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Creates a script to add orphacodes to directory emx file #19

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merged 1 commit into from
Feb 8, 2022

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@svituz svituz commented Feb 8, 2022

PR that creates a script to add Orphacodes to collections in the BBMRI directory EMX file.
The script gets in input the directory EMX file, the Orphanet file with mappings (i.e., the one used by OrphaCodes class) and the output file.
For every ICD-10 diagnosis in the input file, it gets the mappings and if the orphanet mapping type is BTNT or EXACT it
adds the orphacode to the collection.

NB: The script gets the mapping Orphacodes from OrphaCodes class in orphacodes.py. The class marks the mapping type
from icd to orpha as the inverse of orpha to icd, so BTNT become NTBT. That means, that we need to check for the NTBT
mapping level in the script.

@holubp holubp merged commit ce48e71 into BBMRI-ERIC:master Feb 8, 2022
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2 participants