Question

背景：

                    Table$Gene=Gene1
 time n.risk n.event survival std.err lower 95% CI upper 95% CI
    0   2872     208    0.928 0.00484        0.918        0.937
    1   2664     304    0.822 0.00714        0.808        0.836
    2   2360     104    0.786 0.00766        0.771        0.801
    3   2256      48    0.769 0.00787        0.754        0.784
    4   2208      40    0.755 0.00803        0.739        0.771
    5   2256      48    0.769 0.00787        0.754        0.784
    6   2208      40    0.755 0.00803        0.739        0.771

                Table$Gene=Gene2
 time n.risk n.event survival std.err lower 95% CI upper 95% CI
    0   2872     208    0.938 0.00484        0.918        0.937
    1   2664     304    0.822 0.00714        0.808        0.836
    2   2360     104    0.786 0.00766        0.771        0.801
    3   2256      48    0.769 0.00787        0.754        0.784
    4   1000      40    0.744 0.00803        0.739        0.774
#There is a new line ("\n") here too, it just doesn't come out in the code.

我想要的东西看起来很简单。我想将上面的文件转换为如下所示的输出：

Gene1  0.755
Gene2  0.744

即。每个基因，每个部分的生存列中的最后一个数字。

我尝试了多种方法，使用正则表达式，以列表形式读取文件并说出＆＃34; .next（）＆＃34;。我尝试过的一个代码示例：

fileopen = open(sys.argv[1]).readlines()  # Read in the file as a list.
for index,line in enumerate(fileopen):   # Enumerate items in list
    if "Table" in line:  # Find the items with "Table" (This will have my gene name)
            line2 = line.split("=")[1]  # Parse line to get my gene name
            if "\n" in fileopen[index+1]: # This is the problem section.
                print fileopen[index]
            else:
                fileopen[index+1]

正如您在问题部分中所看到的，我试图在此尝试中说：

如果列表中的下一个项目是新行，则打印该项目，否则，下一行是当前行（然后我可以拆分该行以提取特定数字I想）。

如果有人能够纠正这些代码，那么我就可以看到我做错了什么，我很感激。

Answer 1

有点矫枉过正，但不是手动为每个数据项编写解析器，而是使用像pandas这样的现有包来读取csv文件。只需编写一些代码来指定文件中的相关行。未优化的代码（读取文件两次）：

import pandas as pd
def genetable(gene):
    l = open('gene.txt').readlines()
    l += "\n"  # add newline to end of file in case last line is not newline
    lines = len(l)
    skiprows = -1
    for (i, line) in enumerate(l):
        if "Table$Gene=Gene"+str(gene) in line:
            skiprows = i+1
        if skiprows>=0 and line=="\n":
            skipfooter = lines - i - 1
            df = pd.read_csv('gene.txt', sep='\t', engine='python', skiprows=skiprows, skipfooter=skipfooter)
            #  assuming tab separated data given your inputs. change as needed
            # assert df.columns.....
            return df
    return "Not Found"

这将在DataFrame中读取该文件中的所有相关数据

然后

可以这样做：

genetable(2).survival  # series with all survival rates
genetable(2).survival.iloc[-1]   last item in survival

这样做的好处是您可以访问所有项目，可能会更好地拾取文件的任何错误格式，并防止使用不正确的值。如果我自己的代码我会在返回pandas DataFrame之前在列名称上添加断言。想要在早期解析时发现任何错误，以免传播。

Answer 2

这在我尝试时起作用了：

gene = 1
for i in range(len(filelines)):
    if filelines[i].strip() == "":
        print("Gene" + str(gene) + " " + filelines[i-1].split()[3])
        gene += 1

Answer 3

您可以尝试这样的事情（我将您的数据复制到foo.dat）;

In [1]: with open('foo.dat') as input:
   ...:     lines = input.readlines()
   ...:

使用with可确保文件在阅读后关闭。

In [3]: lines = [ln.strip() for ln in lines]

这消除了额外的空白。

In [5]: startgenes = [n for n, ln in enumerate(lines) if ln.startswith("Table")]

In [6]: startgenes
Out[6]: [0, 10]

In [7]: emptylines = [n for n, ln in enumerate(lines) if len(ln) == 0]

In [8]: emptylines
Out[8]: [9, 17]

使用emptylines依赖于记录由仅包含空格的行分隔的事实。

In [9]: lastlines = [n-1 for n, ln in enumerate(lines) if len(ln) == 0]

In [10]: for first, last in zip(startgenes, lastlines):
   ....:     gene = lines[first].split("=")[1]
   ....:     num = lines[last].split()[-1]
   ....:     print gene, num
   ....:     
Gene1 0.771
Gene2 0.774

Answer 4

这是我的解决方案：

>>> with open('t.txt','r') as f:
...     for l in f:
...         if "Table" in l:
...             gene = l.split("=")[1][:-1]
...         elif l not in ['\n', '\r\n']:
...             surv = l.split()[3]
...         else:
...             print gene, surv
...
Gene1 0.755
Gene2 0.744

Answer 5

而不是检查新行，只需在完成阅读文件后打印

lines = open("testgenes.txt").readlines()
table = ""
finalsurvival = 0.0
for line in lines:
    if "Table" in line:
        if table != "": # print previous survival
            print table, finalsurvival
        table = line.strip().split('=')[1]
    else:
        try:                
            finalsurvival = line.split('\t')[4]
        except IndexError:
            continue
print table, finalsurvival

python从文件中打印特定行

5 个答案: