diff --git a/poetry.lock b/poetry.lock index 6347608..a589056 100644 --- a/poetry.lock +++ b/poetry.lock @@ -366,17 +366,6 @@ files = [ {file = "cycler-0.11.0.tar.gz", hash = "sha256:9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f"}, ] -[[package]] -name = "defusedxml" -version = "0.7.1" -description = "XML bomb protection for Python stdlib modules" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" -files = [ - {file = "defusedxml-0.7.1-py2.py3-none-any.whl", hash = "sha256:a352e7e428770286cc899e2542b6cdaedb2b4953ff269a210103ec58f6198a61"}, - {file = "defusedxml-0.7.1.tar.gz", hash = "sha256:1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69"}, -] - [[package]] name = "et-xmlfile" version = "1.1.0" diff --git a/pyproject.toml b/pyproject.toml index 305bcdf..1b689f5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,7 +17,6 @@ classifiers = [ [tool.poetry.dependencies] python = ">=3.9,<3.12" bio = "1.6.2" -defusedxml = "0.7.1" lxml = "5.2.1" mdanalysis = "2.7.0" requests = "2.31.0" diff --git a/src/arctic3d/modules/blast.py b/src/arctic3d/modules/blast.py index cfc0b09..4b85fd7 100644 --- a/src/arctic3d/modules/blast.py +++ b/src/arctic3d/modules/blast.py @@ -1,4 +1,5 @@ """Function to BLAST input sequence and return accession id.""" + import logging import os import shlex @@ -7,7 +8,7 @@ from pathlib import Path from Bio.Blast import NCBIWWW -from defusedxml import lxml as ET +from lxml import etree as ET log = logging.getLogger("arctic3d.log")