From fe8906453a83fd8d0419cb49f429105dcefdc5c8 Mon Sep 17 00:00:00 2001 From: Mostafa Kalhor Date: Wed, 10 Apr 2024 13:23:33 +0200 Subject: [PATCH] still working on errors - fixed typrguard error --- spectrum_io/search_result/xisearch.py | 4 +++- tests/unit_tests/data/peptide_protein_map.tsv.params.txt | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/spectrum_io/search_result/xisearch.py b/spectrum_io/search_result/xisearch.py index e50b877..b4a87b5 100644 --- a/spectrum_io/search_result/xisearch.py +++ b/spectrum_io/search_result/xisearch.py @@ -77,7 +77,6 @@ def filter_xisearch_result(self, df: pd.DataFrame) -> pd.DataFrame: :param df: df to filter :return: filtered df as pd.DataFrame """ - # df = df[df["linear"] != True] df = df[~df["linear"]] df = df[df["linked_aa_p1"].notna() & df["linked_aa_p1"].str.contains("K")] df = df[df["linked_aa_p2"].notna() & df["linked_aa_p2"].str.contains("K")] @@ -152,6 +151,9 @@ def add_mod_sequence( :param mod_b_positions: position of all modifications of peptide b :return: modified sequence a and b """ + mod_a_positions = str(mod_a_positions) # Ensure it's a string + mod_b_positions = str(mod_b_positions) # Ensure it's a string + split_seq_a = [x for x in seq_a] split_seq_b = [x for x in seq_b] diff --git a/tests/unit_tests/data/peptide_protein_map.tsv.params.txt b/tests/unit_tests/data/peptide_protein_map.tsv.params.txt index 8ca4d2e..4424a1b 100644 --- a/tests/unit_tests/data/peptide_protein_map.tsv.params.txt +++ b/tests/unit_tests/data/peptide_protein_map.tsv.params.txt @@ -1 +1 @@ -/cmnfs/home/m.kalhor/miniconda3/envs/oktoberfest/bin/pytest +/cmnfs/home/m.kalhor/miniconda3/envs/oktoberfest/bin/pytest \ No newline at end of file