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:]