baseq (version 0.1.4)

write.list_to_fastq: Write a list of sequence_bases and quality scores to a FASTQ file

Description

This function takes a list of sequence_bases and quality scores and writes them to a FASTQ file. The name of the list is used as the base name for the output file with the .fastq extension. Each sequence in the list is written to the output file in FASTQ format with the sequence name as the header and the quality scores on the following line.

Usage

write.list_to_fastq(sequence_list, output_dir = getwd())

Arguments

sequence_list

A list of sequence_bases where each element of the list is a named list containing "Sequence" and "QualityScore" elements.

output_dir

The directory path where the output file should be written. If not provided, the working directory will be used.

Examples

sequence_bases <- list("ACGT", "ATCG")
quality_scores <- list("IIII", "JJJJ")
sequences <- list(seq1=list(Sequence=sequence_bases[[1]], QualityScore=quality_scores[[1]]),
                       seq2=list(Sequence=sequence_bases[[2]], QualityScore=quality_scores[[2]]))
tempdir <- tempdir()
write.list_to_fastq(sequences, output_dir = tempdir)

# Write to working directory
# write.list_to_fastq(sequences)

# Write to custom directory
# write.list_to_fastq(sequences, output_dir = "/path/to/directory/")