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lemieuxl / pyGenClean

Automated genetic data clean up procedure in Python.
GNU General Public License v3.0
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Check ethnicity error #11

Closed lemieuxl closed 8 years ago

lemieuxl commented 8 years ago

When using the check_ethnicity script, there is an error if the --skip-ref-pops options. The automatic report fails when it tries to read the file ethnicity.outliers (which doesn't exists). The automatic report also needs to change its content if the --skip-ref-pops option is used.

lemieuxl commented 8 years ago 
Traceback (most recent call last):
  File ".../pyGenClean_virt/bin/run_pyGenClean", line 9, in <module>
    load_entry_point('pyGenClean==1.7.1', 'console_scripts', 'run_pyGenClean')()
  File ".../pyGenClean_virt/pyGenClean/run_data_clean_up.py", line 3174, in safe_main
    main()
  File ".../pyGenClean_virt/pyGenClean/run_data_clean_up.py", line 186, in main
    options,
  File ".../pyGenClean_virt/pyGenClean/run_data_clean_up.py", line 1923, in run_check_ethnicity
    with open(script_prefix + ".outliers", "r") as i_file:
IOError: [Errno 2] No such file or directory: 'data_clean_up.2015-10-09_08.00.25/3_check_ethnicity/ethnicity.outliers'