maskCodons

maskCodons - 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 (pwalign::pairwiseAlignment)
gap_extension: gap extension penalty (pwalign::pairwiseAlignment)
keep_insertions: return removed insertion sequences?
mask: if FALSE, don’t mask codons

Value¶

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

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/

Examples¶

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

$sequence_id
[1] 1

$sequence_masked
[1] ""

$masking_note
[1] ""

$insertions
[1] ""

$subject_alignment
[1] "ATC---ATCATC"

$query_alignment
[1] "ATCTTTATCATC"

$sequence_masked_v
[1] "ATCATCATC..."


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

$sequence_id
[1] "test"

$sequence_masked
[1] ""

$masking_note
[1] "1,2"

$insertions
[1] "3-TTT"

$subject_alignment
[1] "AT---CATCATC"

$query_alignment
[1] "ATTTTCATCATC"

$sequence_masked_v
[1] "NNNATCATC..."