write.fastq: Write FASTQ Files

In LocaTT: Geographically-Conscious Taxonomic Assignment for Metabarcoding

Write FASTQ Files

Description

Writes FASTQ files.

Usage

write.fastq(names, sequences, quality_scores, file, comments)

Arguments

names	A character vector of sequence names.
sequences	A character vector of sequences.
quality_scores	A character vector of quality scores.
file	A string specifying the path to a FASTQ file to write.
comments	An optional character vector of sequence comments.

Value

No return value. Writes a FASTQ file.

See Also

read.fastq for reading FASTQ files.
write.fasta for writing FASTA files.
read.fasta for reading FASTA files.

Examples

# Get path to example sequences CSV file.
path_to_CSV_file<-system.file("extdata",
                              "example_query_sequences.csv",
                              package="LocaTT",
                              mustWork=TRUE)

# Read the example sequences CSV file.
df<-read.csv(file=path_to_CSV_file,stringsAsFactors=FALSE)

# Create a temporary file path for the FASTQ file to write.
path_to_FASTQ_file<-tempfile(fileext=".fastq")

# Write the example sequences as a FASTQ file.
write.fastq(names=df$Name,
            sequences=df$Sequence,
            quality_scores=df$Quality_score,
            file=path_to_FASTQ_file,
            comments=df$Comment)

LocaTT documentation built on Nov. 2, 2023, 6:09 p.m.