peptide
+    - Precursor charge
+    - Score CSM
+    - Score peptide
+    - protein accession
+    - position of peptide in protein
+    - decoy peptide
+- Export to pyXlinkViewer
+  - Req: all covered
+- Export to XMAS
+  - Req: all covered
+- Export to Spectral Library
+  - Req:
+  - MGF
+  - CSM:
+    - Modification
+    - RT
+    - Ion Mobility / Compensation Voltage
+- MS Annika FDR
+  - Req: all covered
+- MS Annika Combine Results
+  - Req: all covered
+- CSM Annotation
+  - Req: this is probably MS Annika only, as it requires doublet information

pyxlms-0.0.1/src/pyXLMS.egg-info/SOURCES.txt ADDED Viewed

@@ -0,0 +1,11 @@
+LICENSE
+README.md
+pyproject.toml
+src/pyXLMS/__init__.py
+src/pyXLMS/data.py
+src/pyXLMS.egg-info/PKG-INFO
+src/pyXLMS.egg-info/SOURCES.txt
+src/pyXLMS.egg-info/dependency_links.txt
+src/pyXLMS.egg-info/requires.txt
+src/pyXLMS.egg-info/top_level.txt
+tests/tests.py

pyxlms-0.0.1/src/pyXLMS.egg-info/dependency_links.txt ADDED Viewed

	@@ -0,0 +1 @@
1	+

pyxlms-0.0.1/src/pyXLMS.egg-info/requires.txt ADDED Viewed

@@ -0,0 +1,4 @@
+pandas
+[gui]
+streamlit

pyxlms-0.0.1/src/pyXLMS.egg-info/top_level.txt ADDED Viewed

	@@ -0,0 +1 @@
1	+ pyXLMS

pyxlms-0.0.1/tests/tests.py ADDED Viewed

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+#!/usr/bin/env python3
+# pyXLMS - TESTS
+# 2024 (c) Micha Johannes Birklbauer
+# https://github.com/michabirklbauer/
+# micha.birklbauer@gmail.com
+import pytest
+def test1():
+    from pyXLMS import data
+    x = 1
+    assert data.check_input(x, "x", int)
+def test2():
+    from pyXLMS import data
+    x = [1, 2, 3]
+    assert data.check_input(x, "x", list)
+def test3():
+    from pyXLMS import data
+    x = [1, 2, 3]
+    assert data.check_input(x, "x", list, int)
+def test4():
+    from pyXLMS import data
+    x = 1
+    with pytest.raises(TypeError, match = f"x must be {str}!"):
+        i = data.check_input(x, "x", str)
+def test5():
+    from pyXLMS import data
+    x = [1, 2, 3]
+    with pytest.raises(TypeError, match = f"List values of x must be {str}"):
+        i = data.check_input(x, "x", list, str)
+def test6():
+    from pyXLMS import data
+    crosslink = data.create_crosslink("PEPTIDE", 1, ["PROTEIN"], [1],
+                                      "EDITPEP", 3, ["NIETORP", "PROTEIN"], [5, 2],
+                                      170.3)
+    assert crosslink["data_type"] == "crosslink"
+    assert crosslink["alpha_peptide"] == "EDITPEP"
+    assert crosslink["alpha_peptide_crosslink_position"] == 3
+    assert len(crosslink["alpha_proteins"]) == 2
+    assert crosslink["alpha_proteins"][0] == "NIETORP"
+    assert len(crosslink["alpha_proteins_crosslink_positions"]) == 2
+    assert crosslink["alpha_proteins_crosslink_positions"][0] == 5
+    assert crosslink["beta_peptide"] == "PEPTIDE"
+    assert crosslink["beta_peptide_crosslink_position"] == 1
+    assert len(crosslink["beta_proteins"]) == 1
+    assert crosslink["beta_proteins"][0] == "PROTEIN"
+    assert len(crosslink["beta_proteins_crosslink_positions"]) == 1
+    assert crosslink["beta_proteins_crosslink_positions"][0] == 1
+    assert crosslink["score"] >= 170.25 and crosslink["score"] <= 170.35
+def test7():
+    from pyXLMS import data
+    crosslink = data.create_crosslink("PEPTIDE", 3, ["PROTEIN"], [3],
+                                      "PEPTIDE", 1, ["PROTEIN"], [1],
+                                      170.3)
+    assert crosslink["data_type"] == "crosslink"
+    assert crosslink["alpha_peptide"] == "PEPTIDE"
+    assert crosslink["alpha_peptide_crosslink_position"] == 1
+    assert len(crosslink["alpha_proteins"]) == 1
+    assert crosslink["alpha_proteins"][0] == "PROTEIN"
+    assert len(crosslink["alpha_proteins_crosslink_positions"]) == 1
+    assert crosslink["alpha_proteins_crosslink_positions"][0] == 1
+    assert crosslink["beta_peptide"] == "PEPTIDE"
+    assert crosslink["beta_peptide_crosslink_position"] == 3
+    assert len(crosslink["beta_proteins"]) == 1
+    assert crosslink["beta_proteins"][0] == "PROTEIN"
+    assert len(crosslink["beta_proteins_crosslink_positions"]) == 1
+    assert crosslink["beta_proteins_crosslink_positions"][0] == 3
+    assert crosslink["score"] >= 170.25 and crosslink["score"] <= 170.35
+def test8():
+    from pyXLMS import data
+    with pytest.raises(TypeError, match = f"xl_position_peptide_a must be {int}!"):
+        crosslink = data.create_crosslink("PEPTIDE", "3", ["PROTEIN"], [3],
+                                          "PEPTIDE", 1, ["PROTEIN"], [1],
+                                          170.3)
+def test9():
+    from pyXLMS import data
+    with pytest.raises(TypeError, match = f"List values of xl_position_proteins_a must be {int}"):
+        crosslink = data.create_crosslink("PEPTIDE", 3, ["PROTEIN"], ["3"],
+                                          "PEPTIDE", 1, ["PROTEIN"], [1],
+                                          170.3)
+def test10():
+    from pyXLMS import data
+    with pytest.raises(ValueError, match = "Crosslink position has to be given for every protein! Length of proteins_a and xl_position_proteins_a has to match!"):
+        crosslink = data.create_crosslink("PEPTIDE", 3, ["PROTEIN"], [3, 4],
+                                          "PEPTIDE", 1, ["PROTEIN"], [1],
+                                          170.3)
+def test11():
+    from pyXLMS import data
+    with pytest.raises(ValueError, match = "Crosslink position has to be given for every protein! Length of proteins_b and xl_position_proteins_b has to match!"):
+        crosslink = data.create_crosslink("PEPTIDE", 3, ["PROTEIN"], [3],
+                                          "PEPTIDE", 1, ["PROTEIN"], [1, 2],
+                                          170.3)