select atleast one sequence!

[josenikhid97]

hello @julienfumey , @sebastianduchene , @Wytamma

i have written a script for downloading the 100 sequences everyday from beginning of pandemic to till now. now when I run the script it pops up an error saying that " Select at least one sequence! " and the script is down below

install.packages('devtools', repos = "http://cran.us.r-project.org")

install.packages("devtools")

devtools::install_github("Wytamma/GISAIDR", force = TRUE)

library(GISAIDR)
for (day in dates){
credentials <- login(username = , password = )
df <- query(credentials = credentials,complete = T, high_coverage = T,low_coverage_excl = T,collection_date_complete = T,from = day, to= day,start_index = 1,nrows =100)
df <- df[df$host == 'Human',]
all(df$length > 29000)
list_of_accession_ids <- df$accession_ids
full_df_with_seq <- download(
credentials = credentials,
list_of_accession_ids = list_of_accession_ids,
get_sequence=T)
full_df_with_seq$sequence
export_fasta(full_df_with_seq, out_file_name = paste0(day,".fasta"), date_format='%Y-%m-%d',delimiter='/')}

can you make this piece of code to work

best
jose

[Wytamma]

Hi @josenikhid97 I suspect on of one of the days list_of_accession_ids is empty i.e. no sequences match the query for that day. I'd suggest adding a check for that e.g.

if (nrow(df) > 0) {
  full_df_with_seq <- download(
    credentials = credentials,
    list_of_accession_ids = list_of_accession_ids,
    get_sequence = T
  )
}

[josenikhid97]

Hello, @Wytamma i changed the line of code u mentioned, but it is still the same

@code

credentials<- login(username = ,  password = )
df <- query(credentials = credentials,complete = T, high_coverage = T,low_coverage_excl = T,collection_date_complete = T,from = '2020-08-20', to= '2020-08-20',start_index = 1,nrows =50)
df <- df[df$host == 'Human',]
all(df$length > 29000)
list_of_accession_ids <- df$accession_ids
if (nrow(df) > 0) {
  full_df_with_seq <- download(
    credentials = credentials, 
    list_of_accession_ids = list_of_accession_ids,
    get_sequence= T 
  )
}
full_df_with_seq$sequence
export_fasta(full_df_with_seq, out_file_name = paste0('2020-08-19',".fasta"), date_format='%Y-%m-%d',delimiter='/')

I am attaching the error, I even changed the dates but no luck ;(

thanks in advance,

[Wytamma]

Ah, it looks like you've got a typo

list_of_accession_ids <- df$accession_ids

should be

list_of_accession_ids <- df$accession_id