Skip to contents

Function to fill a `.fastq` file with random reads

fill_fastq.Rd

This function populates a `.fastq` file with random reads for a given patient ID. The function first creates an empty `.fastq` file using the patient ID, then generates a specified number of random reads, and writes them to the file.

Usage

fill_fastq(patient_id, output_dir = tempdir(), n, read_length)

Arguments

patient_id

A character string representing the patient ID.

output_dir

A character string specifying the directory where the `.fastq` file will be saved.

n

An integer specifying the number of reads to generate.

read_length

An integer specifying the length of each read. It should be multiple of 4. Default is 8.

Details

The function first checks if the `.fastq` file already exists. If it does, it appends the new reads to the existing file. If not, it creates a new file. The generated reads are in `.fastq` format, which consists of four lines per read:

  • Line 1: Sequence identifier (e.g., @patient_id_read1)

  • Line 2: Random DNA sequence

  • Line 3: Separator (e.g., +)

  • Line 4: Quality scores

Examples

# Fill a `.fastq` file for patient ID "patient_123" with 2 reads of length 8
fill_fastq("patient_123",output_dir = tempdir(), n = 2, read_length = 8)
#> File already exists. Appending reads to the existing file.
#> Populated /tmp/RtmpCk48DO/patient_123.fastq with 2 reads.