From d52df6e832270add5828b9522a6cbb6a41eca279 Mon Sep 17 00:00:00 2001 From: riasc Date: Sun, 1 Sep 2024 20:39:34 -0500 Subject: [PATCH] renamed protein and pathogen fields --- workflow/scripts/prioritization/filtering.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflow/scripts/prioritization/filtering.py b/workflow/scripts/prioritization/filtering.py index 40384a0..a0b8e78 100644 --- a/workflow/scripts/prioritization/filtering.py +++ b/workflow/scripts/prioritization/filtering.py @@ -95,14 +95,14 @@ def __init__(self, output_dir, mhc_class, vartype): df.insert(len(df.keys()), "pathogen_similarity", score) df.insert(len(df.keys()), "pathogen_evalue", evalue) df.insert(len(df.keys()), "pathogen_bitscore", bitscore) - df.insert(len(df.keys()), "pathogen_organism", organism) + df.insert(len(df.keys()), "pathogen", organism) # calculate proteome similarity prot_score, prot_evalue, prot_bit, prot = self.proteome_similarity(mt_epitope_seq) df.insert(len(df.keys()), "proteome_similarity", prot_score) df.insert(len(df.keys()), "proteome_evalue", prot_evalue) df.insert(len(df.keys()), "proteome_bitscore", prot_bit) - df.insert(len(df.keys()), "proteome_organism", prot) + df.insert(len(df.keys()), "protein", prot) self.outfile = os.path.join(output_dir, f"{vartype}_{mhc_class}_neoepitopes.txt")