From 9c89206431fe20f5dfa04f91a7a7f58c04958055 Mon Sep 17 00:00:00 2001 From: William Steele Date: Mon, 2 Sep 2024 14:31:08 +0100 Subject: [PATCH] Fixed hmmscan path check for python envs. --- lib/python/anarci/anarci.py | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/lib/python/anarci/anarci.py b/lib/python/anarci/anarci.py index 4069994..9b42283 100644 --- a/lib/python/anarci/anarci.py +++ b/lib/python/anarci/anarci.py @@ -43,16 +43,18 @@ ''' +import gzip +import math import os +import shutil import sys +import sysconfig import tempfile -import gzip -import math from functools import partial -from textwrap import wrap -from subprocess import Popen, PIPE from itertools import groupby, islice from multiprocessing import Pool +from subprocess import PIPE, Popen +from textwrap import wrap from Bio.SearchIO.HmmerIO import Hmmer3TextParser as HMMERParser @@ -509,9 +511,11 @@ def run_hmmer(sequence_list,hmm_database="ALL",hmmerpath="", ncpu=None, bit_scor # Run hmmer as a subprocess if hmmerpath: - hmmscan = os.path.join(hmmerpath,"hmmscan") - else: + hmmscan = os.path.join(hmmerpath, "hmmscan") + elif shutil.which("hmmscan") is not None: hmmscan = "hmmscan" + else: + hmmscan = os.path.join(sysconfig.get_paths()["scripts"], "hmmscan") try: if ncpu is None: command = [ hmmscan, "-o", output_filename, HMM, fasta_filename]