Yes I think that's because you use the official interface that GISAID provides; the AA Substitutions column only seems present when one selects records directly on the GISAID website & then presses Download at the bottom, where one can then choose between downloading the metadata or the FASTA sequences...

With manually selected & downloaded GISAID records I get a tsv back with these columns

 [1] "Virus name"                      "Accession ID"                   
 [3] "Collection date"                 "Location"                       
 [5] "Host"                            "Additional location information"
 [7] "Sampling strategy"               "Gender"                         
 [9] "Patient age"                     "Patient status"                 
[11] "Last vaccinated"                 "Passage"                        
[13] "Specimen"                        "Additional host information"    
[15] "Lineage"                         "Clade"                          
[17] "AA Substitutions"

It's only when I used the GISAIDR download function that I get the columns

[1] "id"                      "virus_name"             
[3] "passage_details_history" "accession_id"           
[5] "collection_date"         "submission_date"        
[7] "information"             "length"                 
[9] "host"                    "location"               
[11] "originating_lab"         "submitting_lab"

which misses the AA Substitutions field (confirmed by directly inspecting the gisaidr_data_tmp.tar file)...

I think getting a tsv back with all the columns included could be supported if the download would be driven via RSelenium, similar to how I download the GISAID batch download packages that are available, https://stackoverflow.com/questions/72632118/download-covid-patient-metadata-from-gisaid-website-in-r-using-rselenium.

This would involve:
(1) enter username & password at https://www.epicov.org/epi3/frontend and press Login button
(2) press Search tab
(3) press Select tab at the bottom
(4) paste GISAID access nrs (no more than 10 000 at a time) (or point to csv file with desired access nrs)
(5) press OK button
(6) press Download button at the bottom
(7) Select Patient status metadata or Nucleotide sequences (FASTA)
(8) press Download

Aside from downloading particular records in this way (which should also get the AA substitutions field), I think supporting the download of the batch download packages via RSelenium could be cool too, but you would probably just have to put it in a separate function, as one can then only download the whole database (download+reading it in in R then just takes 2 mins), and not a particular subset.

Difference in metadata columns #27

Description

Metadata

Assignees

Labels

Projects

Milestone

Relationships

Development

Issue actions