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Add Transcripts GnomadAD constraints and clinvar reports in the export #568

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incardon opened this issue Jul 8, 2022 · 1 comment
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enhancement New feature or request

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@incardon
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incardon commented Jul 8, 2022

Is your feature request related to a problem? Please describe.
No

Describe the solution you'd like
Having in the export Transcripts, GnomAD constraints, and clivar reports

Describe alternatives you've considered
None

Additional context
No additional context

@incardon incardon added the enhancement New feature or request label Jul 8, 2022
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incardon commented Jul 11, 2022

Implementation Proposal
RowWithTranscripts that wrap the result table in order to make the exporters working with the additional transcript columns.
load_molecular_impact moved in model.py to be usable in the exporter. Adding test with and without jannovar enables with mockers in the test.
Extend CaseExportTableQueryPartsBuilder with GnomAD constraints
Extend ProjectExportTableQueryPartsBuilder with GnomAD constraints

ExtendQueryPartsGnomadConstraintsJoin add additional fields: "oe_lof", "oe_lof_upper", "oe_lof_lower

Affected Components
Exports

Affected Modules/Files
variants/file_export.py, variants/models.py variants/tests/test_file_export.py factories.py variants/query.py

Required Architectural Changes
A RowWithTranscripts must be created

Implementation Sketch
Create a RowWithTranscripts following the design of RowWith*. All the other fields are in the query, so not need to extend with RowWithSomething.

incardon pushed a commit to incardon/varfish-server that referenced this issue Jul 11, 2022
Related-Issue: varfish-org#568
Projected-Results-Impact: none
incardon pushed a commit to incardon/varfish-server that referenced this issue Jul 11, 2022
Related-Issue: varfish-org#568
Projected-Results-Impact: none
incardon pushed a commit to incardon/varfish-server that referenced this issue Jul 11, 2022
Related-Issue: varfish-org#568
Projected-Results-Impact: none
incardon pushed a commit to incardon/varfish-server that referenced this issue Jul 11, 2022
Related-Issue: varfish-org#568
Projected-Results-Impact: none
incardon pushed a commit to incardon/varfish-server that referenced this issue Jul 11, 2022
Related-Issue: varfish-org#568
Projected-Results-Impact: none
incardon pushed a commit to incardon/varfish-server that referenced this issue Jul 11, 2022
Related-Issue: varfish-org#568
Projected-Results-Impact: none
incardon pushed a commit to incardon/varfish-server that referenced this issue Jul 11, 2022
Related-Issue: varfish-org#568
Projected-Results-Impact: none
incardon pushed a commit to incardon/varfish-server that referenced this issue Jul 11, 2022
Related-Issue: varfish-org#568
Projected-Results-Impact: none
incardon pushed a commit to incardon/varfish-server that referenced this issue Jul 11, 2022
Related-Issue: varfish-org#568
Projected-Results-Impact: none
incardon pushed a commit to incardon/varfish-server that referenced this issue Jul 13, 2022
Related-Issue: varfish-org#568
Projected-Results-Impact: none
incardon pushed a commit to incardon/varfish-server that referenced this issue Jul 22, 2022
Related-Issue: varfish-org#568
Projected-Results-Impact: none
incardon pushed a commit to incardon/varfish-server that referenced this issue Jul 22, 2022
stolpeo pushed a commit that referenced this issue Jul 26, 2022
#592)

Closes: #568
Related-Issue: #568
Projected-Results-Impact: none

Co-authored-by: Incardona Pietro <incardon@mpi-cbg.de>
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