如何将返回值（从上一个函数）读入pandas、python？获取错误信息

Question

在下面的程序中

我想access/pipe下游函数中一个函数的数据。

使用 python 代码如下：

def main():
data1, data2, data3 = read_file()
do_calc(data1, data2, data3)   

def read_file():
    data1 = ""
    data2 = ""
    data3 = ""

    file1 = open('file1.txt', 'r+').read()
    for line in file1
        do something....
        data1 += calculated_values

    file2 = open('file2.txt', 'r+').read()
    for line in file1
        do something...
        data2 += calculated_values    

    file1 = open('file1.txt', 'r+').read()
    for line in file1
        do something...
        data3 += calculated_values

    return data1, data2, data3

def do_calc(data1, data2, data3):
    d1_frame = pd.read_table(data1, sep='\t')
    d2_frame = pd.read_table(data2, sep='\t')
    d3_frame = pd.read_table(data3, sep='\t')

    all_data = [d1_frame, d2_frame, d3_frame]

main()

给定的代码有什么问题？熊猫似乎无法正确读取输入文件，但正在将数据 1、2 和 3 的值打印到屏幕上。

read_hdf 似乎读取了文件但不正确。有没有一种方法可以将函数返回的数据直接读入 pandas（无需将 writing/reading 读入文件）。

错误信息：

Traceback (most recent call last):

  File "calc.py", line 757, in <module>

    main()

  File "calc.py", line 137, in main

    merge_tables(pop1_freq_table, pop2_freq_table, f1_freq_table)

  File "calc.py", line 373, in merge_tables

    df1 = pd.read_table(pop1_freq_table, sep='\t')

  File "/home/everestial007/.local/lib/python3.5/site-packages/pandas/io/parsers.py", line 645, in parser_f

    return _read(filepath_or_buffer, kwds)

  File "/home/everestial007/.local/lib/python3.5/site-packages/pandas/io/parsers.py", line 388, in _read

    parser = TextFileReader(filepath_or_buffer, **kwds)

  File "/home/everestial007/.local/lib/python3.5/site-packages/pandas/io/parsers.py", line 729, in __init__

    self._make_engine(self.engine)

  File "/home/everestial007/.local/lib/python3.5/site-packages/pandas/io/parsers.py", line 922, in _make_engine

    self._engine = CParserWrapper(self.f, **self.options)

  File "/home/everestial007/.local/lib/python3.5/site-packages/pandas/io/parsers.py", line 1389, in __init__

    self._reader = _parser.TextReader(src, **kwds)

  File "pandas/parser.pyx", line 373, in pandas.parser.TextReader.__cinit__ (pandas/parser.c:4019)

  File "pandas/parser.pyx", line 665, in pandas.parser.TextReader._setup_parser_source (pandas/parser.c:7967)

FileNotFoundError: File b'0.667,0.333\n2\t15800126\tT\tT,A\t0.667,0.333\n2\t15800193\tC\tC,T\t0.667,0.333\n2\t15800244\tT\tT,C\......

如有任何解释，我将不胜感激。

Answer 1

read_table 需要一个文件作为输入，但您传递的是一串数据而不是包含文件位置的字符串。您可以将数据写入文件，然后从该文件中读取。假设字符串已经正确格式化：

filename = 'tab_separated_file_1.dat'
with open(filename, 'w') as f:
    f.write(data1)

df1 = pd.read_table(filename, sep='\t')

Answer 2

正如其他答案所说，read_table 需要输入文件——或者更准确地说，"file-like object"。您可以使用 StringIO 对象将 data1、data2 和 data3 字符串包装在一个对象中，该对象将 "behave" 像一个文件一样馈送到 pandas 并对您的代码进行一些调整：

#Import StringIO...
# python 2
from StringIO import StringIO
# python 3
from io import StringIO

def main():
    data1, data2, data3 = read_file()
    do_calc(data1, data2, data3)   

def read_file():
    # use StringIO objects instead of strings...
    data1 = StringIO()
    data2 = StringIO()
    data3 = StringIO()

    file1 = open('file1.txt', 'r+').read()
    for line in file1
        do something....
        # note that " += " became ".write()"
        data1.write(calculated_values)

    file2 = open('file2.txt', 'r+').read()
    for line in file1
        do something...
        data2.write(calculated_values)

    file1 = open('file1.txt', 'r+').read()
    for line in file1
        do something...
        data3.write(calculated_values)

    return data1, data2, data3

def do_calc(data1, data2, data3):
    d1_frame = pd.read_table(data1, sep='\t')
    d2_frame = pd.read_table(data2, sep='\t')
    d3_frame = pd.read_table(data3, sep='\t')

    all_data = [d1_frame, d2_frame, d3_frame]

main()

如何将返回值（从上一个函数）读入pandas、python？获取错误信息

How to read the returned value (from previous function) into pandas, python? Getting error messages

python

main

stdout

function

pandas