Update to docs, allele formatting #159
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standage
commented
Apr 24, 2025
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| def __init__(self, name, rsids, index, xrefs=None, source=None): | ||
| self.name = Marker.check_name(name) | ||
| self.source_name = str(self.name) |
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| self.source_name_map[marker.source.name][marker.name] = self.definition_names[marker.posstr()] | ||
| self.source_name_map[marker.source.name][marker.source_name] = self.definition_names[marker.posstr()] | ||
| continue | ||
| else: | ||
| new_name = marker.name | ||
| if len(self.markers_by_definition) > 1: | ||
| new_name = f"{marker.name}.v{len(self.definition_names) + 1}" | ||
| self.definition_names[marker.posstr()] = new_name | ||
| self.source_name_map[marker.source.name][marker.name] = new_name | ||
| self.source_name_map[marker.source.name][marker.source_name] = new_name |
| - 2413 distinct loci | ||
| [frequencies] | ||
| - 59753 haplotypes | ||
| - 59704 haplotypes |
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Correcting for frequency records using deprecated marker identifiers
standage
commented
Apr 24, 2025
microhapdb/tests/test_frequency.py
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| def test_marker_names_valid(): | ||
| freq_markers = set(microhapdb.frequencies.Marker) | ||
| markers = set(microhapdb.markers.Name) | ||
| invalid = freq_markers - markers | ||
| print(invalid) | ||
| assert len(invalid) == 0 |
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Added this regression test
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Additional issues discovered after running the regression test on the master branch.
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In this PR I'm updating the binder demo notebook. In the process, I changed the allele formatting from
A|T|T|AtoA:T:T:Ato avoid confusion with conventional genetic notation for haplotype phases. (I would love to have dropped the separators altogether, but some legacy functions of the database still need to handle microhaps with indels correctly.)I also found a bug with how non-1KGP allele frequencies were being renamed post-resolution of locus and allele definition identifiers.
It only affected four allele definitions at two loci, and was resolved with a simple change to the build procedure.None of the standard 1KGP allele frequencies or Ae scores were affected.Update: Actually, after running the new regression test on the master branch, I found three more affected loci—see comment below. As before, the 1KGP allele frequencies remain unaffected.