run erro
fanyucai1 opened this issue · 8 comments
hi doctor, my script as follows:
##################################
from civicpy import civic, exports
with open('civic_variants.vcf', 'w', newline='') as file:
w = exports.VCFWriter(file)
all_variants = civic.get_all_variants()
w.addrecords(all_variants)
w.writerecords()
###########################the erro:
Traceback (most recent call last):
File "VEP.py", line 1, in
from civicpy import civic, exports
ImportError: cannot import name 'exports'
what should I do?
Hi @fanyucai1. Would you kindly provide us with the version of CIViCpy you are using that produced this error?
hi doctor, I change my python from 3.6 to 3.7. The erro changed as follows:
WARNING:root:Getting all genes. This may take a couple of minutes...
Traceback (most recent call last):
File "test.py", line 6, in
w.addrecords(all_variants)
File "/usr/local/lib/python3.7/site-packages/civicpy/exports.py", line 122, in addrecords
self.addrecord(record)
File "/usr/local/lib/python3.7/site-packages/civicpy/exports.py", line 112, in addrecord
self.addrecord(evidence)
File "/usr/local/lib/python3.7/site-packages/civicpy/exports.py", line 114, in addrecord
valid = self._validate_evidence_record(civic_record)
File "/usr/local/lib/python3.7/site-packages/civicpy/exports.py", line 235, in _validate_evidence_record
valid = self._validate_sequence_variant(variant)
File "/usr/local/lib/python3.7/site-packages/civicpy/exports.py", line 272, in _validate_sequence_variant
valid = self._validate_coordinates(variant, types)
File "/usr/local/lib/python3.7/site-packages/civicpy/exports.py", line 332, in _validate_coordinates
raise NotImplementedError(f'No logic to handle {variant_type.name} {variant}')
NotImplementedError: No logic to handle transcript_fusion <CIViC variant 2663>
#####################
what should I do?
To help you troubleshoot this problem, please provide the version of CIViCpy that you are using. You may find this by using pip freeze | grep civicpy in your shell.
civicpy==0.0.3.post1
Please upgrade to version 1.0.0rc2 by running pip install civicpy==1.0.0rc2.
the erro as follows:
Traceback (most recent call last):
File "get_civicpy.py", line 5, in
all_variants = civic.get_all_variants()
File "/usr/local/lib/python3.7/site-packages/civicpy/civic.py", line 820, in get_all_variants
variants = _get_elements_by_ids('variant', allow_cached=allow_cached, get_all=True)
File "/usr/local/lib/python3.7/site-packages/civicpy/civic.py", line 661, in _get_elements_by_ids
load_cache()
File "/usr/local/lib/python3.7/site-packages/civicpy/civic.py", line 168, in load_cache
old_cache = pickle.load(pf)
_pickle.UnpicklingError: pickle data was truncated
I find one file called: cache.pkl,where can I download this file?
Closing this issue; stale. For reference, a fresh cache.pkl file should be automatically grabbed from live CIViC in civicpy v1.0 and above.