Fix renaming #111
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Fix renaming #111
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standage
commented
Feb 24, 2023
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| mh21KK-320.v1,Italians,A|A|C|A,0.25000,Turchi2019 | ||
| mh21KK-320.v1,Italians,A|A|C|G,0.10700,Turchi2019 | ||
| mh21KK-320.v1,Italians,G|A|C|A,0.12200,Turchi2019 | ||
| mh21KK-320.v1,Italians,G|A|C|G,0.16800,Turchi2019 | ||
| mh21KK-320.v1,Italians,G|A|T|A,0.07700,Turchi2019 | ||
| mh21KK-320.v1,Italians,G|G|C|A,0.08200,Turchi2019 | ||
| mh21KK-320.v1,Italians,G|G|C|G,0.19400,Turchi2019 |
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These frequencies now correspond to the correct definition (see #110).
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| mh18KK-293.v1,MHDBP-7c055e7ee8,A|G|A|A,0.59300,Staadig2021 | ||
| mh18KK-293.v1,MHDBP-7c055e7ee8,A|G|A|G,0.02000,Staadig2021 | ||
| mh18KK-293.v1,MHDBP-7c055e7ee8,A|T|A|G,0.02000,Staadig2021 | ||
| mh18KK-293.v1,MHDBP-7c055e7ee8,A|T|G|A,0.07300,Staadig2021 | ||
| mh18KK-293.v1,MHDBP-7c055e7ee8,G|G|A|A,0.24700,Staadig2021 | ||
| mh18KK-293.v1,MHDBP-7c055e7ee8,G|T|A|A,0.01300,Staadig2021 | ||
| mh18KK-293.v1,MHDBP-7c055e7ee8,G|T|A|G,0.03300,Staadig2021 |
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Also fixed some Staadig and Gandotra associated frequencies.
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| def resolve(self): | ||
| if len(self) <= 1: | ||
| for marker in self.markers: | ||
| yield marker | ||
| return | ||
| definitions = set(self.markers_by_definition) | ||
| for marker in sorted(self.markers, key=lambda m: (m.sources[0].year, m.name.lower())): | ||
| if marker.posstr() in self.definition_names: | ||
| message = f"Marker {marker.name} as defined in {marker.sources[0].name} was defined previously and is redundant" | ||
| print(message) | ||
| self.source_name_map[marker.sources[0].name][marker.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.sources[0].name][marker.name] = new_name | ||
| marker.name = new_name | ||
| for othermarker in self.markers_by_definition[marker.posstr()]: | ||
| if othermarker != marker: | ||
| marker.sources.append(othermarker.sources[0]) | ||
| yield marker |
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Refactored code for determining which names are applied to which marker definitions.
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| self.source = source | ||
| self.sources = list() | ||
| if source is not None: | ||
| self.sources.append(source) |
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Source list now instead of a single source.
Merged
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The PR updates the database build code and fixes a bug with marker renaming. This fixes the issue noted in #110 with MH allele frequencies coming out of sync with the precise marker definitions to which they correspond.
As an added benefit, markers defined consistently in multiple studies will now have each study noted in its "Source" column. Markers from chr19 are shown below to demonstrate.
closes #110.