feat: add script to get organisms and genomes from ncbi api (#159) #160
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hunterckx
commented
Nov 7, 2024
| "taxon": genome_info["organism"]["organism_name"], | ||
| "taxonomyId": genome_info["organism"]["tax_id"], | ||
| "accession": genome_info["accession"], | ||
| "isRef": (not (refseq_category is None)) and ("reference" in refseq_category), |
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Is there a more appropriate way to derive isRef?
hunterckx
commented
Nov 7, 2024
| assemblies_df = pd.DataFrame(requests.get(ASSEMBLIES_URL).json()["data"])[["ucscBrowser", "genBank", "refSeq"]] | ||
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| gen_bank_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="pairedAccession", right_on="genBank") | ||
| ref_seq_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="accession", right_on="refSeq") |
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Do pairedAccession/genBank and accession/refSeq actually correspond like this? Do we need to be using both pairs?
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hunterckx
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NoopDog
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Nov 16, 2024
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