make specific ftp download paths for a dataframe with ftp_paths and assembly accessions

Usage

make_download_urls(data, type)

Arguments

data: a dataframe with the columns 'ftp_path' and 'asm_acc' ftp_path should be a column produced by the function make_ftp_paths()
type: type of download path to generate, one of: 'fna', 'gbff', 'gff', 'gtf', 'faa', 'cds'

Value

returns the original dataframe with an added column, named "type_download"

Examples

make_download_urls(klebsiella_example_dat, type='fna')
#> # A tibble: 200 × 70
#>    `#label`                   FDA_lab_id HHS_region IFSAC_category LibraryLayout
#>    <chr>                      <chr>      <chr>      <chr>          <chr>        
#>  1 PDT001211141.1|SAMN240097… NULL       NULL       NULL           NULL         
#>  2 PDT000434574.1|SAMN087838… NULL       NULL       NULL           PAIRED       
#>  3 PDT001009222.1|SAMN185110… NULL       NULL       NULL           NULL         
#>  4 PDT000414882.1|SAMN102412… NULL       NULL       NULL           NULL         
#>  5 PDT000431384.1|SAMN075255… NULL       NULL       NULL           PAIRED       
#>  6 PDT001020147.1|SAMN190166… NULL       NULL       NULL           PAIRED       
#>  7 PDT000875073.1|SAMN064386… NULL       NULL       NULL           PAIRED       
#>  8 PDT000172180.4|SAMN059560… NULL       NULL       NULL           NULL         
#>  9 PDT000852554.1|SAMN149675… NULL       NULL       NULL           NULL         
#> 10 PDT001025462.1|SAMN189771… NULL       NULL       NULL           PAIRED       
#> # ℹ 190 more rows
#> # ℹ 65 more variables: PFGE_PrimaryEnzyme_pattern <chr>,
#> #   PFGE_SecondaryEnzyme_pattern <chr>, Platform <chr>, Run <chr>,
#> #   asm_acc <chr>, asm_level <chr>, asm_stats_contig_n50 <dbl>,
#> #   asm_stats_length_bp <dbl>, asm_stats_n_contig <dbl>, assembly_method <chr>,
#> #   attribute_package <chr>, bioproject_acc <chr>, bioproject_center <chr>,
#> #   biosample_acc <chr>, isolate_identifiers <chr>, collected_by <chr>, …