AbSim (version 0.2.6)

repertoireFastas: Converts AbSim's output sequences and names into fasta file format. Each tree within the repertire will be stored in an individual fasta file. Utilizes sink() and cloneAllConnections() from R base

Description

Converts AbSim's output sequences and names into fasta file format. Each tree within the repertire will be stored in an individual fasta file. Utilizes sink() and cloneAllConnections() from R base

Usage

repertoireFastas(ab.repertoire, fasta.name, with.germline)

Arguments

ab.repertoire

The output from the either the singleLineage function or the fullRepertoire function. This takes should be a nested list, with the first element containing a list of sequence arrays, the second element containing the corresponding list of names, and the third element containing a list of trees. The following list elements (containing the sampling information) will be disregarded for repertoire expansion.

fasta.name

The name of the fasta files. Each tree will be numbered corresponding to the index within the ab.repertoire list. For example, the second tree in an ab.repertoire object will be "fasta.name_2.fasta",

with.germline

Logical value specifying if the germline sequences should be included in the fasta file (as the first sequence)

Examples

# NOT RUN {
repertoireFastas(ab.repertoire=ab.repertoire.output,
 fasta.name="sample_trees",
 with.germline=TRUE
# }