Thank you very much for your contribution. We ran experiments/Reginf/s01_preprocessing.py and found that 239 lines were missing and the file Whole_Blood.v8.signif_variant_gene_pairs.bed.gz was missing, but we could only find Whole_Blood.v8.signif_variant_gene_pairs.txt.gz. When running the code, the following error Traceback (most recent call last) is reported:
File "s01_preprocessing.py", line 239, in
eqtl = scglue.genomics.read_bed("./GTEx-v8/Whole_Blood.v8.signif_variant_gene_pairs.txt.gz")
File "/opt/conda/envs/glue/lib/python3.8/site-packages/scglue/genomics.py", line 85, in read_bed
return cls(loaded)
File "/opt/conda/envs/glue/lib/python3.8/site-packages/scglue/utils.py", line 495, in init
df = self.rectify(df)
File "/opt/conda/envs/glue/lib/python3.8/site-packages/scglue/genomics.py", line 52, in correct
df[item] = df[item].astype(int)
File "/opt/conda/envs/glue/lib/python3.8/site-packages/pandas/core/generic.py", line 6324, in astype
new_data = self._mgr.astype(dtype=dtype, copy=copy, errors=errors)
File "/opt/conda/envs/glue/lib/python3.8/site-packages/pandas/core/internals/managers.py", line 451, in astype
return self.apply(
File "/opt/conda/envs/glue/lib/python3.8/site-packages/pandas/core/internals/managers.py", line 352, in apply
applied = getattr(b, f)(**kwargs)
File "/opt/conda/envs/glue/lib/python3.8/site-packages/pandas/core/internals/blocks.py", line 511, in astype
new_values = astype_array_safe(values, dtype, copy=copy, errors=errors)
File "/opt/conda/envs/glue/lib/python3.8/site-packages/pandas/core/dtypes/astype.py", line 242, in astype_array_safe
new_values = astype_array(values, dtype, copy=copy)
File "/opt/conda/envs/glue/lib/python3.8/site-packages/pandas/core/dtypes/astype.py", line 187, in astype_array
values = _astype_nansafe(values, dtype, copy=copy)
File "/opt/conda/envs/glue/lib/python3.8/site-packages/pandas/core/dtypes/astype.py", line 138, in _astype_nansafe
return arr.astype(dtype, copy=True)
ValueError: invalid literal for int() with base 10: 'gene_id'
We are not sure if it is a file error, can you provide an answer?
Thank you very much for your contribution. We ran experiments/Reginf/s01_preprocessing.py and found that 239 lines were missing and the file Whole_Blood.v8.signif_variant_gene_pairs.bed.gz was missing, but we could only find Whole_Blood.v8.signif_variant_gene_pairs.txt.gz. When running the code, the following error Traceback (most recent call last) is reported:
File "s01_preprocessing.py", line 239, in
eqtl = scglue.genomics.read_bed("./GTEx-v8/Whole_Blood.v8.signif_variant_gene_pairs.txt.gz")
File "/opt/conda/envs/glue/lib/python3.8/site-packages/scglue/genomics.py", line 85, in read_bed
return cls(loaded)
File "/opt/conda/envs/glue/lib/python3.8/site-packages/scglue/utils.py", line 495, in init
df = self.rectify(df)
File "/opt/conda/envs/glue/lib/python3.8/site-packages/scglue/genomics.py", line 52, in correct
df[item] = df[item].astype(int)
File "/opt/conda/envs/glue/lib/python3.8/site-packages/pandas/core/generic.py", line 6324, in astype
new_data = self._mgr.astype(dtype=dtype, copy=copy, errors=errors)
File "/opt/conda/envs/glue/lib/python3.8/site-packages/pandas/core/internals/managers.py", line 451, in astype
return self.apply(
File "/opt/conda/envs/glue/lib/python3.8/site-packages/pandas/core/internals/managers.py", line 352, in apply
applied = getattr(b, f)(**kwargs)
File "/opt/conda/envs/glue/lib/python3.8/site-packages/pandas/core/internals/blocks.py", line 511, in astype
new_values = astype_array_safe(values, dtype, copy=copy, errors=errors)
File "/opt/conda/envs/glue/lib/python3.8/site-packages/pandas/core/dtypes/astype.py", line 242, in astype_array_safe
new_values = astype_array(values, dtype, copy=copy)
File "/opt/conda/envs/glue/lib/python3.8/site-packages/pandas/core/dtypes/astype.py", line 187, in astype_array
values = _astype_nansafe(values, dtype, copy=copy)
File "/opt/conda/envs/glue/lib/python3.8/site-packages/pandas/core/dtypes/astype.py", line 138, in _astype_nansafe
return arr.astype(dtype, copy=True)
ValueError: invalid literal for int() with base 10: 'gene_id'
We are not sure if it is a file error, can you provide an answer?