This functions uses an internal mustache template to convert a named vector of sequences into an XML data block for BEAST.
Usage
sequences2xml(sequences, data = list())Arguments
- sequences
parsed from file
- data
**optional** other variables, such as specification of datatype
Details
The internal template uses two parameters, an *alignment_id* and a *datatype*. The *alignment_id* identifies this particular alignment block and is important only when multiple input alignments are used during the BEAST analysis. A good practice might be to use a file name of the sequences as an *alignment_id*.
The *datatype* is much more important an tells BEAST what kind of data the alignment represents. The *beter* will try to guess the most common data types: *standard* (binary or discrete states) or *nucleotide* (DNA nucleotides), but if the data is of any other type, the "datatype" must be specified.
Examples
seq = c("A" = "ACTG", "B" = "CTGA", "C" = "TGAC")
sequences2xml(seq)
#> [1] "<data id=\"alignment\" dataType=\"nucleotide\">\n <sequence taxon=\"A\">ACTG</sequence>\n <sequence taxon=\"B\">CTGA</sequence>\n <sequence taxon=\"C\">TGAC</sequence>\n</data>"
sequences2xml(seq, data=list("alignment_id" = "seq", "datatype"="nucleotide") )
#> [1] "<data id=\"seq\" dataType=\"nucleotide\">\n <sequence taxon=\"A\">ACTG</sequence>\n <sequence taxon=\"B\">CTGA</sequence>\n <sequence taxon=\"C\">TGAC</sequence>\n</data>"