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VLE/KBE-4/cadd_integration #65

Merged
merged 3 commits into from
Sep 30, 2024
Merged

VLE/KBE-4/cadd_integration #65

merged 3 commits into from
Sep 30, 2024

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Akaud
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@Akaud Akaud commented Sep 24, 2024

Implemented cadd tool

fetch_cadd_scores :
Returns CADD scores for a given chromosome and genomic position or range (SNV or region).
Handles single-nucleotide variants (SNVs) by constructing call to cadd tool URLs.

evaluate_cadd_score:
Fetches the highest PHRED score for each genomic position using the fetch_cadd_scores function.
Returns the highest PHRED score for evaluation, or an error message if unavailable.

add_cadd_eval_column :
Adds a new column (cadd_eval(PHRED)) and applies the evaluate_cadd_score function row by row in the DataFrame to compute and store CADD score evaluations.

@Akaud Akaud requested a review from Strexas September 24, 2024 16:37
@Akaud Akaud self-assigned this Sep 24, 2024
@Akaud Akaud added the tool label Sep 24, 2024
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@Strexas Strexas left a comment

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Small changes + script should be in tools folder

@Akaud Akaud requested a review from Strexas September 25, 2024 20:01
@Akaud Akaud merged commit 3f818ab into main Sep 30, 2024
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2 participants