Gap.code: Gap coding

In shipunov: Miscellaneous Functions from Alexey Shipunov

Gap coding

Description

Gap coding of DNA nucleotide alignments

Usage

Gap.code(seqs)

Arguments

seqs	Character vector of aligned (and preferably flank trimmed) DNA sequences.

Details

FastGap-like gap code nucleotide alignments ('ATGCN-' are allowed).

Encodes gap presence as 'A' and absence as 'C'.

Likely too straightforward, and only weakly optimized (really slow).

Value

Outputs character matrix where each column is a gapcoded position.

Author(s)

Alexey Shipunov

References

Borchsenius F. 2009. FastGap 1.2. Department of Biosciences, Aarhus University, Denmark. See "http://www.aubot.dk/FastGap_home.htm".

Examples

write(file=file.path(tempdir(), "tmp.fasta"),  c(
 ">1\nGAAC------ATGC",
 ">2\nGAAC------TTGC",
 ">3\nGAAC---CCTTTGC",
 ">4\nGAA---------GC"))
write(file=file.path(tempdir(), "tmp_expected.fasta"), c(
 ">1\nGAAC------ATGCCA-",
 ">2\nGAAC------TTGCCA-",
 ">3\nGAAC---CCTTTGCCCA",
 ">4\nGAA---------GCA--"))
tmp <- Read.fasta(file=file.path(tempdir(), "tmp.fasta"))
expected <- Read.fasta(file=file.path(tempdir(), "tmp_expected.fasta"))
seqs <- tmp$sequence
gc <- Gap.code(seqs)
tmp$sequence <- apply(cbind(seqs, gc), 1, paste, collapse="")
identical(tmp, expected) # TRUE, isn't it?

shipunov documentation built on Feb. 16, 2023, 9:05 p.m.