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vatlab / varianttools

software tool for the manipulation, annotation, selection, and analysis of variants in the context of next-gen sequencing analysis
https://vatlab.github.io/vat-docs/
GNU General Public License v3.0
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"object name is not a valid python identifier" during vtools associate. #133

Closed BoPeng closed 5 years ago

BoPeng commented 5 years ago

The following test 

python test_associate.py TestAssociate.testBasic

with error message and no output,

  check_attribute_name(name)
/Users/bpeng1/anaconda3/envs/vtools/lib/python3.7/site-packages/tables-3.6.0-py3.7-macosx-10.9-x86_64.egg/tables/path.py:155: NaturalNameWarning: object name is not a valid Python identifier: '0'; it does not match the pattern ``^[a-zA-Z_][a-zA-Z0-9_]*$``; you will not be able to use natural naming to access this object; using ``getattr()`` will still work, though
  check_attribute_name(name)
/Users/bpeng1/anaconda3/envs/vtools/lib/python3.7/site-packages/tables-3.6.0-py3.7-macosx-10.9-x86_64.egg/tables/path.py:155: NaturalNameWarning: object name is not a valid Python identifier: '1'; it does not match the pattern ``^[a-zA-Z_][a-zA-Z0-9_]*$``; you will not be able to use natural naming to access this object; using ``getattr()`` will still work, though
  check_attribute_name(name)
/Users/bpeng1/anaconda3/envs/vtools/lib/python3.7/site-packages/tables-3.6.0-py3.7-macosx-10.9-x86_64.egg/tables/path.py:155: NaturalNameWarning: object name is not a valid Python identifier: '2'; it does not match the pattern ``^[a-zA-Z_][a-zA-Z0-9_]*$``; you will not be able to use natural naming to access this object; using ``getattr()`` will still work, though
  check_attribute_name(name)

The actual commands executed are

vtools admin --load_snapshot proj/assoproj.tar.gz
vtools update variant --from_file output/assogrp1.txt --format fmt/randcol.fmt --var_info grpby
vtools associate variant phen2 --covariate phen1 phen3 phen4 -m "LinRegBurden --alternative 2" -g grpby -f -j 8
jma7 commented 5 years ago

All tests passed now. Forgot to add #133 in the commit message though.