Merge pull request #146 from wilhelm-lab/release/0.7.5

Release/0.7.5
wilhelm-lab · Oct 10, 2024 · 1f1bb24 · 1f1bb24
2 parents 2595491 + f786831
commit 1f1bb24
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Showing 10 changed files with 20 additions and 22 deletions.
diff --git 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
@@ -1,5 +1,5 @@
-name-template: "0.7.4 " # <<COOKIETEMPLE_FORCE_BUMP>>
-tag-template: 0.7.4 # <<COOKIETEMPLE_FORCE_BUMP>>
+name-template: "0.7.5 " # <<COOKIETEMPLE_FORCE_BUMP>>
+tag-template: 0.7.5 # <<COOKIETEMPLE_FORCE_BUMP>>
 exclude-labels:
     - "skip-changelog"
 

diff --git 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
@@ -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
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "spectrum_fundamentals"
-version = "0.7.4"  # <<COOKIETEMPLE_FORCE_BUMP>>
+version = "0.7.5"  # <<COOKIETEMPLE_FORCE_BUMP>>
 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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