API: MoleculePool

Exported functions

Making a pool of molecules

Pseudoseq.Sequencing.Molecules — Type

Molecules(gen::Vector{LongSequence{DNAAlphabet{2}}}, ng::Int = 1)

Create a pool of ng copies of a genome defined by the gen vector of sequences.

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Molecules(rdr::FASTA.Reader, ng::Int = 1)

Create a pool of ng copies of the genome read in from the FASTA.Reader.

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Molecules(file::String, ng::Int)

Create a pool of ng copies of the genome in the fasta formatted file.

Note

The argument iscircular is currently not used.

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Transformations

Amplify

Missing docstring.

Missing docstring for amplify. Check Documenter's build log for details.

Fragment

Pseudoseq.Sequencing.fragment — Method

fragment(p::Molecules, meansize::Int)

Create a new pool of DNA molecules, by breaking up the DNA molecules in some input pool.

This method breaks up a DNA molecule in a pool p, such that the average length of the fragments is approximately meansize.

It fragments a molecule by scattering an appropriate number of breakpoints across the molecule, before cutting the molecule at those breakpoints.

Note

Breakpoints are scattered entirely at random across a molecule. No two or more breakpoints can fall in exactly the same place, as those positions are sampled without replacement.

Note

The appropriate number of breakpoints to scatter across a molecule is calculated as:

\[\frac{L}{S} - 1\]

Where $L$ is the length of the molecule being fragmented, and $S$ is the desired expected fragment size. This calculation assumes breakpoints fall randomly across the molecule (see above note).

Note

If a DNA molecule being fragmented is smaller than the desired meansize, then it will not be broken, it will simply be included in the new pool.

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Pseudoseq.Sequencing.fragment — Method

fragment(meansize::SequenceLength)

Construct a Fragmenter transform that fragments any Molecules passed to it, to an average length of meansize.

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Subsampling

Pseudoseq.Sequencing.subsample — Method

subsample(p::Molecules, n::Int)

Create a new pool of DNA molecules by sampling an input pool.

Note

DNA molecules in the input pool p are selected according to the uniform distribution; no one molecule is more or less likely to be selected than another.

Note

Sampling is done without replacement, so it is impossible for the new pool that is created to recieve one molecule the input pool twice.

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Tagging

Missing docstring.

Missing docstring for tag(p::Molecules, ntags::Int). Check Documenter's build log for details.

Flipping

Missing docstring.

Missing docstring for flip(p::Molecules). Check Documenter's build log for details.