You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
No acmg_db path given and no db_config.json found
Default is: /home/ggama1/programs/tapes/acmg_db
***TAPES: SORT***
2023-08-31 16:08:23.....Output type: FOLDER
2023-08-31 16:08:23.....VEP vcf processing Traceback (most recent call last):
File "/home/ggama1/programs/tapes/tapes.py", line 355, in <module>
main()
File "/home/ggama1/programs/tapes/tapes.py", line 205, in main
full_stuff, soft_used = tf.open_csv_file(file_path, acmg_db_path) # Load annotated csv in pandas
File "/home/ggama1/programs/tapes/src/t_func.py", line 70, in open_csv_file
dataframe = vp.vep_process_vcf(csv_file, acmg_db_path)
File "/home/ggama1/programs/tapes/src/vep_process.py", line 43, in vep_process_vcf
df['CHROM'] = df['CHROM'].str.replace('chr', '')
File "/home/ggama1/.local/lib/python3.7/site-packages/pandas/core/generic.py", line 5458, in __getattr__
return object.__getattribute__(self, name)
File "/home/ggama1/.local/lib/python3.7/site-packages/pandas/core/accessor.py", line 180, in __get__
accessor_obj = self._accessor(obj)
File "/home/ggama1/.local/lib/python3.7/site-packages/pandas/core/strings/accessor.py", line 154, in __init__
self._inferred_dtype = self._validate(data)
File "/home/ggama1/.local/lib/python3.7/site-packages/pandas/core/strings/accessor.py", line 217, in _validate
raise AttributeError("Can only use .str accessor with string values!")
AttributeError: Can only use .str accessor with string values!
Sorting a single sample VEP anotated VCF, based on hg38, gives no error.
The text was updated successfully, but these errors were encountered:
Hi!
I'm trying to use TAPES on a VEP annotated multisample VCF file. I used VEP 109.
python3 /home/ggama1/programs/tapes/tapes.py sort -i /data/scratch/ggama1/vcf_3777_tapestest/M_Valle_20230522_3777samples.10klines.vep.vcf -o /data/scratch/ggama1/vcf_3777_tapestest/tapes/multisample_hg37/ --tab --by_gene --by_sample
Which gives:
Sorting a single sample VEP anotated VCF, based on hg38, gives no error.
The text was updated successfully, but these errors were encountered: