Merge pull request #184 from cidgoh/madeline-1

Adapt to new DH template
cidgoh · Oct 25, 2024 · 3c5bc08 · 3c5bc08
2 parents c889ce1 + 377ad62
commit 3c5bc08
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diff --git a/assets/virus_functionalAnnotation/NC_045512.2/Pokay_functionalAnnotation_SARSCoV2_v1.0.tsv b/assets/virus_functionalAnnotation/NC_045512.2/Pokay_functionalAnnotation_SARSCoV2_v1.0.tsv
diff --git a/assets/virus_functionalAnnotation/NC_045512.2/Pokay_functionalAnnotation_SARSCoV2_v3.0.tsv b/assets/virus_functionalAnnotation/NC_045512.2/Pokay_functionalAnnotation_SARSCoV2_v3.0.tsv
diff --git a/assets/virus_functionalAnnotation/NC_063383.1/pokay_annotations_v_0.2.tsv b/assets/virus_functionalAnnotation/NC_063383.1/pokay_annotations_v_0.2.tsv
@@ -0,0 +1,7 @@
+"organism"	"reference accession"	"reference database name"	"nucleotide position"	"original mutation description"	"nucleotide mutation"	"amino acid mutation"	"amino acid mutation alias"	"gene name"	"gene symbol"	"gene orientation"	"strand orientation"	"protein name"	"protein symbol"	"measured variant functional effect"	"inferred variant functional effect"	"viral life cycle functional effect"	"measured variant functional effect description"	"CVX code"	"DrugBank Accession Number"	"Antibody Registry ID"	"author"	"publication year"	"URL"	"DOI"	"PMID"	"peer review status"	"curator"	"mutation functional annotation resource"
+"Monkeypox virus"	"NC_063383.1"	"RefSeq"	""	"T220A"	""	""	""	""	""	""	""	""	""	"drug resistence"	""	""	"May represent novel Tecovirimat-resistence mutation as likely at the interaction interface for the drug and observed in two site samples (0.44 and 0.49 frequency, culture  contaminated and culture negative respectively) from an HIV-positive patient treated with Tecovirimat."	""	""	""	"Garrigues"	"2023"	""	""	""	"unknown"	"Paul Gordon"	"Pokay"
+"Monkeypox virus"	"NC_063383.1"	"RefSeq"	""	"T220I"	""	""	""	""	""	""	""	""	""	"drug resistence"	""	""	"May represent novel Tecovirimat-resistence mutation as likely at the interaction interface for the drug and observed in two site samples (0.44 and 0.49 frequency, culture  contaminated and culture negative respectively) from an HIV-positive patient treated with Tecovirimat."	""	""	""	"Garrigues"	"2023"	""	""	""	"unknown"	"Paul Gordon"	"Pokay"
+"Monkeypox virus"	"NC_063383.1"	"RefSeq"	""	"T245I"	""	""	""	""	""	""	""	""	""	"drug resistence"	""	""	"May represent novel Tecovirimat-resistence mutation as likely at the interaction interface for the drug and observed in a single site sample (0.12 frequency, culture positive with EC50 0.3820uM) from an HIV-positive patient treated with Tecovirimat, may be dragged along by D294V (known from literature) from same sample with 0.91 frequency."	""	""	""	"Garrigues"	"2023"	""	""	""	"unknown"	"Paul Gordon"	"Pokay"
+"Monkeypox virus"	"NC_063383.1"	"RefSeq"	""	"D294V"	""	""	""	""	""	""	""	""	""	"drug resistence"	""	""	"May represent novel Tecovirimat-resistence mutation as likely at the interaction interface for the drug and observed in a single site sample (0.91 frequency, culture positive with EC50 0.3820uM) from an HIV-positive patient treated with Tecovirimat."	""	""	""	"Garrigues"	"2023"	""	""	""	"unknown"	"Paul Gordon"	"Pokay"
+"Monkeypox virus"	"NC_063383.1"	"RefSeq"	""	"A265D"	""	""	""	""	""	""	""	""	""	"drug resistence"	""	""	"May represent novel Tecovirimat-resistence mutation as likely at the interaction interface for the drug and observed in a single site sample (0.5 frequency, culture contaminated) from an HIV-positive patient treated with Tecovirimat. Novel T220A also found at similar frequency (0.44) in the same sample, as well as A295E which is known from the literature (0.51 frequency)."	""	""	""	"Garrigues"	"2023"	""	""	""	"unknown"	"Paul Gordon"	"Pokay"
+"Monkeypox virus"	"NC_063383.1"	"RefSeq"	""	"T289A"	""	""	""	""	""	""	""	""	""	"drug resistence"	""	""	"May represent novel Tecovirimat-resistence mutation as likely at the interaction interface for the drug and observed in a single site sample (0.41 frequency, culture data pending) from an HIV-positive patient treated with Tecovirimat."	""	""	""	"Garrigues"	"2023"	""	""	""	"unknown"	"Paul Gordon"	"Pokay"