BioGenerics

Abstract formatted input/output type.

Abstract data reader type.

See subtypes(AbstractReader) for all available data readers.

Abstract data writer type.

See subtypes(AbstractWriter) for all available data writers.

stream(io::AbstractFormattedIO)

Return the underlying IO object; subtypes of AbstractFormattedIO must implement this method.

tryread!(reader::AbstractReader, output)

Try to read the next element into output from reader.

If the result could not be read, then nothing will be returned instead.

MissingFieldException <: Exception

An exception type thrown when a missing field of a record is accessed.

intempdir(fn::Function, parent = tempdir())

Execute some function fn in a temporary directory. After the function is executed, the directory is cleaned by doing the equivalent of rm -r.

random_aa(n, probs = [0.24, 0.24, 0.24, 0.24, 0.04])

Create a random amino acid sequence of length n, by sampling the possible amino acid characters.

random_array(n::Integer, elements, probs)

Create a random array of length n, composed of possible elements, which are selected according to their prob.

random_dna(n, probs = [0.24, 0.24, 0.24, 0.24, 0.04])

Create a random DNA sequence of length n, by sampling the nucleotides A, C, G, T, and N, according to their probability in probs.

random_interval(minstart, maxstop)

Create a random interval between a minimum starting point, and a maximum stop point.

random_rna(n, probs = [0.24, 0.24, 0.24, 0.24, 0.04])

Create a random RNA sequence of length n, by sampling the nucleotides A, C, G, U, and N, according to their probability in probs.

random_seq(n::Integer, nts, probs)

Create a random sequence of length n, composed of nts, according to their prob.