dinosaurur
commented
11 months ago Hi, I resolved this error by modifying the code in make_annot.py at lines 23-25, as explained in the following link: numpy.int64 has no attribute isdigit #362.
However, I am not sure if I got the correct output because I can't access the files in the tutorial.
Hi LDSC team,
I was using make_annot.py to create thin annotation files from sample files, for a partitioned heritability analysis. I kept running into an issue where the script was creating annotation files.
Any suggestions?
(base) stxuyuan@ubuntu:~/Documents/HLQ/GWAS/test$ python make_annot.py \ --gene-set-file GTEx_Cortex.GeneSet \ --gene-coord-file ENSG_coord.txt \ --windowsize 100000 \ --bimfile 1000G.EUR.QC.22.bim \ --annot-file GTEx_Cortex.annot.gz
making gene set bed file Traceback (most recent call last): File "make_annot.py", line 50, in
bed_for_annot = gene_set_to_bed(args)
File "make_annot.py", line 17, in gene_set_to_bed
return BedTool(iter_df).sort().merge()
File "/home/stxuyuan/miniconda3/lib/python3.8/site-packages/pybedtools/bedtool.py", line 589, in init
fn = BedTool(iter(fn)).saveas().fn
File "/home/stxuyuan/miniconda3/lib/python3.8/site-packages/pybedtools/bedtool.py", line 923, in decorated
result = method(self, *args, **kwargs)
File "/home/stxuyuan/miniconda3/lib/python3.8/site-packages/pybedtools/bedtool.py", line 3362, in saveas
fn = self._collapse(
File "/home/stxuyuan/miniconda3/lib/python3.8/site-packages/pybedtools/bedtool.py", line 1422, in _collapse
for i in iterable:
File "pybedtools/cbedtools.pyx", line 793, in pybedtools.cbedtools.IntervalIterator.next
File "pybedtools/cbedtools.pyx", line 657, in pybedtools.cbedtools.create_interval_from_list
File "pybedtools/cbedtools.pyx", line 579, in pybedtools.cbedtools.isdigit
AttributeError: 'float' object has no attribute 'isdigit'