readFastq: Read and write FASTQ files

In microseq: Basic Biological Sequence Handling

Read and write FASTQ files

Description

Reads and writes files in the FASTQ format.

Usage

readFastq(in.file)
writeFastq(fdta, out.file)

Arguments

in.file	url/directory/name of (gzipped) FASTQ file to read.
fdta	FASTQ object to write.
out.file	url/directory/name of (gzipped) FASTQ file to write.

Details

These functions handle input/output of sequences in the commonly used FASTQ format, typically used for storing DNA sequences (reads) after sequencing. If filenames (in.file or out.file) have the extension .gz they will automatically be compressed/uncompressed.

The sequences are stored in a tibble, opening up all the possibilities in R for fast and easy manipulations. The content of the file is stored as three columns, ‘⁠Header⁠’, ‘⁠Sequence⁠’ and ‘⁠Quality⁠’. If other columns are added, these will be ignored by writeFastq.

Value

readFastq returns a tibble with the contents of the (gzipped) FASTQ file stored in three columns of text. The first, named ‘⁠Header⁠’, contains the headerlines, the second, named ‘⁠Sequence⁠’, contains the sequences and the third, named ‘⁠Quality⁠’ contains the base quality scores.

writeFastq produces a (gzipped) FASTQ file.

Note

These functions will only handle files where each entry spans one single line, i.e. not the (uncommon) multiline FASTQ format.

Author(s)

Lars Snipen and Kristian Hovde Liland.

See Also

codereadFasta.

Examples

## Not run: 
# We need a FASTQ-file to read, here is one example file:
fq.file <- file.path(file.path(path.package("microseq"),"extdata"),"small.fastq.gz")

# Read and write
fdta <- readFastq(fq.file)
ok <- writeFastq(fdta[1:3,], out.file = "delete_me.fq")

# Make use of dplyr to copy parts of the file to another file
readFastq(fq.file) %>% 
  mutate(Length = str_length(Sequence)) %>% 
  filter(Length > 200) %>% 
  writeFasta(out.file = "long_reads.fa") # writing to FASTA file

## End(Not run)

microseq documentation built on Aug. 21, 2023, 5:10 p.m.