diff --git a/.cookietemple.yml b/.cookietemple.yml index 690429d..c00f97f 100644 --- a/.cookietemple.yml +++ b/.cookietemple.yml @@ -15,5 +15,5 @@ full_name: Victor Giurcoiu email: victor.giurcoiu@tum.de project_name: spectrum_fundamentals project_short_description: Fundamentals public repo -version: 0.7.4 +version: 0.7.5 license: MIT diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml index 9c78e48..92bced3 100644 --- a/.github/release-drafter.yml +++ b/.github/release-drafter.yml @@ -1,5 +1,5 @@ -name-template: "0.7.4 " # <> -tag-template: 0.7.4 # <> +name-template: "0.7.5 " # <> +tag-template: 0.7.5 # <> exclude-labels: - "skip-changelog" diff --git a/cookietemple.cfg b/cookietemple.cfg index 2c55632..afd4846 100644 --- a/cookietemple.cfg +++ b/cookietemple.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.7.4 +current_version = 0.7.5 [bumpversion_files_whitelisted] init_file = spectrum_fundamentals/__init__.py diff --git a/docs/conf.py b/docs/conf.py index 2833a7f..528c6b8 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -52,9 +52,9 @@ # the built documents. # # The short X.Y version. -version = "0.7.4" +version = "0.7.5" # The full version, including alpha/beta/rc tags. -release = "0.7.4" +release = "0.7.5" # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/pyproject.toml b/pyproject.toml index 2c6a528..9ef31fc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "spectrum_fundamentals" -version = "0.7.4" # <> +version = "0.7.5" # <> description = "Fundamental functions, annotation pipeline and constants for oktoberfest" authors = ["Wilhelmlab at Technical University of Munich"] license = "MIT" diff --git a/spectrum_fundamentals/__init__.py b/spectrum_fundamentals/__init__.py index d4fa09a..9bb0ba3 100644 --- a/spectrum_fundamentals/__init__.py +++ b/spectrum_fundamentals/__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__ = "0.7.4" +__version__ = "0.7.5" import logging import logging.handlers diff --git a/spectrum_fundamentals/__main__.py b/spectrum_fundamentals/__main__.py index f03da2d..50831d4 100644 --- a/spectrum_fundamentals/__main__.py +++ b/spectrum_fundamentals/__main__.py @@ -5,7 +5,7 @@ @click.command() -@click.version_option(version="0.7.4", message=click.style("spectrum_fundamentals Version: 0.7.4")) +@click.version_option(version="0.7.5", message=click.style("spectrum_fundamentals Version: 0.7.5")) def main() -> None: """spectrum_fundamentals.""" diff --git a/spectrum_fundamentals/metrics/percolator.py b/spectrum_fundamentals/metrics/percolator.py index 4e54f68..374658f 100644 --- a/spectrum_fundamentals/metrics/percolator.py +++ b/spectrum_fundamentals/metrics/percolator.py @@ -336,9 +336,7 @@ def add_percolator_metadata_columns(self): else: spec_id_cols = ["RAW_FILE", "SCAN_NUMBER", "MODIFIED_SEQUENCE", "PRECURSOR_CHARGE"] self.metrics_val["Peptide"] = self.metadata["MODIFIED_SEQUENCE"].apply(lambda x: "_." + x + "._") - self.metrics_val["Proteins"] = self.metadata[ - "MODIFIED_SEQUENCE" - ] # we don't need the protein ID to get PSM / peptide results, fill with peptide sequence + self.metrics_val["Proteins"] = self.metadata["PROTEINS"] if "SCAN_EVENT_NUMBER" in self.metadata.columns: spec_id_cols.append("SCAN_EVENT_NUMBER") diff --git a/tests/unit_tests/data/perc_input.csv b/tests/unit_tests/data/perc_input.csv index 6d7bfe4..2e7e566 100644 --- a/tests/unit_tests/data/perc_input.csv +++ b/tests/unit_tests/data/perc_input.csv @@ -1,9 +1,9 @@ -,RAW_FILE,SCAN_NUMBER,MODIFIED_SEQUENCE,SEQUENCE,PRECURSOR_CHARGE,MASS,CALCULATED_MASS,SCORE,REVERSE,FRAGMENTATION,MASS_ANALYZER,SCAN_EVENT_NUMBER,RETENTION_TIME,PREDICTED_IRT,COLLISION_ENERGY -0,20210122_0263_TMUCLHan_Peiru_DDA_IP_C797S_02,7978,AAIGEATRL,AAIGEATRL,2,900.50345678,900.50288029264,60.43600000000001,False,HCD,FTMS,1,0.5000000183883155,0.5000000323590892,30.0 -1,20210122_0263_TMUCLHan_Peiru_DDA_IP_C797S_02,12304,AAVPRAAFL,AAVPRAAFL,2,914.53379,914.53379,34.006,True,HCD,FTMS,2,1.000000038995633,1.5000000246189773,30.0 -2,20210122_0263_TMUCLHan_Peiru_DDA_IP_C797S_02,12398,AAYFGVYDTAK,AAYFGVYDTAK,2,1204.5764,1204.5764,39.97399999999999,True,HCD,FTMS,3,1.5000000993570157,2.500000056694346,30.0 -3,20210122_0263_TMUCLHan_Peiru_DDA_IP_C797S_02,11716,AAYYHPSYL,AAYYHPSYL,2,1083.5025,1083.5025,99.919,False,HCD,FTMS,4,2.0000000098074193,3.5000000203256407,30.0 -4,20210122_0263_TMUCLHan_Peiru_DDA_IP_C797S_02,5174,AEDLNTRVA,AEDLNTRVA,2,987.49852,987.49852,87.802,False,HCD,FTMS,5,2.500000083793533,4.5000000747038005,30.0 -5,20210122_0263_TMUCLHan_Peiru_DDA_IP_C797S_02,5174,AEDLNTRVA,AEDLNTRVA,2,987.49852,987.49852,62.802,False,HCD,FTMS,6,3.0000000338727677,5.5000000960095505,30.0 -6,20210122_0263_TMUCLHan_Peiru_DDA_IP_C797S_02,5174,AEDLNTRVA,AEDLNTRVA,2,987.49852,987.49852,79.802,False,HCD,FTMS,7,3.500000001673834,6.5000000134594345,30.0 -7,20210122_0263_TMUCLHan_Peiru_DDA_IP_C797S_02,5174,AEDLNTRVA,AEDLNTRVA,2,987.49852,987.49852,79.802,False,HCD,FTMS,8,4.000000066050141,7.500000085284446,30.0 +,RAW_FILE,SCAN_NUMBER,MODIFIED_SEQUENCE,SEQUENCE,PRECURSOR_CHARGE,MASS,CALCULATED_MASS,SCORE,REVERSE,FRAGMENTATION,MASS_ANALYZER,SCAN_EVENT_NUMBER,RETENTION_TIME,PREDICTED_IRT,COLLISION_ENERGY,PROTEINS +0,20210122_0263_TMUCLHan_Peiru_DDA_IP_C797S_02,7978,AAIGEATRL,AAIGEATRL,2,900.5034568,900.5028803,60.436,FALSE,HCD,FTMS,1,0.500000018,0.500000032,30,sp|O23523|RGGA_ARATH +1,20210122_0263_TMUCLHan_Peiru_DDA_IP_C797S_02,12304,AAVPRAAFL,AAVPRAAFL,2,914.53379,914.53379,34.006,TRUE,HCD,FTMS,2,1.000000039,1.500000025,30,sp|O23523|RGGA_ARATH +2,20210122_0263_TMUCLHan_Peiru_DDA_IP_C797S_02,12398,AAYFGVYDTAK,AAYFGVYDTAK,2,1204.5764,1204.5764,39.974,TRUE,HCD,FTMS,3,1.500000099,2.500000057,30,sp|O23523|RGGA_ARATH +3,20210122_0263_TMUCLHan_Peiru_DDA_IP_C797S_02,11716,AAYYHPSYL,AAYYHPSYL,2,1083.5025,1083.5025,99.919,FALSE,HCD,FTMS,4,2.00000001,3.50000002,30,sp|O23523|RGGA_ARATH +4,20210122_0263_TMUCLHan_Peiru_DDA_IP_C797S_02,5174,AEDLNTRVA,AEDLNTRVA,2,987.49852,987.49852,87.802,FALSE,HCD,FTMS,5,2.500000084,4.500000075,30,sp|O23523|RGGA_ARATH +5,20210122_0263_TMUCLHan_Peiru_DDA_IP_C797S_02,5174,AEDLNTRVA,AEDLNTRVA,2,987.49852,987.49852,62.802,FALSE,HCD,FTMS,6,3.000000034,5.500000096,30,sp|O23523|RGGA_ARATH +6,20210122_0263_TMUCLHan_Peiru_DDA_IP_C797S_02,5174,AEDLNTRVA,AEDLNTRVA,2,987.49852,987.49852,79.802,FALSE,HCD,FTMS,7,3.500000002,6.500000013,30,sp|O23523|RGGA_ARATH +7,20210122_0263_TMUCLHan_Peiru_DDA_IP_C797S_02,5174,AEDLNTRVA,AEDLNTRVA,2,987.49852,987.49852,79.802,FALSE,HCD,FTMS,8,4.000000066,7.500000085,30,sp|O23523|RGGA_ARATH diff --git a/tests/unit_tests/test_percolator.py b/tests/unit_tests/test_percolator.py index 5e736f4..3651d21 100644 --- a/tests/unit_tests/test_percolator.py +++ b/tests/unit_tests/test_percolator.py @@ -395,7 +395,7 @@ def test_calc(self): # np.testing.assert_almost_equal(percolator.metrics_val['ExpMass'][0], 900.50345678) np.testing.assert_string_equal(percolator.metrics_val["Peptide"][0], "_.AAIGEATRL._") np.testing.assert_string_equal( - percolator.metrics_val["Proteins"][0], "AAIGEATRL" + percolator.metrics_val["Proteins"][0], "sp|O23523|RGGA_ARATH" ) # we don't need the protein ID to get PSM / peptide results # features