maskCodons {dowser}

maskCodons Masks codons split by insertions

Description

maskCodons Masks codons split by insertions

Usage

maskCodons(
  id,
  q,
  s,
  keep_alignment = FALSE,
  gap_opening = 5,
  gap_extension = 1,
  keep_insertions = FALSE,
  mask = TRUE
)

Arguments

id

sequence id

q

(query) un-aligned input sequence (sequence)

s

(subject) aligned input sequence (sequence_alignment)

keep_alignment

store q and s alignments

gap_opening

gap opening penalty (Biostrings::pairwiseALignment)

gap_extension

gap extension penalty (Biostrings::pairwiseALignment)

keep_insertions

return removed insertion sequences?

mask

if FALSE, don't mask codons

Details

Performs global alignment of q and s, masks codons in s that are split by insertions (see example) masking_note notes codon positions in subject_alignment sequence that were masked, if found. subject_alignment contains subject sequence aligned to query (q) sequence query_alignment contains query sequence aligned to subject (q) sequence sequence_masked will be NA if frameshift or alignment error detected/

Value

A list with split codons masked, if found (sequence_masked).

See Also

maskSequences, Biostrings::pairwiseAlignment.

Examples

s = "ATCATCATC..."
q = "ATCTTTATCATC"
print(maskCodons(1,q,s,TRUE))

s <- "ATCATCATC..."
q <- "ATTTTCATCATC"
print(maskCodons("test",q,s,keep_alignment=TRUE,keep_insertions=TRUE))