cleanSeqs - Clean up nucleotide sequences

Description

cleanSeqs capitalizes nucleotides, replaces “.” with “-“, and then replaces all characters besides ACGT- with “N”.

Usage

cleanSeqs(seqs)

Arguments

seqs
a vector of nucleotide sequences

Value

A vector of nucleotide sequences

Examples

# Create messy nucleotide sequences
seqs = c("AGAT.taa-GAG...ATA",
"GATACAGTXXXXXAGNNNPPPACA")
# Clean them up
cleanSeqs(seqs)
[1] "AGAT-TAA-GAG---ATA"       "GATACAGTNNNNNAGNNNNNNACA"

See also

sortAlleles and updateAlleleNames can help format a list of allele names.