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oxpig / ANARCI

Antibody Numbering and Antigen Receptor ClassIfication
BSD 3-Clause "New" or "Revised" License
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Using ANARCI through Parapred #60

Closed hanzhiz closed 11 months ago

hanzhiz commented 1 year ago

Hello,

I have a issue with using anarci with through parapred. When importing anarci, cannot import .germlines. Actually in lib there is no germlines.py file. Do you know how to solve it?

Following is the error command:

ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' /usr/local/lib64/python3.6/site-packages/Bio/SearchIO/init.py:211: BiopythonExperimentalWarning: Bio.SearchIO is an experimental submodule which may undergo significant changes prior to its future official release. BiopythonExperimentalWarning) Traceback (most recent call last): File "/usr/local/lib/python3.6/site-packages/parapred-1.0.1-py3.6.egg/parapred/full_seq_processor.py", line 32, in get_CDR_simple File "/root/.local/lib/python3.6/site-packages/anarci/init.py", line 3, in from .anarci import * File "/root/.local/lib/python3.6/site-packages/anarci/anarci.py", line 68, in from .germlines import all_germlines ModuleNotFoundError: No module named 'anarci.germlines'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/usr/local/bin/parapred", line 33, in sys.exit(load_entry_point('parapred==1.0.1', 'console_scripts', 'parapred')()) File "/usr/local/lib/python3.6/site-packages/parapred-1.0.1-py3.6.egg/parapred/parapred.py", line 227, in main File "/usr/local/lib/python3.6/site-packages/parapred-1.0.1-py3.6.egg/parapred/parapred.py", line 197, in process_full_VH_VL_sequence File "/usr/local/lib/python3.6/site-packages/parapred-1.0.1-py3.6.egg/parapred/full_seq_processor.py", line 34, in get_CDR_simple Exception: ImportError function get_CDR_simple() requires the python module anarci Available from http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/ANARCI.php

FBoyles commented 11 months ago

You need to run the script build_pipeline/RUN_pipeline.sh. This downloads germline data and builds HMM models. This script is run as part of the installation process, so should not be necessary if the package was installed correctly. Closing as not a code issue.