extract_read_data: Extract the read data from a fast5 file

In adnaniazi/nanoporePractical: Interactive squiggle browser for Oxford Nanopore data

Description

This function can deal with both multifast5 files and single fast5 files. It can handle files basecalled with standard or the flip flop model.

Usage

extract_read_data(file_path = NA, read_id_fast5_file = NA,
  plot_debug = FALSE, basecalled_with, basecall_group, multifast5, model,
  plotting_library)

Arguments

file_path	a character string [NA]. Path of the single fast5 file. Use it if the file to be read is a single fast file. If the file to be read is multifast5 file, then keep this parameter as NA. Also set multifast5 flag to FALSE
read_id_fast5_file	a list [NA]. A list of 'read_id' and 'fast5_file' path. Use this option when a read from a multifast5 file is to be read. In such a case, you should set file_path to NA, and set multifast5 flag to TRUE.
plot_debug	a logical [FALSE]. Should data for plotting debug info in the plots be computed
basecalled_with	a character string. Specify if the data is from 'albacore' or 'guppy'
basecall_group	a character string. Name of the level in the Fast5 file hierarchy from which to read the data e.g. "Basecall_1D_000"
multifast5	a logical. Set it to TRUE if the file to be processed is multifast5. Set it to FALSE if the file to be processed is a single fast5 file
model	a string. Set to 'flipflop' if the basecalling model is flipflop. Set to 'standard' if the basecalling model is standard model.
plotting_library	a string

Value

a list

Examples

## Not run: 

extract_read_data(file_path = '/path/to/the/file',
                  read_id_fast5_file = NA,
                  plot_debug = F,
                  basecalled_with = 'albacore',
                  basecall_group = 'Basecall_1D_000',
                  multifast5 = TRUE,
                  model = 'standard',
                  plotting_library = 'rbokeh')

## End(Not run)

adnaniazi/nanoporePractical documentation built on May 14, 2019, 3:05 a.m.