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"""
Rudimentary support for PHAST's tree model file format (a simple format for
storing trees and rate matrices).
"""
from numpy import zeros
class TreeModel:
def __init__(self):
self.alphabet = None
self.radix = 0
self.order = 0
self.subst_mod = None
self.background = None
self.tree = None
self.matrix = None
@staticmethod
def from_file(f):
input = iter(f)
tm = TreeModel()
for line in input:
if line.startswith("ALPHABET:"):
tm.alphabet = tuple(line.split()[1:])
tm.radix = len(tm.alphabet)
if line.startswith("ORDER:"):
tm.order = int(line.split()[1])
if line.startswith("SUBST_MOD:"):
tm.subst_mod = line[11:].rstrip()
if line.startswith("BACKGROUND:"):
tm.background = tuple(map(float, line.split()[1:]))
if line.startswith("TREE:"):
tm.tree = line[6:].strip()
if line.startswith("RATE_MAT:"):
matrix = zeros((tm.radix, tm.radix), float)
for i in range(len(tm.alphabet)):
matrix[i] = [float(_) for _ in next(input).split()]
tm.matrix = matrix
return tm
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