Description Usage Arguments Value Author(s) See Also Examples
Guess the format of an MSA file by looking at the file contents.
1 | guess.format.msa(filename, method = "content")
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filename |
A vector of file names |
method |
Either "content" or "extension". "content" implies to open the file and guess the format based on content; "extension" simply guesses based on the extension on the file name (it does not open the file). This argument will be recycled to the length of filename. |
A character vector giving the format of each file (one of "MAF", "FASTA", "LAV", "SS", "PHYLIP", "MPM", or "UNKNOWN").
Melissa J. Hubisz
is.format.msa
1 2 3 4 5 6 | exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
files <- c("ENr334-100k.maf", "ENr334-100k.fa", "ENr334-100k.ss", "sol1.maf", "sol1.gp")
unzip(exampleArchive, files=files)
guess.format.msa(files)
# the last file is not an alignment, which is why it returns UNKNOWN
unlink(files)
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