Merge branch 'development' into feature/timsTOF

.cookietemple.yml

@@ -15,5 +15,5 @@ full_name: Victor Giurcoiu
 email: [email protected]
 project_name: oktoberfest
 project_short_description: Public repo oktoberfest
-version: 0.5.0
+version: 0.5.1
 license: MIT

.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.5.0 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
-tag-template: 0.5.0 # <<COOKIETEMPLE_FORCE_BUMP>>
+name-template: "0.5.1 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
+tag-template: 0.5.1 # <<COOKIETEMPLE_FORCE_BUMP>>
 exclude-labels:
     - "skip-changelog"
 

.github/workflows/build_package.yml

@@ -12,7 +12,7 @@ jobs:
                 python: [3.8, 3.9]
 
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v4
               name: Check out source-code repository
 
             - name: Setup Python

.github/workflows/labeler.yml

@@ -11,9 +11,9 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v2.3.3
+              uses: actions/checkout@v4
 
             - name: Run Labeler
-              uses: crazy-max/ghaction-github-labeler@v4.1.0
+              uses: crazy-max/ghaction-github-labeler@v5.0.0
               with:
                   skip-delete: true

.github/workflows/publish_docs.yml

@@ -7,7 +7,7 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v4
               name: Check out source-code repository
 
             - name: Setup Python

.github/workflows/publish_package.yml

@@ -10,7 +10,7 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v2.3.4
+              uses: actions/checkout@v4
               with:
                   fetch-depth: 2
 

.github/workflows/run_cookietemple_lint.yml

@@ -7,7 +7,7 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v4
               name: Check out source-code repository
 
             - name: Setup Python

.github/workflows/run_tests.yml

@@ -1,8 +1,14 @@
 name: Run oktoberfest Tests
 
 on:
-    - push
-    - pull_request
+    push:
+        branches:
+            - development
+            - main
+            - "release/*"
+    pull_request:
+        branches:
+            - "*"
 
 jobs:
     tests:
@@ -63,7 +69,7 @@ jobs:
 
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v2.3.4
+              uses: actions/checkout@v4
 
             - name: Set up Python ${{ matrix.python-version }}
               uses: actions/setup-python@v4
@@ -98,7 +104,7 @@ jobs:
                   print("::set-output name=result::{}".format(result))
 
             - name: Restore pre-commit cache
-              uses: actions/[email protected].1
+              uses: actions/[email protected].2
               if: matrix.session == 'pre-commit'
               with:
                   path: ~/.cache/pre-commit
@@ -128,7 +134,7 @@ jobs:
         needs: tests
         steps:
             - name: Check out the repository
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
 
             - name: Set up Python 3.8
               uses: actions/setup-python@v4

.github/workflows/sync_project.yml

@@ -17,7 +17,7 @@ jobs:
             - name: Install cookietemple
               run: pip install cookietemple
 
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v4
               with:
                   fetch-depth: 0
                   token: "${{ secrets.CT_SYNC_TOKEN }}"

cookietemple.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.0
+current_version = 0.5.1
 
 [bumpversion_files_whitelisted]
 init_file = oktoberfest/__init__.py

docs/conf.py

@@ -54,9 +54,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = "0.5.0"
+version = "0.5.1"
 # The full version, including alpha/beta/rc tags.
-release = "0.5.0"
+release = "0.5.1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

oktoberfest/__init__.py

@@ -5,7 +5,7 @@
 __author__ = """The Oktoberfest development team (Wilhelmlab at Technical University of Munich)"""
 __copyright__ = f"Copyright {datetime.now():%Y}, Wilhelmlab at Technical University of Munich"
 __license__ = "MIT"
-__version__ = "0.5.0"
+__version__ = "0.5.1"
 
 import logging.handlers
 import sys

oktoberfest/runner.py

@@ -169,7 +169,7 @@ def generate_spectral_lib(config_path: Union[str, Path]):
     if library_input_type == "fasta":
         pp.digest(
             fasta=config.library_input,
-            output=config.output / "prosit_input.csv",
+            output=config.output,
             fragmentation=config.fragmentation,
             digestion=config.digestion,
             cleavages=config.cleavages,

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "oktoberfest"
-version = "0.5.0"  # <<COOKIETEMPLE_FORCE_BUMP>>
+version = "0.5.1"  # <<COOKIETEMPLE_FORCE_BUMP>>
 description = "Public repo oktoberfest"
 authors = ["Victor Giurcoiu <[email protected]>"]
 license = "MIT"

tests/unit_tests/configs/spectral_library_with_digest.json

@@ -0,0 +1,26 @@
+{
+    "type": "SpectralLibraryGeneration",
+    "tag": "",
+    "inputs": {
+        "library_input": "../data/test.fasta",
+        "library_input_type": "fasta"
+    },
+    "output": "../data/",
+    "models": {
+        "intensity": "Prosit_2020_intensity_HCD",
+        "irt": "Prosit_2019_irt"
+    },
+    "outputFormat": "spectronaut",
+    "prediction_server": "koina.proteomicsdb.org:443",
+    "ssl": true,
+    "fastaDigestOptions": {
+        "fragmentation": "HCD",
+        "digestion": "full",
+        "missedCleavages": 2,
+        "minLength": 7,
+        "maxLength": 60,
+        "enzyme": "trypsin",
+        "specialAas": "KR",
+        "db": "concat"
+    }
+}

tests/unit_tests/data/test.fasta

@@ -0,0 +1,54 @@
+>ENSP00000488551.1 pep:known chromosome:GRCh38:CHR_HSCHR7_2_CTG6:142634764:142635309:1 gene:ENSG00000282497.1 transcript:ENST00000631835.1 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+MGPGLLHWMALCLLGTGHGDAMVIQNPRYQVTQFGKPVTLSCSQTLNHNVMYWYQQKSSQ
+APKLLFHYYDKDFNNEADTPDNFQSRRPNTSFCFLDIRSPGLGDAAMYLCATSR
+>ENSP00000374917.3 pep:known chromosome:GRCh38:7:142626649:142627399:1 gene:ENSG00000211747.3 transcript:ENST00000390394.3 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+MLLLLLLLGPGSGLGAVVSQHPSRVICKSGTSVKIECRSLDFQATTMFWYRQFPKQSLML
+MATSNEGSKATYEQGVEKDKFLINHASLTLSTLTVTSAHPEDSSFYICSAR
+>ENSP00000374919.1 pep:known chromosome:GRCh38:7:142645961:142646467:1 gene:ENSG00000211749.1 transcript:ENST00000390396.1 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+MGTRLLGCAALCLLAADSFHAKVTQTPGHLVKGKGQKTKMDCTPEKGHTFVYWYQQNQNK
+EFMLLISFQNEQVLQETEMHKKRFSSQCPKNAPCSLAILSSEPGDTALYLCASSQ
+>ENSP00000452526.1 pep:known chromosome:GRCh38:14:22052514:22053056:1 gene:ENSG00000211801.3 transcript:ENST00000390449.3 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+METLLGLLILWLQLQWVSSKQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPG
+KGLTSLLLIQSSQREQTSGRLNASLDKSSGRSTLYIAASQPGDSATYLCAVR
+>ENSP00000437362.1 pep:known chromosome:GRCh38:14:21887857:21888502:1 gene:ENSG00000211789.2 transcript:ENST00000390437.2 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+MKSLRVLLVILWLQLSWVWSQQKEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQY
+SGKSPELIMFIYSNGDKEDGRFTAQLNKASQYVSLLIRDSQPSDSATYLCAVN
+>ENSP00000374895.3 pep:known chromosome:GRCh38:7:142482548:142483019:1 gene:ENSG00000211725.3 transcript:ENST00000390372.3 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+MGPGLLCWVLLCLLGAGPVDAGVTQSPTHLIKTRGQQVTLRCSPISGHKSVSWYQQVLGQ
+GPQFIFQYYEKEERGRGNFPDRFSARQFPNYSSELNVNALLLGDSALYLCASSL
+>ENSP00000488152.1 pep:known chromosome:GRCh38:CHR_HSCHR7_2_CTG6:142374511:142375050:1 gene:ENSG00000282506.1 transcript:ENST00000631392.1 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+MGTRLLFWVAFCLLGADHTGAGVSQSPSNKVTEKGKDVELRCDPISGHTALYWYRQSLGQ
+GLEFLIYFQGNSAPDKSGLPSDRFSAERTGGSVSTLTIQRTQQEDSAVYLCASSL
+>ENSP00000446355.1 pep:known chromosome:GRCh38:14:21749178:21749705:1 gene:ENSG00000211779.3 transcript:ENST00000390427.3 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+MKTFAGFSFLFLWLQLDCMSRGEDVEQSLFLSVREGDSSVINCTYTDSSSTYLYWYKQEP
+GAGLQLLTYIFSNMDMKQDQRLTVLLNKKDKHLSLRIADTQTGDSAIYFCAES
+>ENSP00000479506.1 pep:known chromosome:GRCh38:7:142580917:142581427:1 gene:ENSG00000275158.1 transcript:ENST00000621184.1 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+MATRLLCCVVLCLLGEELIDARVTQTPRHKVTEMGQEVTMRCQPILGHNTVFWYRQTMMQ
+GLELLAYFRNRAPLDDSGMPKDRFSAEMPDATLATLKIQPSEPRDSAVYFCASGL
+>ENSP00000374920.2 pep:known chromosome:GRCh38:7:142656701:142657213:1 gene:ENSG00000211750.2 transcript:ENST00000390397.2 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+MASLLFFCGAFYLLGTGSMDADVTQTPRNRITKTGKRIMLECSQTKGHDRMYWYRQDPGL
+GLQLIYYSFDVKDINKGEISDGYSVSRQAQAKFSLSLESAIPNQTALYFCATSDL
+>ENSP00000374884.3 pep:known chromosome:GRCh38:7:142384329:142384841:1 gene:ENSG00000211714.3 transcript:ENST00000390361.3 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+MGTRLLCWAALCLLGADHTGAGVSQTPSNKVTEKGKDVELRCDPISGHTALYWYRQSLGQ
+GPEFLIYFQGTGAADDSGLPKDRFFAVRPEGSVSTLKIQRTEQGDSAAYLRASSL
+>ENSP00000480999.1 pep:known chromosome:GRCh38:7:142563740:142564245:1 gene:ENSG00000276953.1 transcript:ENST00000617347.1 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+MGSWTLCCVSLCILVAKHTDAGVIQSPRHEVTEMGQEVTLRCKPISGHDYLFWYRQTMMR
+GLELLIYFNNNVPIDDSGMPEDRFSAKMPNASFSTLKIQPSEPRDSAVYFCASSL
+>ENSP00000479267.1 pep:known chromosome:GRCh38:7:142544212:142544685:1 gene:ENSG00000275791.1 transcript:ENST00000611462.1 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+MGTRLFFYVALCLLWTGHMDAGITQSPRHKVTETGTPVTLRCHQTENHRYMYWYRQDPGH
+GLRLIHYSYGVKDTDKGEVSDGYSVSRSKTEDFLLTLESATSSQTSVYFCAISE
+>ENSP00000477916.1 pep:known chromosome:GRCh38:7:142560423:142560931:1 gene:ENSG00000274752.1 transcript:ENST00000620569.1 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+MDSWTFCCVSLCILVAKHTDAGVIQSPRHEVTEMGQEVTLRCKPISGHNSLFWYRQTMMR
+GLELLIYFNNNVPIDDSGMPEDRFSAKMPNASFSTLKIQPSEPRDSAVYFCASSL
+>ENSP00000451535.1 pep:known chromosome:GRCh38:14:21736152:21736982:1 gene:ENSG00000211778.2 transcript:ENST00000390426.2 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+MRQVARVIVFLTLSTLSLAKTTQPISMDSYEGQEVNITCSHNNIATNDYITWYQQFPSQG
+PRFIIQGYKTKVTNEVASLFIPADRKSSTLSLPRVSLSDTAVYYCLVGD
+>ENSP00000451822.1 pep:known chromosome:GRCh38:14:21965451:21966061:1 gene:ENSG00000211794.3 transcript:ENST00000390442.3 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+MMKSLRVLLVILWLQLSWVWSQQKEVEQDPGPLSVPEGAIVSLNCTYSNSAFQYFMWYRQ
+YSRKGPELLMYTYSSGNKEDGRFTAQVDKSSKYISLFIRDSQPSDSATYLCAMS
+>ENSP00000450505.1 pep:known chromosome:GRCh38:14:21978459:21979120:1 gene:ENSG00000211795.3 transcript:ENST00000390443.3 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+MLLLLVPAFQVIFTLGGTRAQSVTQLDSQVPVFEEAPVELRCNYSSSVSVYLFWYVQYPN
+QGLQLLLKYLSGSTLVESINGFEAEFNKSQTSFHLRKPSVHISDTAEYFCAVS
+>ENSP00000451359.1 pep:known chromosome:GRCh38:14:21990496:21990938:1 gene:ENSG00000211796.1 transcript:ENST00000390444.1 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene
+MKPTLISVLVIIFILRGTRAQRVTQPEKLLSVFKGAPVELKCNYSYSGSPELFWYVQYSR
+QRLQLLLRHISRESIKGFTADLNKGETSFHLKKPFAQEEDSAMYYCALS

tests/unit_tests/test_runner.py

@@ -0,0 +1,15 @@
+import unittest
+from pathlib import Path
+from unittest.mock import patch
+
+from oktoberfest.__main__ import main
+
+
+class TestRunner(unittest.TestCase):
+    """Test class for use cases of runner."""
+
+    def test_speclib_digest(self):
+        """Test the runner for a spectral library generation with a fasta digest."""
+        config_path = Path(__file__).parent / "configs" / "spectral_library_with_digest.json"
+        with patch("sys.argv", ["oktoberfest", f"--config_path={config_path}"]):
+            main()