Extract antibiograms from NCBI biosample metadata #90
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Related to issue #64.
This PR adds new functionality to extract antibiograms from NCBI BioSample metadata.
Example: https://www.ncbi.nlm.nih.gov/biosample/SAMN18874759/
The above BioSample contains an antibiogram in its description field. Before this PR this field was not parsed but instead the text "WEBSEQ WARNING: DESCRIPTION CONTAINS A TABLE. CHECK MANUALLY." was returned within the description variable of the returned data frame.
This PR changes the structure of the object returned by
ncbi_parse()when parsing biosample metadata. It will no longer be a data frame, but a list (!) of data frames. If none of the biosamples contain a table in their description field, it will return a list with a single data frame called "main". If any of the biosamples contain e.g. an antibiogram, these will be merged and the function will return these as a second list item.Note, the function will not explicitly look for antibiograms but any table in the description field. Note, the function is only tested to work with a single table in the description field. I have not yeet found an example with multiple tables, if I'll find one, I'll update, if necessary.