silly hack to parse newick strings
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type PhyloNode | |
label::String | |
children::Vector{PhyloNode} | |
length::Real | |
end | |
function parsenewick(newick::String) | |
newick = rstrip(newick,';') | |
newick = replace(newick,":","+") | |
newick_expr = parse(newick) | |
return parsenewick(newick_expr) | |
end | |
parsenewick(newick::Symbol) = PhyloNode(string(newick), PhyloNode[], -1) | |
function parsenewick(newick::Expr) | |
if newick.head == :tuple | |
children = [parsenewick(child) for child in newick.args] | |
name = "" | |
length = -1 | |
elseif newick.head == :call | |
if newick.args[1] == :+ | |
# + indicates length | |
length = newick.args[3] | |
if typeof(newick.args[2]) == Expr | |
if newick.args[2].head == :tuple | |
children = [parsenewick(child) for child in newick.args[2].args] | |
name = "" | |
elseif newick.args[2].head == :call && newick.args[2].args[1] == :* | |
# * indicates naming | |
name = string(newick.args[2].args[3]) | |
children = [parsenewick(child) for child in newick.args[2].args[2].args] | |
end | |
elseif typeof(newick.args[2]) == Symbol || typeof(newick.args[2]) == Int | |
# tip node | |
name = string(newick.args[2]) | |
children = PhyloNode[] | |
end | |
elseif newick.args[1] == :* | |
# bare * indicates a node with name but no length | |
name = string(newick.args[3]) | |
children = [parsenewick(child) for child in newick.args[2].args] | |
length = -1 | |
end | |
end | |
PhyloNode(name,convert(Vector{PhyloNode},children),length) | |
end |
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