Created
January 14, 2019 09:37
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Getting extra sequence information for a phylotaR sequence
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| library(phylotaR) | |
| data("yeasts") | |
| # not all info is stored on the seq object | |
| str(yeasts@sqs@sqs[[1]]) | |
| # but the accession can be used to download extra info | |
| accssn <- yeasts@sqs@sqs[[1]]@id | |
| library(rentrez) | |
| smmry_obj <- entrez_summary(db = 'nucleotide', id = accssn) | |
| str(smmry_obj) | |
| # e.g. getting country | |
| subtypes <- strsplit(smmry_obj[['subtype']], split = '\\|')[[1]] | |
| subnames <- strsplit(smmry_obj[['subname']], split = '\\|')[[1]] | |
| (subnames[subtypes == 'country']) |
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