def_names: Default column names and types for defined formats

In thackl/gggenomes: A Grammar of Graphics for Comparative Genomics

Default column names and types for defined formats

Description

Intended to be used in readr::read_tsv()-like functions that accept a col_names and a col_types argument.

Usage

def_names(format)

def_types(format)

Arguments

format

specify a format known to gggenomes, such as gff3, gbk, ...

Value

a vector with default column names for the given format

a vector with default column types for the given format

Functions

• def_names(): default column names for defined formats

• def_types(): default column types for defined formats

Defined formats, column types and names

  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

Examples

# read a blast-tabular file with read_tsv
readr::read_tsv(ex("emales/emales-prot-ava.o6"), col_names=def_names("blast"))

thackl/gggenomes documentation built on March 10, 2024, 7:26 a.m.