Adding commands

.github/workflows/python-app.yml

@@ -28,6 +28,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python setup.py install
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

.github/workflows/python-package.yml

@@ -29,6 +29,7 @@ jobs:
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python setup.py install
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

BSA_design_urls_sample.csv

@@ -0,0 +1,7 @@
+Spectra_Filepath	Sample
+https://raw.githubusercontent.com/nf-core/test-datasets/proteomicslfq/testdata/BSA1_F1.mzML	1
+https://raw.githubusercontent.com/nf-core/test-datasets/proteomicslfq/testdata/BSA1_F2.mzML	1
+https://raw.githubusercontent.com/nf-core/test-datasets/proteomicslfq/testdata/BSA2_F1.mzML	2
+https://raw.githubusercontent.com/nf-core/test-datasets/proteomicslfq/testdata/BSA2_F2.mzML	2
+https://raw.githubusercontent.com/nf-core/test-datasets/proteomicslfq/testdata/BSA3_F1.mzML	3
+https://raw.githubusercontent.com/nf-core/test-datasets/proteomicslfq/testdata/BSA3_F2.mzML	3

pyproject.toml

@@ -12,7 +12,11 @@ build-backend = "setuptools.build_meta"
 click = ">=7.0"
 pydantic = ">=1.10,<2"
 python = "^3.7"
-sdrf_pipelines = ">=0.0.26"
+sdrf-pipelines = ">=0.0.26"
+pyopenms = ">=2.6.0"
+ms2rescore = ">=3.0.2"
+psm-utils = "==0.8.0"
+pandas = ">=1.0.0"
 
 [tool.poetry.dev-dependencies]
 pytest = "*"

pyquantms/diann/create_diann_cfg.py

@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 """
 This script converts SDRF parameters to DIA-NN parameters
 License: Apache 2.0
@@ -12,20 +10,13 @@
 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.command("create_diann_cfg")
 @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):
+def create_diann_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)
@@ -53,19 +44,31 @@ def convert_mod(unimod_database, fix_mod: str, var_mod: str) -> Tuple[List, List
             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)
+                    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)
+                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:
+            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)
@@ -75,19 +78,31 @@ def convert_mod(unimod_database, fix_mod: str, var_mod: str) -> Tuple[List, List
             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)
+                    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)
+                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:
+            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)
@@ -107,9 +122,3 @@ def convert_mod(unimod_database, fix_mod: str, var_mod: str) -> Tuple[List, List
 
 def enzyme_cut(enzyme: str) -> str:
     return _ENZYME_SPECIFICITY.get(enzyme) or "--cut"
-
-
-cli.add_command(generate_cfg)
-
-if __name__ == "__main__":
-    cli()