def parseMods(mods, alignerArgs, indices, skipped):
mods.reverse()
while mods:
mod = mods.pop()
if mod == '-' + indices[0]:
alignerArgs.NEWICK_TREE_STRING = mods.pop()
continue
if mod == '-' + indices[1]:
alignerArgs.SEQUENCE_FILES = parseVarArgs(mods)
continue
if mod == '-' + indices[2]:
alignerArgs.OUTPUT_FILE = mods.pop()
continue
if mod == '-' + indices[3]:
alignerArgs.OUTPUT_TREE_FILE = mods.pop()
continue
if mod == '-' + indices[4]:
alignerArgs.OUTPUT_SCORE_FILE = mods.pop()
continue
if mod == '-' + indices[5]:
A = float(mods.pop())
C = float(mods.pop())
G = float(mods.pop())
T = float(mods.pop())
alignerArgs.EXPECTED_CHARACTER_FREQUENCIES = normaliseWV([ A, C, G, T ])
continue
if mod == '-' + indices[6]:
alignerArgs.EMPIRICALLY_ESTIMATE_CHARACTER_FREQUENCIES = True
continue
if mod == '-' + alignerArgs.MAKE_FINAL_ALIGNMENT_INDICE:
alignerArgs.MAKE_FINAL_ALIGNMENT = not alignerArgs.MAKE_FINAL_ALIGNMENT
continue
skipped.append(mod)
return indices[7:]
def parseEstimateTreeMods(mods, treeArgs, indices, skipped):
mods.reverse()
while mods:
mod = mods.pop()
if mod == '-' + indices[0]:
treeArgs.DEFAULT_DISTANCE = float(mods.pop())
continue
if mod == '-' + indices[1]:
treeArgs.ITERATION_NUMBER = int(mods.pop())
assert treeArgs.ITERATION_NUMBER > 0
continue
if mod == '-' + indices[2]:
treeArgs.SEMPHY_PATH = mods.pop()
continue
if mod == '-' + indices[3]:
treeArgs.SEMPHY_ARGS_TREE = mods.pop()[1:]
continue
if mod == '-' + indices[4]:
treeArgs.SEMPHY_ARGS_PAIRS = mods.pop()[1:]
continue
if mod == '-' + indices[5]:
treeArgs.COLUMN_MIN_GAPLESS_NO = int(mods.pop())
continue
if mod == '-' + indices[6]:
treeArgs.DO_SUBTREE_BRANCH_LENGTH_ESTIMATION = False
continue
if mod == '-' + indices[7]:
treeArgs.BRANCH_LENGTH_ESTIMATION_SUBTREE_DISTANCE = float(
mods.pop())
continue
if mod == '-' + indices[8]:
treeArgs.SPECIES_TREE_STRING = mods.pop()
continue
if mod == '-' + indices[9]:
treeArgs.LEAF_SPECIES = parseVarArgs(mods)
continue
skipped.append(mod)
return indices[10:]
def parseEstimateTreeMods(mods, treeArgs, indices, skipped):
mods.reverse()
while mods:
mod = mods.pop()
if mod == '-' + indices[0]:
treeArgs.DEFAULT_DISTANCE = float(mods.pop())
continue
if mod == '-' + indices[1]:
treeArgs.ITERATION_NUMBER = int(mods.pop())
assert treeArgs.ITERATION_NUMBER > 0
continue
if mod == '-' + indices[2]:
treeArgs.SEMPHY_PATH = mods.pop()
continue
if mod == '-' + indices[3]:
treeArgs.SEMPHY_ARGS_TREE = mods.pop()[1:]
continue
if mod == '-' + indices[4]:
treeArgs.SEMPHY_ARGS_PAIRS = mods.pop()[1:]
continue
if mod == '-' + indices[5]:
treeArgs.COLUMN_MIN_GAPLESS_NO = int(mods.pop())
continue
if mod == '-' + indices[6]:
treeArgs.DO_SUBTREE_BRANCH_LENGTH_ESTIMATION = False
continue
if mod == '-' + indices[7]:
treeArgs.BRANCH_LENGTH_ESTIMATION_SUBTREE_DISTANCE = float(mods.pop())
continue
if mod == '-' + indices[8]:
treeArgs.SPECIES_TREE_STRING = mods.pop()
continue
if mod == '-' + indices[9]:
treeArgs.LEAF_SPECIES = parseVarArgs(mods)
continue
skipped.append(mod)
return indices[10:]
