From 6a8a78a85b2a28afbe1a29d8a97390bc2ff9eea4 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 28 Jan 2024 16:20:31 +0100 Subject: [PATCH] Fixing liting --- taranis/reference_alleles.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/taranis/reference_alleles.py b/taranis/reference_alleles.py index 1358103..bbee5a7 100644 --- a/taranis/reference_alleles.py +++ b/taranis/reference_alleles.py @@ -1,5 +1,5 @@ import logging -import numpy as np +# import numpy as np import os import re import rich.console @@ -10,7 +10,7 @@ # from Bio import SeqIO from Bio.Seq import Seq from Bio import SeqIO -from Bio.Blast.Applications import NcbiblastnCommandline +# from Bio.Blast.Applications import NcbiblastnCommandline from collections import OrderedDict from pathlib import Path import taranis.utils @@ -172,7 +172,7 @@ def create_matrix_distance(self): locus_num = len(self.selected_locus) # pdb.set_trace() matrix_df = pd.read_csv("matrix_distance.tsv", sep="\t").fillna(value=0) - + # remove the first line of the matrix that contain only the number of alleles matrix_df = matrix_df.drop(0) locus_list = matrix_df.iloc[0:locus_num, 0]