write_demultiplexed_sequences: Write demultiplexed sequences to fasta/q files in an output...

In cnobles/gintools: Genomic DNA Integration Analysis Tools

Description

This function will read in a sequence file, parse it given 'multiplexed_data' information and write the parsed files to an output directory. Specify the 'type' as "fasta" or "fastq" and give a sequence file path ('read_file_path') and the output folder path ('out_folder'). Data can either be comressed (into .gz format) or uncompressed.

Usage

write_demultiplexed_sequences(read_file_path, multiplexed_data, out_folder,
  type, read_name_pattern = "[\\w\\:\\-\\+]+", compress = TRUE)

Arguments

read_file_path	path to sequence file (fasta/q) to be demultiplexed.
out_folder	path to output directory.
type	character identifying the read class (R1, I1, I2, R2).
read_name_pattern	regular expression to be applied to the sequence names for identification. Default: "[\w\:\-\+]+".
compress	logical indicating if the output files should be gzip compressed (.gz, default) or uncompressed.

Details

write_demultiplexed_sequences will write fasta/q files to an output directory when supplied with grouping information ('multiplexed_data').

Author(s)

Christopher Nobles, Ph.D.

cnobles/gintools documentation built on Aug. 22, 2019, 10:36 a.m.