codon_filter: Filter sequences containing stop codons

In alexpiper/seqateurs: Tools for trimming and processing sequence data

Filter sequences containing stop codons

Description

Filter sequences containing stop codons

Usage

codon_filter(x, genetic_code = NULL, tryrc = TRUE, resolve_draws = "majority")

Arguments

x	Sequences in DNAStringset or DNAbin format
genetic_code	A genetic code for the Amino acid translation. set to 'SGC4' for Invertebrate mitochondrial or see all known codes at Biostrings::GENETIC_CODE_TABLE
tryrc	Whether the reverse complemement should be evaluated if no frame without stop codons was found in the forward orientation.
resolve_draws	How draws should be resolved when multiple possible frames produce sequences with no stop codons. Options are "remove" to completely remove the sequence, or "majority" to pick the most common frame from the entire alignment.

alexpiper/seqateurs documentation built on July 9, 2023, 7:21 a.m.