Dist #34
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Dist #34
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Codecov Report
@@ Coverage Diff @@
## master #34 +/- ##
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+ Coverage 93.11% 93.71% +0.6%
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Files 19 19
Lines 668 700 +32
Branches 120 128 +8
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+ Hits 622 656 +34
Misses 39 39
+ Partials 7 5 -2
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|
standage
commented
May 28, 2019
| 'gt1', help='genotype data (in JSON format) for individual 1' | ||
| '-p', '--ploidy', type=int, metavar='PLD', default=2, | ||
| help='for simulated genotypes, the number of distinct haplotypes ' | ||
| 'present in the sample; default is 2 (for a single diploid genotype)' |
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It should be possible to infer the ploidy automatically when populating SimulatedGenotype objects from BED data. I don't like having to state this explicitly, but we'll leave it in for now.
| if locus in gt2.data: | ||
| allele2 = gt2.data[locus]['genotype'] | ||
| allele1 = gt1.alleles(locus) | ||
| allele2 = gt2.alleles(locus) |
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Updated the SimulatedGenotype and ObservedGenotype classes so that their alleles() and loci() methods perform identically to take advantage of duck typing.
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This update enables more seamless comparisons between simulated and observed genotypes, both at the Python level and the CLI. The
mixturemodule can now also output a BED file containing genotype data from all contributors to enable equality and distance comparisons. Closes #33.