Check and convert poly(A) length file format

Detects whether an input poly(A) length file originates from nanopolish or tailfindr and, if necessary, converts it to the nanopolish-like format expected by the ninetails legacy (Guppy/Fast5) pipeline. Tailfindr cDNA output is explicitly rejected because the legacy pipeline supports only DRS (direct RNA sequencing) data.

Usage

check_polya_length_filetype(input)

Arguments

input

Character string or data frame. Either the path to a poly(A) length file (nanopolish .tsv or tailfindr .csv) or an in-memory data frame. Only DRS data are accepted for tailfindr input.

Value

A named list with two elements:

data

Data frame / tibble. Standardised poly(A) length data in nanopolish-like format, ready for downstream ninetails processing.

file_type

Character. One of "nanopolish" or "tailfindr_drs", indicating the detected input format.

Details

File-type detection is based on column names:

nanopolish

Identified by the presence of a qc_tag column. Returned as-is.

tailfindr DRS

Identified by the presence of read_id, tail_start, tail_end, samples_per_nt, and tail_length. Converted via convert_tailfindr_output.

tailfindr cDNA

Identified by the presence of a tail_is_valid column. Raises an error because cDNA data are not compatible with this pipeline.

If none of the above patterns match, an error is raised.

This function is part of the legacy pipeline (Guppy basecaller, multi-Fast5 files). It may be retired if the Fast5 format is deprecated.

See also

convert_tailfindr_output for the tailfindr conversion logic, extract_polya_data for subsequent processing of the standardised output, check_tails_guppy for the legacy pipeline entry point.

Examples

if (FALSE) { # \dontrun{

# run on nanopolish output
test <- ninetails::check_polya_length_filetype(
  input = system.file('extdata', 'test_data',
                      'nanopolish_output.tsv',
                      package = 'ninetails'))

# run on tailfindr output
test <- ninetails::check_polya_length_filetype(
  input = system.file('extdata', 'test_data',
                      'tailfindr_output.csv',
                      package = 'ninetails'))

} # }