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Fixed hmmscan path check for python envs. #92

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Fixed hmmscan path check for python envs. #92

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16 changes: 10 additions & 6 deletions lib/python/anarci/anarci.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -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]
Expand Down