truncate_alignment | R Documentation |
Simply truncating a Stockholm alignment file that includes secondary structure annotations may result in invalid base pairing, when only one half of a pair is removed. This function converts these half-pairs to "X", indicating unpairable bases.
truncate_alignment(alnfile, outfile, start = 1L, stop = 1000000L)
alnfile |
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outfile |
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start |
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stop |
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NULL (invisibly)
aln <- system.file(file.path("extdata", "fungi_32S.cm"), package = "LSUx")
truncate_alignment(aln, tempfile("trunc", fileext = ".stk"), 1, 500)
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