Esempio n. 1
0
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:]
Esempio n. 2
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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:]
Esempio n. 3
0
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:]