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Check if the provided directory contains Fast5 files in the correct format

Source: R/ninetails_misc_helper_functions.R
check_fast5_filetype.Rd

Analyzes the structure of the first Fast5 file in the given directory and checks whether it fulfills the analysis requirements: the file must be a multi-Fast5, basecalled by Guppy basecaller, and contain the provided basecall group and RNA reads. Otherwise the function throws a descriptive error.

Usage

check_fast5_filetype(workspace, basecall_group)

Arguments

workspace

Character string. Full path of the directory containing the basecalled multi-Fast5 files.

basecall_group

Character string. Name of the level in the Fast5 file hierarchy from which data should be extracted (e.g., "Basecall_1D_000").

Value

Prints to console: data type (RNA), Fast5 file type (multi-Fast5), basecaller used, basecaller version, and basecalling model. Called for its side effect; returns invisibly.

Acknowledgements

This lookup function is inspired by adnaniazi's explore-basecaller-and-fast5type.R from tailfindr: https://github.com/adnaniazi/tailfindr/blob/master/R/explore-basecaller-and-fast5type.R.

See also

is_multifast5 for the multi-Fast5 format check, is_RNA for the RNA content check, check_tails_guppy where this function is called during pipeline initialization

Examples

if (FALSE) { # \dontrun{

check_fast5_filetype(
  workspace = '/path/to/guppy/workspace',
  basecall_group = 'Basecall_1D_000'
)

} # }