Merge pull request #115 from wilhelm-lab/patch/0.4.4

Patch/0.4.4

.cookietemple.yml

@@ -15,5 +15,5 @@ full_name: Mario Picciani
 email: [email protected]
 project_name: spectrum_io
 project_short_description: IO related functionalities for oktoberfest.
-version: 0.4.3
+version: 0.4.4
 license: MIT

.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.4.3 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
-tag-template: 0.4.3 # <<COOKIETEMPLE_FORCE_BUMP>>
+name-template: "0.4.4 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
+tag-template: 0.4.4 # <<COOKIETEMPLE_FORCE_BUMP>>
 exclude-labels:
     - "skip-changelog"
 

.github/workflows/publish_docs.yml

@@ -30,7 +30,7 @@ jobs:
 
             - name: Deploy
               if: ${{ github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main'}}
-              uses: peaceiris/actions-gh-pages@v3
+              uses: peaceiris/actions-gh-pages@v4
               with:
                   github_token: ${{ secrets.GITHUB_TOKEN }}
                   publish_dir: ./docs/_build/html

.github/workflows/release_drafter.yml

@@ -14,6 +14,6 @@ jobs:
     update_release_draft:
         runs-on: ubuntu-latest
         steps:
-            - uses: release-drafter/release-drafter@v5
+            - uses: release-drafter/release-drafter@v6
               env:
                   GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/run_tests.yml

@@ -165,4 +165,4 @@ jobs:
               run: nox --force-color --session=coverage -- xml -i
 
             - name: Upload coverage report
-              uses: codecov/codecov-action@v3.1.1
+              uses: codecov/codecov-action@v4.4.1

cookietemple.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.3
+current_version = 0.4.4
 
 [bumpversion_files_whitelisted]
 init_file = spectrum_io/__init__.py

docs/conf.py

@@ -53,9 +53,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = "0.4.3"
+version = "0.4.4"
 # The full version, including alpha/beta/rc tags.
-release = "0.4.3"
+release = "0.4.4"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "spectrum_io"
-version = "0.4.3"  # <<COOKIETEMPLE_FORCE_BUMP>>
+version = "0.4.4"  # <<COOKIETEMPLE_FORCE_BUMP>>
 description = "IO related functionalities for oktoberfest."
 authors = ["Wilhelmlab at Technical University of Munich"]
 license = "MIT"
@@ -28,8 +28,8 @@ pandas = "^1.3.0"
 h5py = "^3.1.0"
 pymzml = "^2.5.0"
 pyteomics = "^4.3.3"
-lxml= '^4.5.2'
-spectrum-fundamentals = ">=0.5.2,<0.6.0"
+lxml= '>=4.5.2,<6.0.0'
+spectrum-fundamentals = ">=0.5.4,<0.6.0"
 alphatims = "^1.0.8"
 sortedcontainers = "^2.4.0"
 

spectrum_io/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = "Mario Picciani"
 __email__ = "[email protected]"
-__version__ = "0.4.3"
+__version__ = "0.4.4"
 
 import logging
 import logging.handlers

spectrum_io/__main__.py

@@ -5,7 +5,7 @@
 
 
 @click.command()
-@click.version_option(version="0.4.3", message=click.style("spectrum_io Version: 0.4.3"))
+@click.version_option(version="0.4.4", message=click.style("spectrum_io Version: 0.4.4"))
 def main() -> None:
     """spectrum_io."""
 

spectrum_io/d/bruker.py

@@ -184,5 +184,6 @@ def read_and_aggregate_timstof(source: Path, tims_meta_file: Path) -> pd.DataFra
     df_combined["RAW_FILE"] = source.stem
     df_combined["MASS_ANALYZER"] = "TOF"
     df_combined["FRAGMENTATION"] = "HCD"
+    df_combined["INSTRUMENT_TYPES"] = "TIMSTOF"
 
     return df_combined

spectrum_io/search_result/sage.py

@@ -58,7 +58,7 @@ def update_columns_for_prosit(df: pd.DataFrame, tmt_labeled: str) -> pd.DataFram
         )
 
         # removing .mzML
-        df["RAW_FILE"] = df["RAW_FILE"].str.replace(".mzML", "", regex=True)
+        df["RAW_FILE"] = df["RAW_FILE"].str.replace(r"\.mz[M|m][l|L]", "", regex=True)
         # extracting only the scan number
         df["SCAN_NUMBER"] = [int(x.rsplit("=", 1)[-1]) for x in df["SCAN_NUMBER"]]
         # creating a column of decoys and targets

spectrum_io/search_result/search_results.py

@@ -22,7 +22,7 @@ def filter_valid_prosit_sequences(df: pd.DataFrame) -> pd.DataFrame:
     # retain only peptides that fall within [7, 30] length supported by Prosit
     df = df[(df["PEPTIDE_LENGTH"] <= 30) & (df["PEPTIDE_LENGTH"] >= 7)]
     # remove unsupported mods to exclude
-    unsupported_mods = [r"Acetyl \(Protein N\-term\)", "ac", r"\[[0-9]+\]"]
+    unsupported_mods = [r"Acetyl \(Protein N\-term\)", "ac", r"\[[0-9]+\]", r"\+"]
     exclude_mods_pattern = re.compile("|".join(unsupported_mods))
     df = df[~df["MODIFIED_SEQUENCE"].str.contains(exclude_mods_pattern)]
     # remove non-canonical aas

tests/unit_tests/data/sage_output.tsv

@@ -1,17 +1,17 @@
 peptide	proteins	num_proteins	filename	scannr	rank	label	expmass	calcmass	charge	peptide_len	missed_cleavages	isotope_error	precursor_ppm	fragment_ppm	hyperscore	delta_next	delta_best	rt	aligned_rt	predicted_rt	delta_rt_model	matched_peaks	longest_b	longest_y	longest_y_pct	matched_intensity_pct	scored_candidates	poisson	sage_discriminant_score	posterior_error	spectrum_q	peptide_q	protein_q	ms1_intensity	ms2_intensity
 [+229.1629]-HLDGGAEQSLLFVAGM[+15.9949]R	rev_sp|P26006-1|ITA3_HUMAN;rev_sp|P26006|ITA3_HUMAN	2	GN20170722_SK_HLA_G0103_R1_01.mzML	controllerType=0 controllerNumber=1 scan=50989	1	-1	2199.172	2045.0568	2	17	0	0.0	72623.49	7.826053	18.084579770792818	0.20642824189008735	0.0	113.94822	0.9495685	0.0	0.9495685	4	2	1	0.05882353	1.318411	84602	-2.0562283019710534	-0.37137848	-0.35820845	0.30232558	0.5880901	0.5815684	926232.0	7361.109
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-[+229.1629]-LTVEC[+57.0214]MPTIASDDLPVGTLQESEVSM[+15.9949]TGPG	rev_tr|C9JVX2|C9JVX2_HUMAN	1	GN20170722_SK_HLA_G0103_R1_01.mzML	controllerType=0 controllerNumber=1 scan=45450	1	-1	3533.4688	3378.6082	3	30	0	0.0	44808.7	2.583788	18.628243636678995	0.4911733270242351	0.0	102.02221	0.8501851	0.0	0.8501851	4	1	2	0.06666667	1.6194082	80638	-2.046675752396668	-0.3724502	-0.35820845	0.30232558	0.5880901	0.5815684	643726.75	8588.239
+[+229.1629]-LTVEC[+57.0215]MPTIASDDLPVGTLQESEVSM[+15.9949]TGPG	rev_tr|C9JVX2|C9JVX2_HUMAN	1	GN20170722_SK_HLA_G0103_R1_01.mzML	controllerType=0 controllerNumber=1 scan=45450	1	-1	3533.4688	3378.6082	3	30	0	0.0	44808.7	2.583788	18.628243636678995	0.4911733270242351	0.0	102.02221	0.8501851	0.0	0.8501851	4	1	2	0.06666667	1.6194082	80638	-2.046675752396668	-0.3724502	-0.35820845	0.30232558	0.5880901	0.5815684	643726.75	8588.239
 [+229.1629]-VNM[+15.9949]RTSSSIQNEDEATSMELIAPGP	sp|Q9Y5Y9|SCNAA_HUMAN;tr|A0A2R8Y6J6|A0A2R8Y6J6_HUMAN;tr|A0A590UJM0|A0A590UJM0_HUMAN	3	GN20170722_SK_HLA_G0103_R1_01.mzML	controllerType=0 controllerNumber=1 scan=45493	1	1	3074.5525	2921.3948	3	25	1	0.0	51087.08	5.391072	19.979716393086438	0.2293833747943026	0.0	102.12942	0.85107845	0.0	0.85107845	5	1	2	0.08	1.4697478	154744	-2.71207222963538	-0.3737817	-0.35820845	0.30232558	0.5880901	0.5815684	1085421.8	8865.469
 [+229.1629]-VGEQEAPHEGGHPGSDSARASMADWLR	sp|Q9H093|NUAK2_HUMAN	1	GN20170722_SK_HLA_G0103_R1_01.mzML	controllerType=0 controllerNumber=1 scan=41946	1	1	3229.3804	3075.4417	3	27	1	0.0	48832.06	2.6081188	20.936078174830033	0.05364075290029291	0.0	93.63916	0.7803263	0.0	0.7803263	4	1	1	0.037037037	6.790568	109802	-2.034297610829216	-0.37500644	-0.35820845	0.30232558	0.5880901	0.5815684	604286.9	36628.875
-[+229.1629]-EM[+15.9949]VSPTDSC[+57.0214]VRVSVRDLPQFHVSVVDM[+15.9949]DR	rev_sp|Q9HCN3|PGAP6_HUMAN;rev_tr|K4DI83|K4DI83_HUMAN	2	GN20170722_SK_HLA_G0103_R1_01.mzML	controllerType=0 controllerNumber=1 scan=39750	1	-1	3924.602	3620.7583	3	29	2	0.0	80537.9	4.2269964	17.954540767022678	0.13827490088740646	0.0	88.40008	0.73666734	0.0	0.73666734	4	1	2	0.06896552	2.1663432	50127	-2.0296029706779146	-0.375757	-0.35820845	0.30232558	0.5880901	0.5815684	1711349.0	6906.8516
+[+229.1629]-EM[+15.9949]VSPTDSC[+57.0215]VRVSVRDLPQFHVSVVDM[+15.9949]DR	rev_sp|Q9HCN3|PGAP6_HUMAN;rev_tr|K4DI83|K4DI83_HUMAN	2	GN20170722_SK_HLA_G0103_R1_01.mzML	controllerType=0 controllerNumber=1 scan=39750	1	-1	3924.602	3620.7583	3	29	2	0.0	80537.9	4.2269964	17.954540767022678	0.13827490088740646	0.0	88.40008	0.73666734	0.0	0.73666734	4	1	2	0.06896552	2.1663432	50127	-2.0296029706779146	-0.375757	-0.35820845	0.30232558	0.5880901	0.5815684	1711349.0	6906.8516
 [+229.1629]-K[+229.1629]M[+15.9949]EEDIYTNLSK[+229.1629]METVLGQSMSSLPLSYR	sp|Q8WXH0-2|SYNE2_HUMAN;sp|Q8WXH0|SYNE2_HUMAN;tr|A0A0A0MRE3|A0A0A0MRE3_HUMAN;tr|G3V5X4|G3V5X4_HUMAN	4	GN20170722_SK_HLA_G0103_R1_01.mzML	controllerType=0 controllerNumber=1 scan=45441	2	1	4205.6133	4053.1077	4	29	2	0.0	36932.02	7.9742827	19.962357128713123	0.0	0.0	101.99851	0.8499876	0.0	0.8499876	4	1	2	0.06896552	2.6182032	65126	-1.9825140292603154	-0.37760013	-0.35820845	0.30232558	0.5880901	0.5815684	1558514.0	15372.994
-[+229.1629]-TC[+57.0214]SK[+229.1629]SQGSWGNREIVIIDTPDMFSWK[+229.1629]	sp|Q9UG22|GIMA2_HUMAN	1	GN20170722_SK_HLA_G0103_R1_01.mzML	controllerType=0 controllerNumber=1 scan=36758	1	1	3881.789	3728.9263	3	26	2	0.0	40170.414	8.588704	18.776753308950084	2.853361183504054	0.0	81.83095	0.6819246	0.0	0.6819246	4	1	1	0.03846154	2.170038	54463	-2.02115128698497	-0.3785715	-0.35820845	0.30232558	0.5880901	0.5815684	1264436.8	13284.256
+[+229.1629]-TC[+57.0215]SK[+229.1629]SQGSWGNREIVIIDTPDMFSWK[+229.1629]	sp|Q9UG22|GIMA2_HUMAN	1	GN20170722_SK_HLA_G0103_R1_01.mzML	controllerType=0 controllerNumber=1 scan=36758	1	1	3881.789	3728.9263	3	26	2	0.0	40170.414	8.588704	18.776753308950084	2.853361183504054	0.0	81.83095	0.6819246	0.0	0.6819246	4	1	1	0.03846154	2.170038	54463	-2.02115128698497	-0.3785715	-0.35820845	0.30232558	0.5880901	0.5815684	1264436.8	13284.256
 [+229.1629]-M[+15.9949]SLGRAAPSAPGR	rev_sp|P51693-2|APLP1_HUMAN;rev_sp|P51693|APLP1_HUMAN;rev_tr|K7EMS1|K7EMS1_HUMAN	3	GN20170722_SK_HLA_G0103_R1_01.mzML	controllerType=0 controllerNumber=1 scan=49100	1	-1	1669.267	1514.819	2	13	1	0.0	97012.45	4.073574	20.66450790410668	0.2021918361478079	0.0	109.23304	0.91027534	0.0	0.91027534	5	1	3	0.23076923	1.8854505	176106	-2.684809584132347	-0.37956935	-0.35820845	0.30232558	0.5880901	0.5815684	611105.25	12195.32
-[+229.1629]-C[+57.0214]LIQM[+15.9949]GAAVEAK[+229.1629]AYNGNTALHVAASLQYR	tr|H7C5S1|H7C5S1_HUMAN	1	GN20170722_SK_HLA_G0103_R1_01.mzML	controllerType=0 controllerNumber=1 scan=37376	1	1	3897.3843	3593.885	3	29	1	0.0	81027.46	5.0039053	21.88178474607965	0.07848479239995854	0.0	83.277466	0.6939789	0.0	0.6939789	4	1	2	0.06896552	2.1495197	58331	-2.045800246831915	-0.37965888	-0.35820845	0.30232558	0.5880901	0.5815684	18796730.0	52520.473
+[+229.1629]-C[+57.0215]LIQM[+15.9949]GAAVEAK[+229.1629]AYNGNTALHVAASLQYR	tr|H7C5S1|H7C5S1_HUMAN	1	GN20170722_SK_HLA_G0103_R1_01.mzML	controllerType=0 controllerNumber=1 scan=37376	1	1	3897.3843	3593.885	3	29	1	0.0	81027.46	5.0039053	21.88178474607965	0.07848479239995854	0.0	83.277466	0.6939789	0.0	0.6939789	4	1	2	0.06896552	2.1495197	58331	-2.045800246831915	-0.37965888	-0.35820845	0.30232558	0.5880901	0.5815684	18796730.0	52520.473
 [+229.1629]-M[+15.9949]EESLNIVK[+229.1629]YTAFLYNDQLIWSGLEQDDMR	sp|P86790|CCZ1B_HUMAN;sp|P86791|CCZ1_HUMAN	2	GN20170722_SK_HLA_G0103_R1_01.mzML	controllerType=0 controllerNumber=1 scan=41296	1	1	4398.7207	4095.037	3	30	1	0.0	71507.48	3.7571762	22.91659667770412	2.159702635767953	0.0	92.108765	0.76757306	0.0	0.76757306	4	2	2	0.06666667	18.10546	11995	-2.0440490580574484	-0.38045537	-0.35820845	0.30232558	0.5880901	0.5815684	1328658.9	71828.805
-[+229.1629]-LNVEGTERGSC[+57.0214]GRK[+229.1629]	sp|O75078-2|ADA11_HUMAN;sp|O75078|ADA11_HUMAN;tr|B4DKD2|B4DKD2_HUMAN;tr|K7EKA8|K7EKA8_HUMAN	4	GN20170722_SK_HLA_G0103_R1_01.mzML	controllerType=0 controllerNumber=1 scan=40784	2	1	2174.1533	2020.0887	3	14	2	0.0	73464.8	5.374492	21.842498887625368	0.6170763228642393	0.0	90.874275	0.75728565	0.0	0.75728565	5	3	2	0.14285715	2.8490458	237683	-2.6522210241481585	-0.3812077	-0.35820845	0.30232558	0.5880901	0.5815684	1290087.5	21134.262
-[+229.1629]-C[+57.0214]NRGWTALHESVSR	sp|Q96Q27-1|ASB2_HUMAN;sp|Q96Q27|ASB2_HUMAN;tr|G3V2Z2|G3V2Z2_HUMAN;tr|G3V4B2|G3V4B2_HUMAN	4	GN20170722_SK_HLA_G0103_R1_01.mzML	controllerType=0 controllerNumber=1 scan=51002	2	1	2055.9688	1900.9526	2	14	1	0.0	78351.875	5.277066	17.823081883875247	0.012034867562086049	0.0	113.98048	0.9498373	0.0	0.9498373	4	1	1	0.071428575	1.2503061	115129	-2.0307522097044646	-0.3828116	-0.35820845	0.30232558	0.5880901	0.5815684	977832.06	5506.2334
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tests/unit_tests/test_sage.py

@@ -12,7 +12,8 @@ class TestSage(unittest.TestCase):
     def test_read_sage(self):
         """Test function for reading sage results and transforming to Prosit format."""
         expected_sage_internal_path = Path(__file__).parent / "data" / "sage_output_internal.csv"
-        internal_search_results_df = Sage(Path(__file__).parent / "data" / "sage_output.tsv").read_result()
+        internal_search_results_df = (
+            Sage(Path(__file__).parent / "data" / "sage_output.tsv").read_result().reset_index(drop=True)
+        )
         expected_df = pd.read_csv(expected_sage_internal_path)
-
         pd.testing.assert_frame_equal(internal_search_results_df, expected_df)