Question

我试图运行我的代码，但错误被弹出。这是我的代码，谢谢！我检查了每个return语句和缩进块。这是我使用的呼叫命令： python3 generate_seqs.py -t -p -r -o

'''python
#!/usr/bin/env python3
ERROR_GTR_PARAMS_FILE = "Invalid GTR parameters file"
ERROR_ROOT_SEQ = "Invalid root sequence. Must be path to FASTA file or integer"

from decimal import *
from math import log
from random import uniform
from numpy import matrix
from scipy.linalg import expm
try:
    import Queue as Q  # ver. < 3.0
except ImportError:
    import queue as Q
import treeswift

def randomChoice(prob):
    faces = sorted(die.keys())
    probs = [die[key] for key in faces]
    cdf = [probs[0]]
    while len(cdf) < len(probs):
        cdf.append(cdf[-1] + probs[len(cdf)])

    num = uniform(0, 1)
    index = 0
    while cdf[index] < num:
        index += 1

    return faces[index]

是进化序列 ''' prob_A，prob_C，prob_G，prob_T = gtr_probs＃如果方便的话可以使用这些 rate_CT，rate_AT，rate_GT，rate_AC，rate_CG，rate_AG = gtr_rates＃如果方便的话可以使用它们 seqs = dict（）＃这将是您的输出（键=叶子标签（str）和值=序列（str））＃TODO您的代码在这里 rate_dict = {'AC'：rate_AC， “ CT”：rate_CT， 'AT'：rate_AT， 'GT'：rate_GT， “ CG”：rate_CG， 'AG'：rate_AG}

    prob_dict = {'A': prob_A,
                 'C': prob_C,
                 'G': prob_G,
                 'T': prob_T}

    R = gtr2matrix(rate_dict,prob_dict)
    root = tree.seed_node
    root.seq = root_seq
    todo = Q.Queue()

    for child in root.child_nodes():
        todo.put(child)

    while not todo.empty():
        node = todo.get()
        node.seq = evolveSeq(node.parent_node.seq, node.edge_length, R)
        for child in node.child_nodes():
            todo.put(child)

    for leaf in tree.leaf_node_iter():
        seqs[leaf.taxon.label] = leaf.seq

    return seqs

'''python

-bash：Python中意外令牌“ newline”附近的语法错误

0 个答案: