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cov-lineages / scorpio

serious constellations of reoccurring phylogenetically-independent origin
GNU General Public License v3.0
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Giving input file without `-i` causes stack trace #41

Closed rambaut closed 2 years ago

rambaut commented 2 years ago

Just putting the name of a file at the end of the command line (i.e., forgetting the -i) gives an obtuse error:

  File "/Users/rambaut/miniconda3/envs/pangolin/bin/scorpio", line 8, in <module>
    sys.exit(main())
  File "/Users/rambaut/miniconda3/envs/pangolin/lib/python3.8/site-packages/scorpio/__main__.py", line 281, in main
    args.func(args)
  File "/Users/rambaut/miniconda3/envs/pangolin/lib/python3.8/site-packages/scorpio/subcommands/haplotype.py", line 7, in run
    type_constellations(options.input,
  File "/Users/rambaut/miniconda3/envs/pangolin/lib/python3.8/site-packages/scorpio/scripts/type_constellations.py", line 868, in type_constellations
    with open(in_fasta, "r") as f:
TypeError: expected str, bytes or os.PathLike object, not NoneType