First commit.

.gitignore

@@ -157,4 +157,4 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+.idea/

pyquantms/diann/create_diann_cfg.py

@@ -0,0 +1,115 @@
+#!/usr/bin/env python
+
+"""
+This script converts SDRF parameters to DIA-NN parameters
+License: Apache 2.0
+Authors: Dai Chengxin, Yasset Perez-Riverol
+"""
+
+import re
+from typing import List, Tuple
+
+import click
+from sdrf_pipelines.openms.unimod import UnimodDatabase
+
+CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
+
+
+@click.group(context_settings=CONTEXT_SETTINGS)
+def cli():
+    pass
+
+
+@click.command("generate")
+@click.option("--enzyme", "-e", help="")
+@click.option("--fix_mod", "-f", help="")
+@click.option("--var_mod", "-v", help="")
+@click.pass_context
+def generate_cfg(ctx, enzyme, fix_mod, var_mod):
+    cut = enzyme_cut(enzyme)
+    unimod_database = UnimodDatabase()
+    fix_ptm, var_ptm = convert_mod(unimod_database, fix_mod, var_mod)
+
+    var_ptm_str = " --var-mod "
+    fix_ptm_str = " --fixed-mod "
+    diann_fix_ptm = ""
+    diann_var_ptm = ""
+    for mod in fix_ptm:
+        diann_fix_ptm += fix_ptm_str + mod
+    for mod in var_ptm:
+        diann_var_ptm += var_ptm_str + mod
+
+    with open("diann_config.cfg", "w") as file:
+        file.write("--cut " + cut + diann_fix_ptm + diann_var_ptm)
+
+
+def convert_mod(unimod_database, fix_mod: str, var_mod: str) -> Tuple[List, List]:
+    pattern = re.compile(r"\((.*?)\)")
+    var_ptm = []
+    fix_ptm = []
+
+    if fix_mod != "":
+        for mod in fix_mod.split(","):
+            tag = 0
+            for modification in unimod_database.modifications:
+                if modification.get_name() == mod.split(" ")[0]:
+                    diann_mod = modification.get_name() + "," + str(modification._delta_mono_mass)
+                    tag = 1
+                    break
+            if tag == 0:
+                print("Warning: Currently only supported unimod modifications for DIA pipeline. Skipped: " + mod)
+                continue
+            site = re.findall(pattern, " ".join(mod.split(" ")[1:]))[0]
+            if site == "Protein N-term":
+                site = "*n"
+            elif site == "N-term":
+                site = "n"
+
+            if "TMT" in diann_mod or "Label" in diann_mod or "iTRAQ" in diann_mod or "mTRAQ" in diann_mod:
+                fix_ptm.append(diann_mod + "," + site + "," + "label")
+            else:
+                fix_ptm.append(diann_mod + "," + site)
+
+    if var_mod != "":
+        for mod in var_mod.split(","):
+            tag = 0
+            for modification in unimod_database.modifications:
+                if modification.get_name() == mod.split(" ")[0]:
+                    diann_mod = modification.get_name() + "," + str(modification._delta_mono_mass)
+                    tag = 1
+                    break
+            if tag == 0:
+                print("Warning: Currently only supported unimod modifications for DIA pipeline. Skipped: " + mod)
+                continue
+            site = re.findall(pattern, " ".join(mod.split(" ")[1:]))[0]
+            if site == "Protein N-term":
+                site = "*n"
+            elif site == "N-term":
+                site = "n"
+
+            if "TMT" in diann_mod or "Label" in diann_mod or "iTRAQ" in diann_mod or "mTRAQ" in diann_mod:
+                var_ptm.append(diann_mod + "," + site + "," + "label")
+            else:
+                var_ptm.append(diann_mod + "," + site)
+
+    return fix_ptm, var_ptm
+
+
+_ENZYME_SPECIFICITY = {
+    "Trypsin": "K*,R*,!*P",
+    "Trypsin/P": "K*,R*",
+    "Arg-C": "R*,!*P",
+    "Asp-N": "*B,*D",
+    "Chymotrypsin": "F*,W*,Y*,L*,!*P",
+    "Lys-C": "K*,!*P",
+}
+
+
+def enzyme_cut(enzyme: str) -> str:
+    return _ENZYME_SPECIFICITY.get(enzyme) or "--cut"
+
+
+cli.add_command(generate_cfg)
+
+if __name__ == "__main__":
+    cli()