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Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/compound_annotation/van_krevelen_data_generator/van_krevelen_data_generator.py","line":118,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/compound_annotation/van_krevelen_data_generator/van_krevelen_data_generator.py:118"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/compound_annotation/van_krevelen_data_generator/van_krevelen_data_generator.py","line":129,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/compound_annotation/van_krevelen_data_generator/van_krevelen_data_generator.py:129"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/drug_metabolism/drug_metabolite_screener/drug_metabolite_screener.py","line":170,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/drug_metabolism/drug_metabolite_screener/drug_metabolite_screener.py:170"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/drug_metabolism/mass_difference_network_builder/mass_difference_network_builder.py","line":63,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/drug_metabolism/mass_difference_network_builder/mass_difference_network_builder.py:63"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/drug_metabolism/mass_difference_network_builder/mass_difference_network_builder.py","line":136,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/drug_metabolism/mass_difference_network_builder/mass_difference_network_builder.py:136"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/drug_metabolism/mass_difference_network_builder/mass_difference_network_builder.py","line":144,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/drug_metabolism/mass_difference_network_builder/mass_difference_network_builder.py:144"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/export/gnps_fbmn_exporter/gnps_fbmn_exporter.py","line":59,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/export/gnps_fbmn_exporter/gnps_fbmn_exporter.py:59"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/export/gnps_fbmn_exporter/gnps_fbmn_exporter.py","line":146,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/export/gnps_fbmn_exporter/gnps_fbmn_exporter.py:146"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/export/gnps_fbmn_exporter/gnps_fbmn_exporter.py","line":179,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/export/gnps_fbmn_exporter/gnps_fbmn_exporter.py:179"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/export/gnps_fbmn_exporter/gnps_fbmn_exporter.py","line":195,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/export/gnps_fbmn_exporter/gnps_fbmn_exporter.py:195"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/export/kovats_ri_calculator/kovats_ri_calculator.py","line":42,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/export/kovats_ri_calculator/kovats_ri_calculator.py:42"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/export/kovats_ri_calculator/kovats_ri_calculator.py","line":166,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/export/kovats_ri_calculator/kovats_ri_calculator.py:166"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/export/kovats_ri_calculator/kovats_ri_calculator.py","line":170,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/export/kovats_ri_calculator/kovats_ri_calculator.py:170"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/export/sirius_exporter/sirius_exporter.py","line":36,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/export/sirius_exporter/sirius_exporter.py:36"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/export/sirius_exporter/sirius_exporter.py","line":85,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/export/sirius_exporter/sirius_exporter.py:85"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/feature_processing/adduct_group_analyzer/adduct_group_analyzer.py","line":125,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/feature_processing/adduct_group_analyzer/adduct_group_analyzer.py:125"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/feature_processing/adduct_group_analyzer/adduct_group_analyzer.py","line":134,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/feature_processing/adduct_group_analyzer/adduct_group_analyzer.py:134"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/feature_processing/blank_subtraction_tool/blank_subtraction_tool.py","line":93,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/feature_processing/blank_subtraction_tool/blank_subtraction_tool.py:93"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/feature_processing/blank_subtraction_tool/blank_subtraction_tool.py","line":99,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/feature_processing/blank_subtraction_tool/blank_subtraction_tool.py:99"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/feature_processing/blank_subtraction_tool/blank_subtraction_tool.py","line":112,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/feature_processing/blank_subtraction_tool/blank_subtraction_tool.py:112"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/feature_processing/duplicate_feature_detector/duplicate_feature_detector.py","line":134,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/feature_processing/duplicate_feature_detector/duplicate_feature_detector.py:134"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/feature_processing/duplicate_feature_detector/duplicate_feature_detector.py","line":142,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/feature_processing/duplicate_feature_detector/duplicate_feature_detector.py:142"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/feature_processing/isf_detector/isf_detector.py","line":189,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/feature_processing/isf_detector/isf_detector.py:189"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/feature_processing/isf_detector/isf_detector.py","line":199,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/feature_processing/isf_detector/isf_detector.py:199"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/feature_processing/mass_defect_filter/mass_defect_filter.py","line":141,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/feature_processing/mass_defect_filter/mass_defect_filter.py:141"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/feature_processing/mass_defect_filter/mass_defect_filter.py","line":159,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/feature_processing/mass_defect_filter/mass_defect_filter.py:159"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/feature_processing/mass_defect_filter/mass_defect_filter.py","line":164,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/feature_processing/mass_defect_filter/mass_defect_filter.py:164"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/feature_processing/targeted_feature_extractor/targeted_feature_extractor.py","line":153,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/feature_processing/targeted_feature_extractor/targeted_feature_extractor.py:153"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/feature_processing/targeted_feature_extractor/targeted_feature_extractor.py","line":160,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/feature_processing/targeted_feature_extractor/targeted_feature_extractor.py:160"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/formula_tools/adduct_calculator/adduct_calculator.py","line":119,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/formula_tools/adduct_calculator/adduct_calculator.py:119"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/formula_tools/formula_mass_calculator/formula_mass_calculator.py","line":117,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/formula_tools/formula_mass_calculator/formula_mass_calculator.py:117"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/formula_tools/formula_mass_calculator/formula_mass_calculator.py","line":126,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/formula_tools/formula_mass_calculator/formula_mass_calculator.py:126"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/formula_tools/formula_mass_calculator/formula_mass_calculator.py","line":133,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/formula_tools/formula_mass_calculator/formula_mass_calculator.py:133"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/formula_tools/formula_validator_golden_rules/formula_validator_golden_rules.py","line":244,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/formula_tools/formula_validator_golden_rules/formula_validator_golden_rules.py:244"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/formula_tools/formula_validator_golden_rules/formula_validator_golden_rules.py","line":252,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/formula_tools/formula_validator_golden_rules/formula_validator_golden_rules.py:252"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/formula_tools/mass_decomposition_tool/mass_decomposition_tool.py","line":183,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/formula_tools/mass_decomposition_tool/mass_decomposition_tool.py:183"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/formula_tools/mass_decomposition_tool/mass_decomposition_tool.py","line":188,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/formula_tools/mass_decomposition_tool/mass_decomposition_tool.py:188"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/formula_tools/metabolite_formula_annotator/metabolite_formula_annotator.py","line":180,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/formula_tools/metabolite_formula_annotator/metabolite_formula_annotator.py:180"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/formula_tools/metabolite_formula_annotator/metabolite_formula_annotator.py","line":187,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/formula_tools/metabolite_formula_annotator/metabolite_formula_annotator.py:187"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/formula_tools/molecular_formula_finder/molecular_formula_finder.py","line":260,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/formula_tools/molecular_formula_finder/molecular_formula_finder.py:260"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/formula_tools/molecular_formula_finder/molecular_formula_finder.py","line":265,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/formula_tools/molecular_formula_finder/molecular_formula_finder.py:265"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/formula_tools/rdbe_calculator/rdbe_calculator.py","line":95,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/formula_tools/rdbe_calculator/rdbe_calculator.py:95"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/formula_tools/rdbe_calculator/rdbe_calculator.py","line":103,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/formula_tools/rdbe_calculator/rdbe_calculator.py:103"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/identification/accurate_mass_searcher/accurate_mass_searcher.py","line":69,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/identification/accurate_mass_searcher/accurate_mass_searcher.py:69"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/identification/accurate_mass_searcher/accurate_mass_searcher.py","line":92,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/identification/accurate_mass_searcher/accurate_mass_searcher.py:92"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/identification/accurate_mass_searcher/accurate_mass_searcher.py","line":129,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/identification/accurate_mass_searcher/accurate_mass_searcher.py:129"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/identification/accurate_mass_searcher/accurate_mass_searcher.py","line":133,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/identification/accurate_mass_searcher/accurate_mass_searcher.py:133"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/identification/metabolite_spectral_matcher/metabolite_spectral_matcher.py","line":73,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/identification/metabolite_spectral_matcher/metabolite_spectral_matcher.py:73"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/isotope_labeling/isotope_label_detector/isotope_label_detector.py","line":157,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/isotope_labeling/isotope_label_detector/isotope_label_detector.py:157"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/isotope_labeling/isotope_label_detector/isotope_label_detector.py","line":168,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/isotope_labeling/isotope_label_detector/isotope_label_detector.py:168"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/isotope_labeling/mid_natural_abundance_corrector/mid_natural_abundance_corrector.py","line":156,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/isotope_labeling/mid_natural_abundance_corrector/mid_natural_abundance_corrector.py:156"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/isotope_labeling/mid_natural_abundance_corrector/mid_natural_abundance_corrector.py","line":169,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/isotope_labeling/mid_natural_abundance_corrector/mid_natural_abundance_corrector.py:169"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/lipidomics/lipid_ecn_rt_predictor/lipid_ecn_rt_predictor.py","line":62,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/lipidomics/lipid_ecn_rt_predictor/lipid_ecn_rt_predictor.py:62"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/lipidomics/lipid_ecn_rt_predictor/lipid_ecn_rt_predictor.py","line":164,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/lipidomics/lipid_ecn_rt_predictor/lipid_ecn_rt_predictor.py:164"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/lipidomics/lipid_ecn_rt_predictor/lipid_ecn_rt_predictor.py","line":168,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/lipidomics/lipid_ecn_rt_predictor/lipid_ecn_rt_predictor.py:168"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/lipidomics/lipid_species_resolver/lipid_species_resolver.py","line":224,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/lipidomics/lipid_species_resolver/lipid_species_resolver.py:224"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/lipidomics/lipid_species_resolver/lipid_species_resolver.py","line":232,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/lipidomics/lipid_species_resolver/lipid_species_resolver.py:232"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/lipidomics/lipid_species_resolver/lipid_species_resolver.py","line":236,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/lipidomics/lipid_species_resolver/lipid_species_resolver.py:236"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/spectral_analysis/isotope_pattern_analyzer/isotope_pattern_analyzer.py","line":400,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/spectral_analysis/isotope_pattern_analyzer/isotope_pattern_analyzer.py:400"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/spectral_analysis/isotope_pattern_analyzer/isotope_pattern_analyzer.py","line":409,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/spectral_analysis/isotope_pattern_analyzer/isotope_pattern_analyzer.py:409"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/spectral_analysis/massql_query_tool/massql_query_tool.py","line":146,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/spectral_analysis/massql_query_tool/massql_query_tool.py:146"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/spectral_analysis/neutral_loss_scanner/neutral_loss_scanner.py","line":143,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/spectral_analysis/neutral_loss_scanner/neutral_loss_scanner.py:143"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/spectral_analysis/spectral_entropy_scorer/spectral_entropy_scorer.py","line":213,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/spectral_analysis/spectral_entropy_scorer/spectral_entropy_scorer.py:213"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/metabolomics/spectral_analysis/spectral_entropy_scorer/spectral_entropy_scorer.py","line":254,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/metabolomics/spectral_analysis/spectral_entropy_scorer/spectral_entropy_scorer.py:254"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/dia_analysis/chromatogram_extractor/chromatogram_extractor.py","line":50,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/dia_analysis/chromatogram_extractor/chromatogram_extractor.py:50"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/dia_analysis/dia_scorer/dia_scorer.py","line":42,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/dia_analysis/dia_scorer/dia_scorer.py:42"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/dia_analysis/dia_scorer/dia_scorer.py","line":187,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/dia_analysis/dia_scorer/dia_scorer.py:187"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/dia_analysis/mrm_decoy_generator/mrm_decoy_generator.py","line":128,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/dia_analysis/mrm_decoy_generator/mrm_decoy_generator.py:128"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/dia_analysis/mrm_decoy_generator/mrm_decoy_generator.py","line":183,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/dia_analysis/mrm_decoy_generator/mrm_decoy_generator.py:183"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/dia_analysis/mrm_feature_finder/mrm_feature_finder.py","line":48,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/dia_analysis/mrm_feature_finder/mrm_feature_finder.py:48"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/dia_analysis/mrm_rt_normalizer/mrm_rt_normalizer.py","line":100,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/dia_analysis/mrm_rt_normalizer/mrm_rt_normalizer.py:100"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/dia_analysis/mrm_rt_normalizer/mrm_rt_normalizer.py","line":133,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/dia_analysis/mrm_rt_normalizer/mrm_rt_normalizer.py:133"},{"rule_id":"opengrep/python.lang.correctness.common-mistakes.string-concat-in-list","severity":"medium","message":"Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list?","path":"tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py","line":25,"fingerprint":"python.lang.correctness.common-mistakes.string-concat-in-list:tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:25"},{"rule_id":"opengrep/python.lang.correctness.common-mistakes.string-concat-in-list","severity":"medium","message":"Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list?","path":"tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py","line":27,"fingerprint":"python.lang.correctness.common-mistakes.string-concat-in-list:tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:27"},{"rule_id":"opengrep/python.lang.correctness.common-mistakes.string-concat-in-list","severity":"medium","message":"Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list?","path":"tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py","line":29,"fingerprint":"python.lang.correctness.common-mistakes.string-concat-in-list:tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:29"},{"rule_id":"opengrep/python.lang.correctness.common-mistakes.string-concat-in-list","severity":"medium","message":"Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list?","path":"tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py","line":31,"fingerprint":"python.lang.correctness.common-mistakes.string-concat-in-list:tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:31"},{"rule_id":"opengrep/python.lang.correctness.common-mistakes.string-concat-in-list","severity":"medium","message":"Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list?","path":"tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py","line":33,"fingerprint":"python.lang.correctness.common-mistakes.string-concat-in-list:tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:33"},{"rule_id":"opengrep/python.lang.correctness.common-mistakes.string-concat-in-list","severity":"medium","message":"Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list?","path":"tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py","line":35,"fingerprint":"python.lang.correctness.common-mistakes.string-concat-in-list:tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:35"},{"rule_id":"opengrep/python.lang.correctness.common-mistakes.string-concat-in-list","severity":"medium","message":"Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list?","path":"tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py","line":37,"fingerprint":"python.lang.correctness.common-mistakes.string-concat-in-list:tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:37"},{"rule_id":"opengrep/python.lang.correctness.common-mistakes.string-concat-in-list","severity":"medium","message":"Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list?","path":"tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py","line":39,"fingerprint":"python.lang.correctness.common-mistakes.string-concat-in-list:tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:39"},{"rule_id":"opengrep/python.lang.correctness.common-mistakes.string-concat-in-list","severity":"medium","message":"Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list?","path":"tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py","line":41,"fingerprint":"python.lang.correctness.common-mistakes.string-concat-in-list:tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:41"},{"rule_id":"opengrep/python.lang.correctness.common-mistakes.string-concat-in-list","severity":"medium","message":"Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list?","path":"tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py","line":47,"fingerprint":"python.lang.correctness.common-mistakes.string-concat-in-list:tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:47"},{"rule_id":"opengrep/python.lang.correctness.common-mistakes.string-concat-in-list","severity":"medium","message":"Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list?","path":"tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py","line":49,"fingerprint":"python.lang.correctness.common-mistakes.string-concat-in-list:tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:49"},{"rule_id":"opengrep/python.lang.correctness.common-mistakes.string-concat-in-list","severity":"medium","message":"Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list?","path":"tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py","line":51,"fingerprint":"python.lang.correctness.common-mistakes.string-concat-in-list:tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:51"},{"rule_id":"opengrep/python.lang.correctness.common-mistakes.string-concat-in-list","severity":"medium","message":"Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list?","path":"tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py","line":53,"fingerprint":"python.lang.correctness.common-mistakes.string-concat-in-list:tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:53"},{"rule_id":"opengrep/python.lang.correctness.common-mistakes.string-concat-in-list","severity":"medium","message":"Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list?","path":"tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py","line":55,"fingerprint":"python.lang.correctness.common-mistakes.string-concat-in-list:tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:55"},{"rule_id":"opengrep/python.lang.correctness.common-mistakes.string-concat-in-list","severity":"medium","message":"Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list?","path":"tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py","line":58,"fingerprint":"python.lang.correctness.common-mistakes.string-concat-in-list:tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:58"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/fasta_utils/fasta_decoy_validator/fasta_decoy_validator.py","line":111,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/fasta_utils/fasta_decoy_validator/fasta_decoy_validator.py:111"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/fasta_utils/fasta_in_silico_digest_stats/fasta_in_silico_digest_stats.py","line":103,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/fasta_utils/fasta_in_silico_digest_stats/fasta_in_silico_digest_stats.py:103"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/fasta_utils/fasta_statistics_reporter/fasta_statistics_reporter.py","line":109,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/fasta_utils/fasta_statistics_reporter/fasta_statistics_reporter.py:109"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/fasta_utils/fasta_subset_extractor/fasta_subset_extractor.py","line":99,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/fasta_utils/fasta_subset_extractor/fasta_subset_extractor.py:99"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/file_conversion/consensus_map_to_matrix/consensus_map_to_matrix.py","line":72,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/file_conversion/consensus_map_to_matrix/consensus_map_to_matrix.py:72"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/file_conversion/idxml_to_tsv_exporter/idxml_to_tsv_exporter.py","line":45,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/file_conversion/idxml_to_tsv_exporter/idxml_to_tsv_exporter.py:45"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/file_conversion/mgf_mzml_converter/mgf_mzml_converter.py","line":74,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/file_conversion/mgf_mzml_converter/mgf_mzml_converter.py:74"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/file_conversion/mgf_mzml_converter/mgf_mzml_converter.py","line":319,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/file_conversion/mgf_mzml_converter/mgf_mzml_converter.py:319"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/file_conversion/ms_data_ml_exporter/ms_data_ml_exporter.py","line":101,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/file_conversion/ms_data_ml_exporter/ms_data_ml_exporter.py:101"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/file_conversion/ms_data_to_csv_exporter/ms_data_to_csv_exporter.py","line":46,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/file_conversion/ms_data_to_csv_exporter/ms_data_to_csv_exporter.py:46"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/file_conversion/ms_data_to_csv_exporter/ms_data_to_csv_exporter.py","line":69,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/file_conversion/ms_data_to_csv_exporter/ms_data_to_csv_exporter.py:69"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/file_conversion/ms_data_to_csv_exporter/ms_data_to_csv_exporter.py","line":96,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/file_conversion/ms_data_to_csv_exporter/ms_data_to_csv_exporter.py:96"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/file_conversion/mztab_summarizer/mztab_summarizer.py","line":37,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/file_conversion/mztab_summarizer/mztab_summarizer.py:37"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/file_conversion/mztab_summarizer/mztab_summarizer.py","line":136,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/file_conversion/mztab_summarizer/mztab_summarizer.py:136"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/identification/mzml_metadata_extractor/mzml_metadata_extractor.py","line":122,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/identification/mzml_metadata_extractor/mzml_metadata_extractor.py:122"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/identification/peptide_spectral_match_validator/peptide_spectral_match_validator.py","line":122,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/identification/peptide_spectral_match_validator/peptide_spectral_match_validator.py:122"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/identification/peptide_spectral_match_validator/peptide_spectral_match_validator.py","line":193,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/identification/peptide_spectral_match_validator/peptide_spectral_match_validator.py:193"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/identification/psm_feature_extractor/psm_feature_extractor.py","line":39,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/identification/psm_feature_extractor/psm_feature_extractor.py:39"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/identification/psm_feature_extractor/psm_feature_extractor.py","line":212,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/identification/psm_feature_extractor/psm_feature_extractor.py:212"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/identification/semi_tryptic_peptide_finder/semi_tryptic_peptide_finder.py","line":189,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/identification/semi_tryptic_peptide_finder/semi_tryptic_peptide_finder.py:189"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/identification/semi_tryptic_peptide_finder/semi_tryptic_peptide_finder.py","line":208,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/identification/semi_tryptic_peptide_finder/semi_tryptic_peptide_finder.py:208"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/identification/sequence_tag_generator/sequence_tag_generator.py","line":182,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/identification/sequence_tag_generator/sequence_tag_generator.py:182"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/amino_acid_composition_analyzer/amino_acid_composition_analyzer.py","line":124,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/amino_acid_composition_analyzer/amino_acid_composition_analyzer.py:124"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/amino_acid_composition_analyzer/amino_acid_composition_analyzer.py","line":127,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/amino_acid_composition_analyzer/amino_acid_composition_analyzer.py:127"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/charge_state_predictor/charge_state_predictor.py","line":148,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/charge_state_predictor/charge_state_predictor.py:148"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/isoelectric_point_calculator/isoelectric_point_calculator.py","line":210,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/isoelectric_point_calculator/isoelectric_point_calculator.py:210"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/isoelectric_point_calculator/isoelectric_point_calculator.py","line":213,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/isoelectric_point_calculator/isoelectric_point_calculator.py:213"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/modification_mass_calculator/modification_mass_calculator.py","line":150,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/modification_mass_calculator/modification_mass_calculator.py:150"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/modification_mass_calculator/modification_mass_calculator.py","line":160,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/modification_mass_calculator/modification_mass_calculator.py:160"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/modification_mass_calculator/modification_mass_calculator.py","line":168,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/modification_mass_calculator/modification_mass_calculator.py:168"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/modified_peptide_generator/modified_peptide_generator.py","line":172,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/modified_peptide_generator/modified_peptide_generator.py:172"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/modified_peptide_generator/modified_peptide_generator.py","line":175,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/modified_peptide_generator/modified_peptide_generator.py:175"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/peptide_detectability_predictor/peptide_detectability_predictor.py","line":160,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/peptide_detectability_predictor/peptide_detectability_predictor.py:160"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/peptide_detectability_predictor/peptide_detectability_predictor.py","line":167,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/peptide_detectability_predictor/peptide_detectability_predictor.py:167"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/peptide_mass_fingerprint/peptide_mass_fingerprint.py","line":156,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/peptide_mass_fingerprint/peptide_mass_fingerprint.py:156"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/peptide_modification_analyzer/peptide_modification_analyzer.py","line":97,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/peptide_modification_analyzer/peptide_modification_analyzer.py:97"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/peptide_modification_analyzer/peptide_modification_analyzer.py","line":100,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/peptide_modification_analyzer/peptide_modification_analyzer.py:100"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/peptide_property_calculator/peptide_property_calculator.py","line":232,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/peptide_property_calculator/peptide_property_calculator.py:232"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/peptide_property_calculator/peptide_property_calculator.py","line":241,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/peptide_property_calculator/peptide_property_calculator.py:241"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/peptide_property_calculator/peptide_property_calculator.py","line":244,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/peptide_property_calculator/peptide_property_calculator.py:244"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/peptide_uniqueness_checker/peptide_uniqueness_checker.py","line":91,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/peptide_uniqueness_checker/peptide_uniqueness_checker.py:91"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/peptide_uniqueness_checker/peptide_uniqueness_checker.py","line":103,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/peptide_uniqueness_checker/peptide_uniqueness_checker.py:103"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/rt_prediction_additive/rt_prediction_additive.py","line":127,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/rt_prediction_additive/rt_prediction_additive.py:127"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/rt_prediction_additive/rt_prediction_additive.py","line":133,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/rt_prediction_additive/rt_prediction_additive.py:133"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/rt_prediction_additive/rt_prediction_additive.py","line":142,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/rt_prediction_additive/rt_prediction_additive.py:142"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/peptide_analysis/rt_prediction_additive/rt_prediction_additive.py","line":145,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/peptide_analysis/rt_prediction_additive/rt_prediction_additive.py:145"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/protein_analysis/peptide_to_protein_mapper/peptide_to_protein_mapper.py","line":57,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/protein_analysis/peptide_to_protein_mapper/peptide_to_protein_mapper.py:57"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/protein_analysis/peptide_to_protein_mapper/peptide_to_protein_mapper.py","line":148,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/protein_analysis/peptide_to_protein_mapper/peptide_to_protein_mapper.py:148"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/protein_analysis/protein_coverage_calculator/protein_coverage_calculator.py","line":104,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/protein_analysis/protein_coverage_calculator/protein_coverage_calculator.py:104"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/protein_analysis/protein_coverage_calculator/protein_coverage_calculator.py","line":114,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/protein_analysis/protein_coverage_calculator/protein_coverage_calculator.py:114"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/protein_analysis/protein_group_reporter/protein_group_reporter.py","line":171,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/protein_analysis/protein_group_reporter/protein_group_reporter.py:171"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/protein_analysis/protein_group_reporter/protein_group_reporter.py","line":190,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/protein_analysis/protein_group_reporter/protein_group_reporter.py:190"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/protein_analysis/spectral_counting_quantifier/spectral_counting_quantifier.py","line":170,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/protein_analysis/spectral_counting_quantifier/spectral_counting_quantifier.py:170"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/protein_analysis/spectral_counting_quantifier/spectral_counting_quantifier.py","line":207,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/protein_analysis/spectral_counting_quantifier/spectral_counting_quantifier.py:207"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/protein_analysis/spectral_counting_quantifier/spectral_counting_quantifier.py","line":210,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/protein_analysis/spectral_counting_quantifier/spectral_counting_quantifier.py:210"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/ptm_analysis/glycopeptide_mass_calculator/glycopeptide_mass_calculator.py","line":141,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/ptm_analysis/glycopeptide_mass_calculator/glycopeptide_mass_calculator.py:141"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/ptm_analysis/phospho_enrichment_qc/phospho_enrichment_qc.py","line":158,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/ptm_analysis/phospho_enrichment_qc/phospho_enrichment_qc.py:158"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/ptm_analysis/phospho_enrichment_qc/phospho_enrichment_qc.py","line":167,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/ptm_analysis/phospho_enrichment_qc/phospho_enrichment_qc.py:167"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/ptm_analysis/phospho_motif_analyzer/phospho_motif_analyzer.py","line":200,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/ptm_analysis/phospho_motif_analyzer/phospho_motif_analyzer.py:200"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/ptm_analysis/phospho_motif_analyzer/phospho_motif_analyzer.py","line":215,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/ptm_analysis/phospho_motif_analyzer/phospho_motif_analyzer.py:215"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/ptm_analysis/phospho_motif_analyzer/phospho_motif_analyzer.py","line":222,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/ptm_analysis/phospho_motif_analyzer/phospho_motif_analyzer.py:222"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/ptm_analysis/phosphosite_class_filter/phosphosite_class_filter.py","line":173,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/ptm_analysis/phosphosite_class_filter/phosphosite_class_filter.py:173"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/ptm_analysis/phosphosite_class_filter/phosphosite_class_filter.py","line":196,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/ptm_analysis/phosphosite_class_filter/phosphosite_class_filter.py:196"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/ptm_analysis/phosphosite_class_filter/phosphosite_class_filter.py","line":204,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/ptm_analysis/phosphosite_class_filter/phosphosite_class_filter.py:204"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/ptm_analysis/ptm_site_localization_scorer/ptm_site_localization_scorer.py","line":230,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/ptm_analysis/ptm_site_localization_scorer/ptm_site_localization_scorer.py:230"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/ptm_analysis/ptm_site_localization_scorer/ptm_site_localization_scorer.py","line":233,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/ptm_analysis/ptm_site_localization_scorer/ptm_site_localization_scorer.py:233"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/acquisition_rate_analyzer/acquisition_rate_analyzer.py","line":97,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/acquisition_rate_analyzer/acquisition_rate_analyzer.py:97"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/collision_energy_analyzer/collision_energy_analyzer.py","line":109,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/collision_energy_analyzer/collision_energy_analyzer.py:109"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/identification_qc_reporter/identification_qc_reporter.py","line":113,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/identification_qc_reporter/identification_qc_reporter.py:113"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/identification_qc_reporter/identification_qc_reporter.py","line":127,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/identification_qc_reporter/identification_qc_reporter.py:127"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/injection_time_analyzer/injection_time_analyzer.py","line":113,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/injection_time_analyzer/injection_time_analyzer.py:113"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/lc_ms_qc_reporter/lc_ms_qc_reporter.py","line":94,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/lc_ms_qc_reporter/lc_ms_qc_reporter.py:94"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/mass_error_distribution_analyzer/mass_error_distribution_analyzer.py","line":129,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/mass_error_distribution_analyzer/mass_error_distribution_analyzer.py:129"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/mass_error_distribution_analyzer/mass_error_distribution_analyzer.py","line":139,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/mass_error_distribution_analyzer/mass_error_distribution_analyzer.py:139"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/missed_cleavage_analyzer/missed_cleavage_analyzer.py","line":99,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/missed_cleavage_analyzer/missed_cleavage_analyzer.py:99"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/missed_cleavage_analyzer/missed_cleavage_analyzer.py","line":110,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/missed_cleavage_analyzer/missed_cleavage_analyzer.py:110"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/missed_cleavage_analyzer/missed_cleavage_analyzer.py","line":113,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/missed_cleavage_analyzer/missed_cleavage_analyzer.py:113"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/ms1_feature_intensity_tracker/ms1_feature_intensity_tracker.py","line":44,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/ms1_feature_intensity_tracker/ms1_feature_intensity_tracker.py:44"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/ms1_feature_intensity_tracker/ms1_feature_intensity_tracker.py","line":211,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/ms1_feature_intensity_tracker/ms1_feature_intensity_tracker.py:211"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/mzqc_generator/mzqc_generator.py","line":130,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/mzqc_generator/mzqc_generator.py:130"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/precursor_charge_distribution/precursor_charge_distribution.py","line":121,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/precursor_charge_distribution/precursor_charge_distribution.py:121"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/precursor_isolation_purity/precursor_isolation_purity.py","line":121,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/precursor_isolation_purity/precursor_isolation_purity.py:121"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/precursor_recurrence_analyzer/precursor_recurrence_analyzer.py","line":165,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/precursor_recurrence_analyzer/precursor_recurrence_analyzer.py:165"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/run_comparison_reporter/run_comparison_reporter.py","line":126,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/run_comparison_reporter/run_comparison_reporter.py:126"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quality_control/sample_complexity_estimator/sample_complexity_estimator.py","line":115,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quality_control/sample_complexity_estimator/sample_complexity_estimator.py:115"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/quantification/peptide_protein_quantifier/peptide_protein_quantifier.py","line":99,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/quantification/peptide_protein_quantifier/peptide_protein_quantifier.py:99"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/rna/rna_digest/rna_digest.py","line":120,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/rna/rna_digest/rna_digest.py:120"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/rna/rna_fragment_spectrum_generator/rna_fragment_spectrum_generator.py","line":209,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/rna/rna_fragment_spectrum_generator/rna_fragment_spectrum_generator.py:209"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/rna/rna_mass_calculator/rna_mass_calculator.py","line":150,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/rna/rna_mass_calculator/rna_mass_calculator.py:150"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/signal_processing/peak_type_estimator/peak_type_estimator.py","line":63,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/signal_processing/peak_type_estimator/peak_type_estimator.py:63"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/signal_processing/signal_to_noise_estimator/signal_to_noise_estimator.py","line":60,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/signal_processing/signal_to_noise_estimator/signal_to_noise_estimator.py:60"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/specialized/cleavage_site_profiler/cleavage_site_profiler.py","line":230,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/specialized/cleavage_site_profiler/cleavage_site_profiler.py:230"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/specialized/cleavage_site_profiler/cleavage_site_profiler.py","line":245,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/specialized/cleavage_site_profiler/cleavage_site_profiler.py:245"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/specialized/cleavage_site_profiler/cleavage_site_profiler.py","line":251,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/specialized/cleavage_site_profiler/cleavage_site_profiler.py:251"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/specialized/immunopeptide_filter/immunopeptide_filter.py","line":115,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/specialized/immunopeptide_filter/immunopeptide_filter.py:115"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/specialized/immunopeptide_filter/immunopeptide_filter.py","line":134,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/specialized/immunopeptide_filter/immunopeptide_filter.py:134"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding=\"utf-8\").","path":"tools/proteomics/specialized/immunopeptide_filter/immunopeptide_filter.py","line":138,"fingerprint":"python.lang.best-practice.unspecified-open-encoding:tools/proteomics/specialized/immunopeptide_filter/immunopeptide_filter.py:138"},{"rule_id":"opengrep/python.lang.best-practice.unspecified-open-encoding","severity":"medium","message":"Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. 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