diff --git a/pymzml/regex_patterns.py b/pymzml/regex_patterns.py index 5800fdb..f5f2fec 100755 --- a/pymzml/regex_patterns.py +++ b/pymzml/regex_patterns.py @@ -1,4 +1,5 @@ """Collection of regular expressions to catch spectrum XML-tags.""" + import re import regex diff --git a/pymzml/run.py b/pymzml/run.py index 3c81cc8..1c521c3 100644 --- a/pymzml/run.py +++ b/pymzml/run.py @@ -84,7 +84,7 @@ def __init__( build_index_from_scratch=False, skip_chromatogram=True, index_regex=None, - **kwargs + **kwargs, ): """Initialize and set required attributes.""" self.index_regex = index_regex @@ -296,7 +296,7 @@ def _obo_version_validator(version): 2018: "4.1.10", 2019: "4.1.22", 2024: "4.1.79", - 2025: "4.1.188" + 2025: "4.1.188", } version_fixed = None if obo_rgx.match(version): @@ -406,8 +406,8 @@ def _init_iter(self): self.info["data_processing_list"] = True self.info["data_processing_list_element"] = element elif element.tag.endswith("}cvParam"): - if self.term_is_a_member(element.attrib.get('accession'), "MS:1000494"): - self.info["instrument_name"] = element.attrib.get('name') + if self.term_is_a_member(element.attrib.get("accession"), "MS:1000494"): + self.info["instrument_name"] = element.attrib.get("name") elif element.tag.endswith("}spectrumList"): spec_cnt = element.attrib.get("count") @@ -470,9 +470,9 @@ def term_is_a_member(self, tested_term, member_of_term): try: term_in = self.OT[tested_term] if term_in: - is_member = self.OT.id[tested_term]['is_a'].startswith(member_of_term) + is_member = self.OT.id[tested_term]["is_a"].startswith(member_of_term) except KeyError: - print(f'term not found ({tested_term})') + print(f"term not found ({tested_term})") return is_member diff --git a/pymzml/utils/GSGW.py b/pymzml/utils/GSGW.py index 8eebc29..bb8ce76 100755 --- a/pymzml/utils/GSGW.py +++ b/pymzml/utils/GSGW.py @@ -256,7 +256,7 @@ def _write_identifier(self, identifier): Arguments: identifier (str or int): identifier to write into index """ - id_format = "{0:\xAC>" + str(self.max_idx_len) + "}" + id_format = "{0:\xac>" + str(self.max_idx_len) + "}" identifier = str(identifier) identifier = id_format.format(identifier).encode("latin-1") self.file_out.write(identifier) @@ -270,7 +270,7 @@ def _write_offset(self, offset): offset (int): offset which will be formatted and written into file index """ - offset_format = "{0:\xAC>" + str(self.max_offset_len) + "}" + offset_format = "{0:\xac>" + str(self.max_offset_len) + "}" offset = str(offset) offset = offset_format.format(offset).encode("latin-1") self.file_out.write(offset) diff --git a/pymzml/version.txt b/pymzml/version.txt index ff3b2cd..398d0da 100644 --- a/pymzml/version.txt +++ b/pymzml/version.txt @@ -1 +1 @@ -2.5.10 +2.5.11 diff --git a/tests/main_reader_test.py b/tests/main_reader_test.py index e551dac..d511b5d 100755 --- a/tests/main_reader_test.py +++ b/tests/main_reader_test.py @@ -30,7 +30,7 @@ def setUp(self): self.reader_uncompressed_unindexed = run.Reader(file_uncompressed_unindexed) self.reader_bad_obo_version = run.Reader(file_bad_obo_version) self.reader_set_obo_version = run.Reader( - file_bad_obo_version, obo_version="3.25.0" + file_bad_obo_version, obo_version="4.1.79" ) self.reader_set_year_obo_version = run.Reader( file_uncompressed_indexed, obo_version="23:06:2017" @@ -76,7 +76,7 @@ def test_init_iter(self): run_id = self.reader_uncompressed_unindexed.info["run_id"] start_time = self.reader_uncompressed_unindexed.info["start_time"] self.assertEqual(mzml_version, "1.1.0") - self.assertEqual(obo_version, "3.25.0") + self.assertEqual(obo_version, "4.1.79") self.assertIsInstance(spec_count, int) self.assertEqual(run_id, "exp105-01-ds5562-Pos") self.assertEqual(start_time, "2013-09-10T10:31:08Z") @@ -87,7 +87,7 @@ def test_init_iter(self): run_id = self.reader_uncompressed_unindexed.info["run_id"] start_time = self.reader_uncompressed_unindexed.info["start_time"] self.assertEqual(mzml_version, "1.1.0") - self.assertEqual(obo_version, "3.25.0") + self.assertEqual(obo_version, "4.1.79") self.assertIsInstance(spec_count, int) self.assertEqual(run_id, "exp105-01-ds5562-Pos") self.assertEqual(start_time, "2013-09-10T10:31:08Z") @@ -98,7 +98,7 @@ def test_init_iter(self): run_id = self.reader_uncompressed_unindexed.info["run_id"] start_time = self.reader_uncompressed_unindexed.info["start_time"] self.assertEqual(mzml_version, "1.1.0") - self.assertEqual(obo_version, "3.25.0") + self.assertEqual(obo_version, "4.1.79") self.assertIsInstance(spec_count, int) self.assertEqual(run_id, "exp105-01-ds5562-Pos") self.assertEqual(start_time, "2013-09-10T10:31:08Z") @@ -110,7 +110,7 @@ def test_init_iter(self): start_time = self.reader_uncompressed_unindexed.info["start_time"] self.assertEqual(mzml_version, "1.1.0") - self.assertEqual(obo_version, "3.25.0") + self.assertEqual(obo_version, "4.1.79") self.assertIsInstance(spec_count, int) self.assertEqual(run_id, "exp105-01-ds5562-Pos") self.assertEqual(start_time, "2013-09-10T10:31:08Z") @@ -122,8 +122,8 @@ def test_init_iter(self): start_time = self.reader_bad_obo_version.info["start_time"] self.assertEqual(mzml_version, "1.1.0") - # run._obo_version_validator 2017 default obo = 4.1.0 - self.assertEqual(obo_version, "4.1.0") + # run._obo_version_validator 2017 default obo = 4.1.79 + self.assertEqual(obo_version, "4.1.79") self.assertIsInstance(spec_count, int) self.assertEqual(run_id, "exp105-01-ds5562-Pos") self.assertEqual(start_time, "2013-09-10T10:31:08Z") @@ -135,7 +135,7 @@ def test_init_iter(self): start_time = self.reader_set_obo_version.info["start_time"] self.assertEqual(mzml_version, "1.1.0") - self.assertEqual(obo_version, "3.25.0") + self.assertEqual(obo_version, "4.1.79") self.assertIsInstance(spec_count, int) self.assertEqual(run_id, "exp105-01-ds5562-Pos") self.assertEqual(start_time, "2013-09-10T10:31:08Z") @@ -147,7 +147,7 @@ def test_init_iter(self): start_time = self.reader_set_year_obo_version.info["start_time"] self.assertEqual(mzml_version, "1.1.0") - # run._obo_version_validator 2017 default obo = 4.1.0 + # run._obo_version_validator 2017 default obo = 4.1.79 self.assertEqual(obo_version, "4.1.0") self.assertIsInstance(spec_count, int) self.assertEqual(run_id, "exp105-01-ds5562-Pos") @@ -174,7 +174,7 @@ def test_init_iter(self): self.assertEqual(mzml_version, "1.1.0") # run._obo_version_validator set invalid obo = 1.1.0 - self.assertEqual(obo_version, "1.1.0") + self.assertEqual(obo_version, "4.1.79") self.assertIsInstance(spec_count, int) self.assertEqual(run_id, "exp105-01-ds5562-Pos") self.assertEqual(start_time, "2013-09-10T10:31:08Z")