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Description
According to the documentation "HMMER", "NAME", "LENG", "ALPH", "HMM" are mandatory tags in the header of hmm files but I found that:
- omitting the "ALPH" line will generate a segmentation fault (not raise an exception), and
- omitting the "HMM" line will not raise an exception
It seems to me that this is an issue with the HMMER parser since this behaviour also arises when using the CLI, i.e.
hmmconvert ill_formated.hmm.
Here is the relevant code to reproduce the behavior (I'm using a MacbookPro with an Intel processor and MacOS Sonoma):
- Create an environment
conda create --name test_pyhmmer bioconda::pyhmmer
conda activate test_pyhmmer-
Download and unzip the attached hmm files and test script
test_files_and_script.zip -
Try validating the hmm files with the attached script
# Expected behavior: exception raised
# Observed behavior: segmentation fault
cd my_downloads_are_here
./validate_hmm_profiles.py no_alph.hmm# Expected behavior: exception raised
# Observed behavior: no exception raised
./validate_hmm_profiles.py no_hmm.hmmJust as a reference, this is what the validation script is doing...
from pyhmmer.plan7 import HMMFile
import sys
with HMMFile(sys.argv[1]) as hmm_file:
for hmm_profile in hmm_file:
hmm_profile.validate(tolerance=0.0001)