Read and write FASTQ files
Reads and writes files in the FASTQ format.
readFastq(in.file) writeFastq(fdta, out.file)
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. |
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.
writeFastq produces a (gzipped) FASTQ file.
These functions will only handle files where each entry spans one single line, i.e. not the (uncommon) multiline FASTQ format.
Lars Snipen and Kristian Hovde Liland.
codereadFasta.
## 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.