python套件 pbh5tools: PacBio rawdata 格式轉換

2016-09-06更新:pbh5tools是PacBio公司早期推出的数据分析工具,其后已经被SMRTanalysis工具所替换。SMRTanalysis的安装与使用都更简单,Linux安装之后可以直接在网页里面进行数据分析操作。

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转载自:http://jeffreyy.pixnet.net/

PacBio 是第三代定序技術 (Third generation sequencing)的技術公司,目前的最新機型為RSII,最長長度可到30kb。

出來的rawdata其檔案格式為hdf5,其中有兩種,一個是bas.h5和bax.h5,其PacBio的文件有寫到以下:

“Due to the increased throughput and read lengths achieved by the PacBio® RS II upgrade, this information is now contained in one bas.h5 file and three bax.h5 files.”

http://files.pacb.com/software/instrument/2.0.0/bas.h5%20Reference%20Guide.pdf

hdf5 格式並無法直接觀看,如果要看序列,必須要經過格式轉換,PacBio有出一個軟體為pbh5tools來進行hdf5的格式轉換。

 

pbh5tools是以python寫的套件,所以安裝前需要安裝其他python套件,在安裝python套件用pip比較好,pip會兼顧各個依存的套件版本,少用easy-install。

安裝 PIP 來管理 Python Packages

除了python套件外,其他的套件還有python-devel 和 hdf5與其相關套件。

 

其安裝其他requirement套件指令為:

sudo yum install python-pip python-devel.x86_64 hdf5-devel.x86_64 hdf5.x86_64 hdf5-mpich-devel.x86_64 hdf5-mpich.x86_64 hdf5-openmpi.x86_64 hdf5-openmpi-devel.x86_64

# 上述yum指令,对于没有root权限的Linux用户,该如何解决???(FL 2016-02-06备注)

sudo pip install --upgrade pip
sudo pip install --upgrade nose
sudo pip install --upgrade Cython
sudo pip install --upgrade numpy
sudo pip install --upgrade six
sudo pip install --upgrade setuptools
sudo pip install --upgrade pkgconfig
sudo pip install --upgrade pysam
sudo pip install --upgrade h5py
sudo pip install --upgrade pbcore

 

其中,pbcore需要python 2.7,故如果系統為python 2.6又無法利用yum升級上去,就必須手動安裝python 2.7,並注意需雙版本依存。

參考資料:

http://ruiaylin.github.io/2014/12/12/python%20update/

https://github.com/h2oai/h2o-2/wiki/Installing-python-2.7-on-centos-6.3.-Follow-this-sequence-exactly-for-centos-machine-only

How to install Python 2.7 and Python 3.3 on CentOS 6

How to Install Python 2.7.10 on CentOS/RHEL 7/6 and Fedora

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