GISAIDR
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Wytamma
Programmatically interact with the GISAID database.
This seems to be on the GISAID side, but here is an illustration: ```R > chunk nrow(chunk) [1] 1000 > chunk$accession_id[duplicated(chunk$accession_id)] [1] "EPI_ISL_2911581" "EPI_ISL_2941558" "EPI_ISL_2941560" "EPI_ISL_2941562" "EPI_ISL_2941569" ```
Just a small possible enhancement, but would it be possible to have the `download `function automatically split the queries in chunks for searches when the length of `list_of_accession_ids` is >4000....
With the following query: ```R african_entries nrow(african_entries) [1] 1000 ``` I.e. it is doing the right thing but printing misleading output. P.S. how can I check which commit my current...
Hi, @Wytamma How can I download the data (e.g., H1N1) from the GISAID EpiFlu database using GISAIDR? Best, Yang
Currently the full metadata can only be downloaded with the sequence data. Is there a way to only get the metadata without downloading sequences? (#16)
When I download a metadata file there is no AA Substitutions column... I'm not sure why we have different columns. It seems maybe different users are getting different results from...
Would it also be possible to support searching by AA substitutions? E.g. I would like to be able to search for E_T11A,NSP3_S403L (picks up more BA.2.75 than searching by lineage)...
Need a test for the `export_fasta` function.
When updating GISAIDR sometimes multiple versions (the old and new) are installed at the same time. Currently can fix by running detach("package:GISAIDR", unload=TRUE) before updating. However, is there an automatic...
Columns are currently returned as strings but they should be cast into appropriate types before being returned to the user e.g. `date = as.Date(date)`.