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Requesting help:about QTL_to_PredictDB: AttributeError: 'NoneType' object has no attribute 'endswith' #172

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jambo611 opened this issue Apr 3, 2023 · 0 comments

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@jambo611
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jambo611 commented Apr 3, 2023

$ python ${main} --input_file ${home} --snp_column SNP_COLUMN --snpid_format rsid --pvalue_column PVALUE_COLUMN --gene_column GENE_COLUMN --beta_column BETA_COLUMN --ref_allele_column REF_ALLELE_COLUMN --alt_allele_column ALT_ALLELE_COLUMN --chromosome_column CHROMOSOME_COLUMN --position_column POSITION_COLUMN --output_file eas.chr.db
Traceback (most recent call last):
File "/public/home/leixia/software/QTL_to_PredictDB/Main.py", line 180, in
run(args)
File "/public/home/leixia/software/QTL_to_PredictDB/Main.py", line 110, in run
for i, chunk in enumerate(DFS.read_eQTL_file(eqtl_file, args, snpid_regex)):
File "/public/home/leixia/software/QTL_to_PredictDB/DataFrameStreamer.py", line 275, in read_eQTL_file
snp_dictionary = build_snp_dictionary(params.snp_annot_file, params, rsid_as_key=True)
File "/public/home/leixia/software/QTL_to_PredictDB/DataFrameStreamer.py", line 88, in build_snp_dictionary
_open = gzip.open if filepath.endswith(".gz") else open
AttributeError: 'NoneType' object has no attribute 'endswith'

I wonder why the report was wrong, requesting help

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