fasta_to_nexus: convert fasta to nexus data block.

In dongzhuoer/mcapomorphy: Molecular Classfication based on amino acid apomorphy

Description

internal function for write_paup()

Usage

fasta_to_nexus(fasta, datatype, missing = "?", gap = "-")

Arguments

fasta	tibble. see Value of biozhuoer::read_fasta(). Sequence must be aligned (in the same length). 'U' would be replaced by 'X' since paup doesn't recognized it
datatype	string. what kind of data is you fasta. ('dna', 'rna', 'protein', or 'standard')
missing	string. symbol used for missing data
gap	string. symbol used for gap

Details

the return value will be printed when call at console, if the file is big, it will take a while, and you can't do anything. Consider fasta_to_nexus() -> x to avoid automatically printing.

Alternatively, you can use seaview But it may take several seconds if each sequence lies on only one line in the original file, because seaview always force the line width less than 80.

Value

character. A Nexus data block. Note that begining '#nexus' isn't included.

Examples

fasta <- biozhuoer::read_fasta(system.file('extdata', 'EOG090F05Z3.fasta', package = 'mcapomorphy'))
fasta_to_nexus(fasta, 'protein');

dongzhuoer/mcapomorphy documentation built on Jan. 9, 2020, 3:28 a.m.