Read sequence index

Read sequence index

read_seq_len(
  file,
  col_names = def_names("seq_len"),
  col_types = def_types("seq_len"),
  ...
)

read_fai(file, col_names = def_names("fai"), col_types = def_types("fai"), ...)

Arguments

file

with sequence length information

col_names

Either TRUE, FALSE or a character vector of column names.

If TRUE, the first row of the input will be used as the column names, and will not be included in the data frame. If FALSE, column names will be generated automatically: X1, X2, X3 etc.

If col_names is a character vector, the values will be used as the names of the columns, and the first row of the input will be read into the first row of the output data frame.

Missing (NA) column names will generate a warning, and be filled in with dummy names ...1, ...2 etc. Duplicate column names will generate a warning and be made unique, see name_repair to control how this is done.

col_types

One of NULL, a cols() specification, or a string. See vignette("readr") for more details.

If NULL, all column types will be inferred from guess_max rows of the input, interspersed throughout the file. This is convenient (and fast), but not robust. If the guessed types are wrong, you'll need to increase guess_max or supply the correct types yourself.

Column specifications created by list() or cols() must contain one column specification for each column. If you only want to read a subset of the columns, use cols_only().

Alternatively, you can use a compact string representation where each character represents one column:

• c = character

• i = integer

• n = number

• d = double

• l = logical

• f = factor

• D = date

• T = date time

• t = time

• ? = guess

• _ or - = skip

By default, reading a file without a column specification will print a message showing what readr guessed they were. To remove this message, set show_col_types = FALSE or set `options(readr.show_col_types = FALSE).

...

additional parameters, passed to read_tsv

Functions

• read_seq_len(): read seqs from a single file in fasta, gbk or gff3 format.

• read_fai(): read seqs from a single file in seqkit/samtools fai format.