pyXLMS 0.0.1__py3-none-any.whl

pyXLMS/data.py

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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.dist-info/LICENSE

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+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.dist-info/METADATA

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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.dist-info/RECORD

@@ -0,0 +1,7 @@
+pyXLMS/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pyXLMS/data.py,sha256=a8dtzLAAaKemmoERc8DfY-38Q8sWS3320DP8nTLmPRM,5627
+pyXLMS-0.0.1.dist-info/LICENSE,sha256=N_5mStWCiIu4tlY6BGEE-LP5Ak_E_TukpIB-xyeHbEk,1082
+pyXLMS-0.0.1.dist-info/METADATA,sha256=tRd4cnsamsOOh8bPk3uG4bvD_cCkjqdHbyWlOzMEs3g,3128
+pyXLMS-0.0.1.dist-info/WHEEL,sha256=Mdi9PDNwEZptOjTlUcAth7XJDFtKrHYaQMPulZeBCiQ,91
+pyXLMS-0.0.1.dist-info/top_level.txt,sha256=PSI-LSbSAP8H1vK38x0D4s8PejAinkrL2Dclm3-G35I,7
+pyXLMS-0.0.1.dist-info/RECORD,,

pyXLMS-0.0.1.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (73.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

pyXLMS-0.0.1.dist-info/top_level.txt

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+pyXLMS