FastaRead — FASTA file reader module

This module provides the type FastaReader which allows to parse FASTA files in Julia. It is designed to be lightweight and fast, and it’s inspired to kseq.h. It reads files on the fly, keeping only one entry at a time in memory, and it can read gzip-compressed files.

Here is a quick example:

julia> using FastaRead

julia> fr = FastaReader("somefile.fasta")

julia> for (name, seq) in fr
         println("$name : $seq")
       end

julia> close(fr)

Installation

You can install FastaRead from Julia’s package manager:

julia> Pkg.add("FastaRead")

Usage

There is one central type provided by the module, FastaReader, which takes a file name as argument, and has a parameter to set the output type:

FastaReader{T}(filename::String)

creates an object which is able to parse FASTA files. The file can be in plain text format or in gzip-compressed format. The type T determines the output type of the sequences: the default is ASCIIString, which is the fastest option; another fast output type is Vector{Uint8}, which is less readable but has the advantage of being mutable; any other container T for which convert(T, ::Vector{Uint8}) is defined will work, but it will pass through a conversion step and therefore be slower.

The data can be read out by iterating the FastaReader object:

for (name, seq) in FastaReader("somefile.fasta")
    # do something with name and seq
end

As shown, the iterator returns a tuple containing the description (always an ASCIIString) and the data (whose type is set when creating the FastaReader object (e.g. FastaReader{Vector{Uint8}}(filename)).

The FastaReader type has a field num_parsed which contains the number of entries parsed so far.

Other ways to read out the data are via the readentry() and readall() functions.

readentry(fr::FastaReader)

This function can be used to read entries one at a time:

fr = FastaReader("somefile.fasta")
name, seq = readentry(fr)

See also the eof() function.

readall(fr::FastaReader)

This function extends Base.readall(): it parses a whole FASTA file at once, and returns an array of tuples, each one containing the description and the sequence.

rewind(fr::FastaReader)

This function rewinds the reader, so that it can restart the parsing again without closing and re-opening it. It also resets the value of the num_parsed field.

eof(fr::FastaReader)

This function extends Base.eof() and tests for end-of-file condition; it is useful when using readentry():

fr = FastaReader("somefile.fasta")
while !eof(fr)
    name, seq = readentry(fr)
    # do something
end
close(fr)

close(fr::FastaReader)

This function extends Base.close() and closes the stream associated with the FastaReader; the reader must not be used any more after this function is called.