Intended to be used in readr::read_tsv()-like functions that accept a
col_names and a col_types argument.
def_names(format)
def_types(format)specify a format known to gggenomes, such as gff3, gbk, ...
a vector with default column names for the given format
a vector with default column types for the given format
def_names(): default column names for defined formats
def_types(): default column types for defined formats
gff3 ccciicccc seq_id,source,type,start,end,score,strand,phase,attributes
paf ciiicciiiiid seq_id,length,start,end,strand,seq_id2,length2,start2,end2,map_match,map_length,map_quality
blast ccdiiiiiiidd seq_id,seq_id2,pident,length,mismatch,gapopen,start,end,start2,end2,evalue,bitscore
bed ciicdc seq_id,start,end,name,score,strand
fai ci--- seq_id,seq_desc,length
seq_len cci seq_id,seq_desc,length
vcf cicccdccc seq_id,start,feat_id,ref,alt,qual,filter,info,format
# read a blast-tabular file with read_tsv
readr::read_tsv(ex("emales/emales-prot-ava.o6"), col_names=def_names("blast"))
#> Rows: 827 Columns: 12
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (2): seq_id, seq_id2
#> dbl (10): pident, length, mismatch, gapopen, start, end, start2, end2, evalu...
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> # A tibble: 827 × 12
#> seq_id seq_id2 pident length mismatch gapopen start end start2 end2
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Cflag_017B_0… Cflag_… 1 119 0 0 1 119 1 119
#> 2 Cflag_017B_0… RCC970… 1 119 0 0 1 119 1 119
#> 3 Cflag_017B_0… E4-10_… 0.991 119 1 0 1 119 1 119
#> 4 Cflag_017B_0… BVI_06… 0.991 119 1 0 1 119 1 119
#> 5 Cflag_017B_0… E4-10_… 0.983 119 2 0 1 119 1 119
#> 6 Cflag_017B_0… BVI_00… 0.983 119 2 0 1 119 1 119
#> 7 E4-10_112_00… E4-10_… 1 406 0 0 1 406 1 406
#> 8 E4-10_112_00… E4-10_… 1 406 0 0 1 406 1 406
#> 9 E4-10_112_00… BVI_06… 0.997 406 1 0 1 406 1 406
#> 10 E4-10_112_00… BVI_00… 0.987 406 5 0 1 406 1 406
#> # ℹ 817 more rows
#> # ℹ 2 more variables: evalue <dbl>, bitscore <dbl>