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sqanti hides import errors and makes it hard to debug #212

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diekhans opened this issue Aug 12, 2023 · 0 comments
Open

sqanti hides import errors and makes it hard to debug #212

diekhans opened this issue Aug 12, 2023 · 0 comments
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enhancement New feature or request

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@diekhans
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this magic made it very hard to debug a problem loading. It is nice that it gives a hint, but the hint was not correct
and catch and discarding the error message means having to modify the code to debug.

Please do not discard error messages.

try:
    from err_correct_w_genome import err_correct
    from sam_to_gff3 import convert_sam_to_gff3
    from STAR import STARJunctionReader
    from BED import LazyBEDPointReader
    import coordinate_mapper as cordmap
except ImportError:
    print("Unable to import err_correct_w_genome or sam_to_gff3.py! Please make sure cDNA_Cupcake/sequence/ is in $PYTHONPATH.", file=sys.stderr)
    sys.exit(-1)

@aarzalluz aarzalluz added the enhancement New feature or request label Aug 12, 2023
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