FASTX
Read and write files in FASTA and FASTQ format, the most common biological sequence file format.
Installation
You can install FASTX from the julia REPL. Press ]
to enter pkg mode again, and enter the following:
(v1.8) pkg> add FASTX
Quickstart
"FASTX" is a shorthand for the two related formats FASTA and FASTQ, which are handled by the two modules FASTX.FASTA
and FASTX.FASTQ
, respectively.
- Construct records from raw parts
julia> record = FASTARecord("some header", dna"TAGAAGA");
julia> (identifier(record), description(record), sequence(record))
("some", "some header", "TAGAAGA")
julia> sequence(LongDNA{2}, record)
7nt DNA Sequence:
TAGAAGA
- Validate files
julia> validate_fasta(IOBuffer(">ABC\nDEF")) === nothing
true
julia> validate_fastq(IOBuffer("@ABC\nTAG\n+\nDDD")) === nothing
true
- Read FASTX files
record = FASTAReader(first, IOBuffer(">ABC\nDEF"))
sequence(record) == "DEF" # should be true
# Or with do-syntax
FASTAReader(GzipDecompressorStream(open(path))) do reader
for record in reader
# do something with record
end
end
- Write FASTX files
FASTQWriter(open(path, "w")) do writer
for record in records
write(writer, record)
end
end
See more details in the sections in the sidebar.
Contributing
We appreciate contributions from users including reporting bugs, fixing issues, improving performance and adding new features.
Take a look at the contributing files detailed contributor and maintainer guidelines, and code of conduct.