Nose tool #14
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Nose tool #14
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averagehat
requested changes
Oct 25, 2019
…nto nose_tool This merge is needed due to recomemnded code changes # Please enter a commit message to explain why this merge is necessary,
averagehat
requested changes
Nov 4, 2019
| #Having difficulty instantiating attributes for match_primer for actual and expected | ||
| actual = match_primers( primer= [MappingCoordinate(10, 40)], alts= [Alt(24, 'G')], bamReads=[BamRead( 234, 5, 9, 154, 'ACGACGGCGCACACGGCAGCAGCAGCGACGCGGGGTTTATATATGGCACGAGCGCGCAGCGACGCAGCGCGCTTGAGACGAGGGTAGAGAGTGCGACGCCGCGCAGGAGAGGGGAGAGG') | ||
| expected = match_primers( primer= [MappingCoordinate(10, 40)], alts= [Alt(24, 'G')], bamReads=[BamRead( 234, 5, 9, 154, 'ACGACGGCGCACACGGCAGCAGCAGCGACGCGGGGTTTATATATGGCACGAGCGCGCAGCGACGCAGCGCGCTTGAGACGAGGGTAGAGAGTGCGACGCCGCGCAGGAGAGGGGAGAGG') | ||
| eq_(3, 5, "Actual {0} is not Expected {1}".format(actual, expected)) |
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You need to compare the actual and expected here
| other: List[Tuple[str, int]] # e.g. N, insertion, etc | ||
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| def match_primers(primers: List[MappingCoordinate], alts: List[Alt], bamReads: Iterator[BamRead]) -> List[PrimerCount]: |
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You need to delete this function or give it an empty body, i.e.
def foo():
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| #def test_primer_annotate(Alt: [str, int], consensus: , MappingCoordinate:[int, int], BamRead[int, int, int, int, str,str] PrimerCount) -> None: | ||
| def match_primers(primers= [MappingCoordinate(int,int)], alts= [Alt(int,str], bamReads=[BamRead(int, int,int, int, str)] -> PrimerCount: List[PrimerCount(int,int,int,int,int,int,int,int)]: |
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this function should be called test_match_primers and accept no arguments
| ok_(True, "True is true") | ||
| #Having difficulty instantiating attributes for match_primer for actual and expected | ||
| actual = match_primers( primer= [MappingCoordinate(10, 40)], alts= [Alt(24, 'G')], bamReads=[BamRead( 234, 5, 9, 154, 'ACGACGGCGCACACGGCAGCAGCAGCGACGCGGGGTTTATATATGGCACGAGCGCGCAGCGACGCAGCGCGCTTGAGACGAGGGTAGAGAGTGCGACGCCGCGCAGGAGAGGGGAGAGG') | ||
| expected = match_primers( primer= [MappingCoordinate(10, 40)], alts= [Alt(24, 'G')], bamReads=[BamRead( 234, 5, 9, 154, 'ACGACGGCGCACACGGCAGCAGCAGCGACGCGGGGTTTATATATGGCACGAGCGCGCAGCGACGCAGCGCGCTTGAGACGAGGGTAGAGAGTGCGACGCCGCGCAGGAGAGGGGAGAGG') |
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expected and actual seem to be the same. actual should be the result of a call to the function we are testing. expected should be defined separately, in this case, it would be a PrimerCount object. See https://realpython.com/python-testing/#how-to-structure-a-simple-test
averagehat
reviewed
Dec 13, 2019
| querySequence='ACGACGGCGCACACGGCAGCAGCAGCGACGCGGGGTTTATATATGGCACGAGCGCGCAGCGACGCAGCGCGCTTGAGACGAGGGTAGAGAGTGCGACGCCGCGCAGGAGAGGGGAGAGG') ] | ||
| result = match_primers(primers=coordinates, alts=alts, bamReads=mapperReadsOverlappingPosition, thresh=20) | ||
| expected = PrimerCount(24, 'G', altTotal=1, alt_Primers_overlap=1, altPrimersWithinEnd=1, primer_base='A') | ||
| # TODO FIX SO IT FAILS again |
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need to check that the result fits the expected
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nose_tool test code for primer matching (beta)