Add descriptions into appended column list #204
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Add option to include descriptions The added descriptions include the following - GENE_SUMMARY - VARIANT_SUMMARY - TUMOR_TYPE_SUMMARY - DIAGNOSTIC_SUMMARY - PROGNOSTIC_SUMMARY
calvinlu3
reviewed
Jun 30, 2023
test_Annotation.py
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| @@ -33,13 +33,15 @@ | |||
| HIGHEST_PX_LEVEL_INDEX = HIGHEST_DX_LEVEL_INDEX + 5 | |||
| UNKNOWN = 'Unknown' | |||
| NUMBER_OF_ANNOTATION_COLUMNS = 27 | |||
| NUMBER_OF_ANNOTATION_COLUMNS_WITH_DESCRIPTIONS = 32 | |||
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Would NUMBER_OF_ANNOTATION_COLUMNS_WITH_DESCRIPTIONS = NUMBER_OF_ANNOTATION_COLUMNS + len(DESCRIPTION_HEADERS) be better?
| @@ -210,6 +210,9 @@ def setsampleidsfileterfile(f): | |||
| SV_TYPE_HEADER = ['SV_CLASS_NAME', 'SV_TYPE', 'CLASS'] | |||
| SV_TYPES = ['DELETION', 'TRANSLOCATION', 'DUPLICATION', 'INSERTION', 'INVERSION', 'FUSION', 'UNKNOWN'] | |||
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| DESCRIPTION_HEADERS = ['GENE_SUMMARY', 'VARIANT_SUMMARY', 'TUMOR_TYPE_SUMMARY', 'DIAGNOSTIC_SUMMARY', | |||
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Do we also want to support mutation effect description?
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@calvinlu3 I was gonna say no, but looking at the request from the user, seems like I should support it.
zhx828
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The added descriptions include the following
This fixes #199