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germlines returns null ,but had value before, please help! thank you #64

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qiuqingpo opened this issue Jul 17, 2023 · 0 comments
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@qiuqingpo
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qiuqingpo commented Jul 17, 2023

@broncio123 @FBoyles
my test code is bellow:


# Import the anarci function.
from anarci import anarci

# Format the sequences that we want to number. 
sequences = [ ("12e8:H","AVVLTQTASPVSAAVGGTVTINCQASQSVYKNNRLAWYQQKPGQPPKLLIYGASTLASGVPSRFKGSGSGTQFTLTISDLECDDAATYYCAGGYSGNINVFGGGTEVVVK")]

# Hand the list of sequences to the anarci function. Number them with the IMGT scheme
results = anarci(sequences, scheme="imgt",output=False,assign_germline=True,allowed_species=['human',
                      'mouse','rat','rabbit','rhesus','pig','alpaca'])

# Unpack the results. We get three lists
numbering, alignment_details, hit_tables = results
print ("numbering: %s alignment_details: %s"%(numbering, alignment_details))

the result of the alignment_details

alignment_details: [[{'id': 'rabbit_K', 'description': '', 'evalue': 3.1e-60, 'bitscore': 192.9, 'bias': 4.8, 'query_start': 0, 'query_end': 110, 'species': 'rabbit', 'chain_type': 'K', 'scheme': 'imgt', 'query_name': '12e8:H', 'germlines': {}}

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