Merge pull request #30 from hgb-bin-proteomics/develop

add exporter for xiFDR >= 2.2.1

Author: michabirklbauer

README.md

@@ -60,7 +60,10 @@ Results can then be exported by selecting `File > Export > To Microsoft Excel…
   Files needed:
   - result.xlsx - MS Annika CSM result file (unvalidated) exported to .xlsx
   ```
+  # for xiFDR version < 2.2.1
   python xiFdrExporter_msannika.py result.xlsx
+  # for xiFDR version >= 2.2.1
+  python xiFdr2.2.1Exporter_msannika.py result.xlsx
   ```
 - **Exporting to [pyXlinkViewer (pyMOL)](https://github.com/BobSchiffrin/PyXlinkViewer)**  
   Files needed:
@@ -188,7 +191,7 @@ optional arguments:
   --version             show program's version number and exit
 ```
 
-Example usage:
+Example usage (xiFDR version < 2.2.1):
 
 ```
 python xiFdrExporter_msannika.py XLpeplib_Beveridge_QEx-HFX_DSS_R1.xlsx
@@ -200,6 +203,18 @@ Or using the Windows binary:
 xiFdrExporter_msannika.exe XLpeplib_Beveridge_QEx-HFX_DSS_R1.xlsx
 ```
 
+Example usage (xiFDR version 2.2.1 or later):
+
+```
+python xiFdr2.2.1Exporter_msannika.py XLpeplib_Beveridge_QEx-HFX_DSS_R1.xlsx
+```
+
+Or using the Windows binary:
+
+```
+xiFdr2.2.1Exporter_msannika.exe XLpeplib_Beveridge_QEx-HFX_DSS_R1.xlsx
+```
+
 ## Export to [PyXlinkViewer for pyMOL](https://github.com/BobSchiffrin/PyXlinkViewer)
 
 A schematic workflow of the implementation can be seen in [*this figure*](img/workflow_pyMOLexporter.png).

binaries/windows/xiFdr2.2.1Exporter_msannika.exe

@@ -0,0 +1,111 @@
+#!/usr/bin/env python3
+
+# Exporter of MS Annika CSM Results to xiFDR 2.2.1 input format
+# 2024 (c) Micha Johannes Birklbauer
+# https://github.com/michabirklbauer/
+# micha.birklbauer@gmail.com
+
+import argparse
+import pandas as pd
+
+__version = "1.0.2"
+__date = "202405017"
+
+"""
+DESCRIPTION:
+A script to export MS Annika CSM results (.xlsx) to a xiFDR input file (.csv).
+This version only works for xiFDR 2.2.1 and later!
+CSMs should be unfiltered, therefore include decoys and not be validated for any
+FDR.
+USAGE:
+xiFdr2.2.1Exporter_msannika.py f [f]
+                                 [-o OUTPUT]
+                                 [-h]
+                                 [--version]
+positional arguments:
+  f                     Crosslink-Spectrum-Matches (CSMs) exported from
+                        MS Annika in Microsoft Excel (.xlsx) format.
+optional arguments:
+  -o OUTPUT, --output OUTPUT
+                        Prefix of the output file.
+  -h, --help            show this help message and exit
+  --version             show program's version number and exit
+"""
+
+# Exporter class with constructor that takes one MS Annika CSM result file as
+# input. CSMs should not be in any way filtered and exported to Microsoft Excel
+# .xlsx format from Proteome Discoverer.
+class MSAnnika_Exporter:
+
+    def __init__(self, input_file: str):
+        self.input_file = input_file
+
+    # static method to generate pandas dataframe of xiFDR export without class
+    # instance. Takes the file name of the CSM file as input.
+    @staticmethod
+    def generate_df(input_file: str) -> pd.DataFrame:
+
+        df = pd.read_excel(input_file)
+        df.rename(columns = {"Spectrum File": "run",
+                             "First Scan": "scan",
+                             "Sequence A": "peptide1",
+                             "Sequence B": "peptide2",
+                             "Crosslinker Position A": "peptide link 1",
+                             "Crosslinker Position B": "peptide link 2",
+                             "Charge": "precursor charge",
+                             "Combined Score": "score",
+                             "Score Alpha": "peptide1 score",
+                             "Score Beta": "peptide2 score",
+                             "Accession A": "accession1",
+                             "Accession B": "accession2",
+                             "A in protein": "peptide position 1",
+                             "B in protein": "peptide position 2"},
+                  inplace = True,
+                  errors = "raise")
+        df["is decoy 1"] = df["Alpha T/D"].apply(lambda x: "false" if "t" in str(x).lower() else "true")
+        df["is decoy 2"] = df["Beta T/D"].apply(lambda x: "false" if "t" in str(x).lower() else "true")
+        df["peptide position 1"] = df["peptide position 1"].apply(lambda x: ";".join([str(int(y) + 1) for y in str(x).split(";")]))
+        df["peptide position 2"] = df["peptide position 2"].apply(lambda x: ";".join([str(int(y) + 1) for y in str(x).split(";")]))
+
+        return df
+
+    # classmethod implementation of the static generate_df
+    def __generate_csv_df(self) -> pd.DataFrame:
+        return self.generate_df(self.input_file)
+
+    # export function, takes one argument "output_file" which sets the prefix
+    # of generated output file
+    def export(self, output_file: str = None) -> pd.DataFrame:
+        csv = self.__generate_csv_df()
+
+        if output_file is None:
+            output_file = ".".join(self.input_file.split(".")[:-1])
+
+        csv.to_csv(output_file + "_xiFDR.csv", index = False)
+
+        return csv
+
+# initialize exporter and export xiFDR csv file
+def main() -> None:
+    parser = argparse.ArgumentParser()
+    parser.add_argument(metavar = "f",
+                        dest = "file",
+                        help = "Name/Path of the MS Annika CSM result file (in .xlsx format) to process.",
+                        type = str,
+                        nargs = 1)
+    parser.add_argument("-o", "--output",
+                        dest = "output",
+                        default = None,
+                        help = "Prefix of the output file.",
+                        type = str)
+    parser.add_argument("--version",
+                        action = "version",
+                        version = __version)
+    args = parser.parse_args()
+
+    exporter = MSAnnika_Exporter(args.file[0])
+
+    exporter.export(args.output)
+
+if __name__ == "__main__":
+    main()