Study import QC (ref genome validation + reported trait cleaning) #331
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(will be imported/used by the study import pipeline)
ens-lgil
reviewed
Feb 26, 2024
curation/imports/scoring_file.py
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| else: | ||
| match_rate: float = float(match) / (match + mismatch) | ||
| report_func(f'Match rate: {match_rate}') | ||
| if match_rate < 0.9: |
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Should we store the threshold (i.e. 0.9) in a variable, preferably in the config file ?
curation/scripts/qc_ref_genome.py
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| def get_variation_from_ensembl(rsids: list[str], ref_genome): | ||
| url = 'https://grch37.rest.ensembl.org/variation/human/' if ref_genome == '37' else 'https://rest.ensembl.org/variation/human/' |
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Should we store the 2 Ensembl URLs in a dictionnary instead ?
e.g.:
servers = {
'37': 'https://grch37.rest.ensembl.org',
'38': 'https://rest.ensembl.org/'
}
The root url is also stored in server line 12
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Do we have any README or flowchart describing how it works? |
ens-lgil
approved these changes
Feb 26, 2024
ens-lgil
approved these changes
Mar 5, 2024
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