[英]Pandas groupby nunique output to list
I have as input a dataset like the following: 我输入了如下数据集:
labels = ['chrom', 'start', 'end', 'read']
my_data = [['chr1', 784344, 800125, 'read1'],
['chr1', 784344, 800124, 'read2'],
['chr1', 784344, 800124, 'read3']]
Which I convert to a pandas dataframe using: 使用以下内容转换为pandas数据帧:
my_data_pd = pd.DataFrame.from_records(my_data, columns=labels)
and that looks like this: 这看起来像这样:
chrom start end read
0 chr1 784344 800125 read1
1 chr1 784344 800124 read2
2 chr1 784344 800124 read3
What I want to do is the following: I wan't merge the rows that have indentical chrom,start,end values, and count the number of disntinct occurences of the values in the 'read' column for those rows that were merged. 我想要做的是以下内容:我不会合并具有缩进的chrom,start,end值的行,并计算那些合并的行的“read”列中值的意外出现次数。 Finally, I want to convert convert that output to a list/tuple, as in this example (note that the last column has the count information):
最后,我想将转换输出转换为list / tuple,如本例所示(注意最后一列有计数信息):
[('chr1', 784344, 800125,1), ('chr1', 784344, 800124,2)]
What I have been able to do: 我能做到的:
Unsing Pandas Groupby and the nunique() with the command: 使用命令解开Pandas Groupby和nunique() :
my_data_pd.groupby(['chrom','start','end'],sort=False).read.nunique()
I arrive to a Pandas.Series object that looks to what I want: 我到达了一个看起来像我想要的Pandas.Series对象:
chrom start end
chr1 784344 800125 1
800124 2
Name: read, dtype: int64
However, when I convert it to a list/tuple using: 但是,当我使用以下命令将其转换为list / tuple时:
sortedd.index.tolist()
the last column gets excluded, leading to the resulting output: 排除最后一列,导致结果输出:
[('chr1', 784344, 800125), ('chr1', 784344, 800124)]
Any idea about how can I get around trough this problem? 关于如何解决这个问题的任何想法?
For all those that might come up with a solution, I am doing this inside a big program thousands of times, so speed is a big issue. 对于那些可能提出解决方案的人来说,我在一个大型程序中做了好几千次,所以速度是个大问题。 Thats the reason I am avoiding other tools like BedTools and pybedtools
这就是我避免使用BedTools和pybedtools等其他工具的原因
Thanks! 谢谢!
You can set_index
你可以
set_index
sortedd.to_frame('val').set_index('val',append=True).index.tolist()
Out[277]: [('chr1', 784344, 800125, 1), ('chr1', 784344, 800124, 2)]
First reset_index
and then in list comprehension
convert to tuples
: 首先
reset_index
然后在list comprehension
reset_index
中转换为tuples
:
L = [tuple(x) for x in sortedd.reset_index().values.tolist()]
print (L)
[('chr1', 784344, 800125, 1), ('chr1', 784344, 800124, 2)]
You can use multi index ie 你可以使用多索引即
idx = pd.MultiIndex.from_arrays(sortedd.reset_index().values.T)
idx.tolist()
[('chr1', 784344, 800125, 1), ('chr1', 784344, 800124, 2)]
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