癌症中克隆种群结构统计推断分析软件PyClone安装小记

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PyClone 是一种用于推断癌症中克隆种群结构的统计模型。它是一种贝叶斯聚类方法，用于将深度测序的体细胞突变集分组到假定的克隆簇中，同时估计其细胞流行率（prevalences）并解释由于分段拷贝数变化（segmental copy-number changes）和正常细胞污染（normal-cell contamination）引起的等位基因失衡。单细胞测序验证证明了 PyClone 的准确性。

The input data for PyClone consists of a set read counts from a deep sequencing experiment, the copy number of the genomic region containing the mutation and an estimate of tumour content.

简易安装

官方推荐使用 MiniConda 来安装 PyClone。为了保证环境的稳定，可为 PyClone 单独建立一个环境，因为 PyClone 基于 Python2.7。在这里，我们使用 Anaconda3(conda 4.5.11) 来安装 PyClone。

# 创建基于 Python2.7 名字为 pyclone 独立环境
conda create --name pyclone python=2

# 激活 pyclone 环境
source activate pyclone

# 退出 pyclone 环境
source deactivate

# 安装 PyClone
conda install pyclone -c aroth85

Anaconda3 中安装完 PyClone，激活环境后，执行 PyClone -h 出现 RuntimeWarning。同样的，我们在 pyclone 的环境中导入 pandas 模板，出现一样的 RuntimeWarning：

(pyclone) shenweiyan@ecs-steven 13:38:25 /home/shenweiyan
$ PyClone -h
/usr/local/software/anaconda3/envs/pyclone/lib/python2.7/site-packages/pandas/_libs/__init__.py:4: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .tslib import iNaT, NaT, Timestamp, Timedelta, OutOfBoundsDatetime
/usr/local/software/anaconda3/envs/pyclone/lib/python2.7/site-packages/pandas/__init__.py:26: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88

......

  from pandas._libs import algos, lib, writers as libwriters
/usr/local/software/anaconda3/envs/pyclone/lib/python2.7/site-packages/statsmodels/nonparametric/kde.py:22: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .linbin import fast_linbin
/usr/local/software/anaconda3/envs/pyclone/lib/python2.7/site-packages/statsmodels/nonparametric/smoothers_lowess.py:11: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._smoothers_lowess import lowess as _lowess
usage: PyClone [-h] [--version]
               {setup_analysis,run_analysis,run_analysis_pipeline,build_mutations_file,plot_clusters,plot_loci,build_table}
               ...

positional arguments:
  {setup_analysis,run_analysis,run_analysis_pipeline,build_mutations_file,plot_clusters,plot_loci,build_table}
    setup_analysis      Setup a config file and mutations files for a PyClone
                        analysis.
    run_analysis        Run an MCMC sampler to sample from the posterior of
                        the PyClone model.
    run_analysis_pipeline
                        Run a full PyClone analysis.
    build_mutations_file
                        Build a YAML format file with mutation data and states
                        prior to be used for PyClone analysis.
    plot_clusters       Plot features of the clusters.
    plot_loci           Plot features of the loci.
    build_table         Build results table which contains cluster ids and
                        (mean) cellular prevalence estimates.

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

(pyclone) shenweiyan@ecs-steven 14:47:17 /home/shenweiyan
$ python
Python 2.7.15 | packaged by conda-forge | (default, Oct 12 2018, 14:10:50)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> >>> import pandas
/usr/local/software/anaconda3/envs/pyclone/lib/python2.7/site-packages/pandas/_libs/__init__.py:4: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .tslib import iNaT, NaT, Timestamp, Timedelta, OutOfBoundsDatetime
/usr/local/software/anaconda3/envs/pyclone/lib/python2.7/site-packages/pandas/__init__.py:26: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import (hashtable as _hashtable,

......

/usr/local/software/anaconda3/envs/pyclone/lib/python2.7/site-packages/pandas/io/pytables.py:50: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos, lib, writers as libwriters
>>> pandas.__version__
u'0.23.4'

原因与解决：(参考 anaconda-issues：#6678、numpy issues：#11628)

The pandas were build agains different version of numpy. we need to rebuild pandas agains the local numpy.

# 方法一（耗时长）
pip install --no-binary pandas -I pandas

# 方法二
conda install numpy==1.14.5 --yes

手动安装

要手动安装 PyClone，请确保安装了必要的库（如下所列）。之后就可以像任何其他 Python 包一样通过 python setup.py install 安装 PyClone。

PyClone 必须满足依赖包如下：

PyDP >= 0.2.3
PyYAML >= 3.10
matplotlib >= 1.2.0 - Required for plotting.
numpy >= 1.6.2 - Required for plotting and clustering.
pandas >= 0.11 - Required for multi sample plotting.
scipy >= 0.11 - Required for plotting and clustering.
seaborn >= 0.6.0

手动安装 PyClone:

$ git clone https://github.com/aroth85/pyclone.git
$ cd pyclone
$ python setup.py install
running install
running bdist_egg
running egg_info
creating PyClone.egg-info
writing PyClone.egg-info/PKG-INFO

......

Installed /usr/local/software/python2.7/pyclone/lib/python2.7/site-packages/PyClone-0.13.1-py2.7.egg
Processing dependencies for PyClone==0.13.1
Finished processing dependencies for PyClone==0.13.1

到这里，PyClone 就安装完成了，关于该软件具体的使用说明，请参考 PyClone -h 或者 PyClone wiki: Usage。