前言：nanopore的下机数据是fast5格式，通常在下游分析之前，需要转换成fastq，poretools是一款开源工具，可以针对原始的fast5文件进行各种操作。
查看官方说明文档，可访问poretools主页
poretools主页
- 软件安装
poretools是基于python2开发，所以可以先使用conda构建python2的环境
conda create -n PoreTools python=2.7.14
conda activate PoreTools
git clone https://github.com/arq5x/poretools
cd poretools
#如果你像我一样，没有root权限，那么安装命令是下面这一条
python setup.py install --user
2.报错解决
在执行python setup.py install --user时，报错：
0.6.0
running install
running bdist_egg
running egg_info
writing requirements to poretools.egg-info/requires.txt
writing poretools.egg-info/PKG-INFO
writing top-level names to poretools.egg-info/top_level.txt
writing dependency_links to poretools.egg-info/dependency_links.txt
writing entry points to poretools.egg-info/entry_points.txt
reading manifest file 'poretools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'poretools.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/Event.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/Fast5File.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/__init__.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/combine.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/events.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/fasta.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/fastq.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/formats.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/hist.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/index.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/metadata.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/nucdist.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/occupancy.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/organise.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/poretools_main.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/qual_v_pos.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/qualdist.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/readstats.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/squiggle.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/statistics.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/stats.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/tabular.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/times.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/version.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/winner.py -> build/bdist.linux-x86_64/egg/poretools
copying build/lib/poretools/yield_plot.py -> build/bdist.linux-x86_64/egg/poretools
creating build/bdist.linux-x86_64/egg/poretools/scripts
copying build/lib/poretools/scripts/__init__.py -> build/bdist.linux-x86_64/egg/poretools/scripts
copying build/lib/poretools/scripts/poretools-script.py -> build/bdist.linux-x86_64/egg/poretools/scripts
byte-compiling build/bdist.linux-x86_64/egg/poretools/Event.py to Event.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/Fast5File.py to Fast5File.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/combine.py to combine.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/events.py to events.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/fasta.py to fasta.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/fastq.py to fastq.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/formats.py to formats.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/hist.py to hist.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/index.py to index.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/metadata.py to metadata.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/nucdist.py to nucdist.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/occupancy.py to occupancy.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/organise.py to organise.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/poretools_main.py to poretools_main.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/qual_v_pos.py to qual_v_pos.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/qualdist.py to qualdist.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/readstats.py to readstats.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/squiggle.py to squiggle.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/statistics.py to statistics.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/stats.py to stats.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/tabular.py to tabular.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/times.py to times.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/version.py to version.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/winner.py to winner.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/yield_plot.py to yield_plot.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/scripts/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/poretools/scripts/poretools-script.py to poretools-script.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying poretools.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying poretools.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying poretools.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying poretools.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying poretools.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying poretools.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying poretools.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating 'dist/poretools-0.6.0-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing poretools-0.6.0-py2.7.egg
removing '/home/ljf/.local/lib/python2.7/site-packages/poretools-0.6.0-py2.7.egg' (and everything under it)
creating /home/ljf/.local/lib/python2.7/site-packages/poretools-0.6.0-py2.7.egg
Extracting poretools-0.6.0-py2.7.egg to /home/ljf/.local/lib/python2.7/site-packages
poretools 0.6.0 is already the active version in easy-install.pth
Installing poretools script to /home/ljf/.local/bin
Installed /home/ljf/.local/lib/python2.7/site-packages/poretools-0.6.0-py2.7.egg
Processing dependencies for poretools==0.6.0
Searching for pandas
Reading https://pypi.org/simple/pandas/
Downloading https://files.pythonhosted.org/packages/53/87/6438c197fc70ca6b3056cfb60b3dfedca25bedb631bce1f72d6a10502d15/pandas-1.0.4.tar.gz#sha256=b35d625282baa7b51e82e52622c300a1ca9f786711b2af7cbe64f1e6831f4126
Best match: pandas 1.0.4
Processing pandas-1.0.4.tar.gz
Writing /tmp/easy_install-_oW1dE/pandas-1.0.4/setup.cfg
Running pandas-1.0.4/setup.py -q bdist_egg --dist-dir /tmp/easy_install-_oW1dE/pandas-1.0.4/egg-dist-tmp-Rxph_5
Traceback (most recent call last):
File "setup.py", line 42, in
'Topic :: Scientific/Engineering :: Bio-Informatics'
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/__init__.py", line 145, in setup
return distutils.core.setup(**attrs)
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/command/install.py", line 67, in run
self.do_egg_install()
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/command/install.py", line 117, in do_egg_install
cmd.run(show_deprecation=False)
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 424, in run
self.easy_install(spec, not self.no_deps)
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 666, in easy_install
return self.install_item(None, spec, tmpdir, deps, True)
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 713, in install_item
self.process_distribution(spec, dist, deps)
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 758, in process_distribution
[requirement], self.local_index, self.easy_install
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/pkg_resources/__init__.py", line 782, in resolve
replace_conflicting=replace_conflicting
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1065, in best_match
return self.obtain(req, installer)
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1077, in obtain
return installer(requirement)
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 685, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 711, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 896, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1164, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1150, in run_setup
run_setup(setup_script, args)
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/sandbox.py", line 253, in run_setup
raise
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/contextlib.py", line 35, in __exit__
self.gen.throw(type, value, traceback)
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
yield
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/contextlib.py", line 35, in __exit__
self.gen.throw(type, value, traceback)
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/sandbox.py", line 166, in save_modules
saved_exc.resume()
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/sandbox.py", line 141, in resume
six.reraise(type, exc, self._tb)
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/sandbox.py", line 154, in save_modules
yield saved
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
yield
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/sandbox.py", line 250, in run_setup
_execfile(setup_script, ns)
File "/home/ljf/miniconda3/envs/PoreTools/lib/python2.7/site-packages/setuptools/sandbox.py", line 44, in _execfile
code = compile(script, filename, 'exec')
File "/tmp/easy_install-_oW1dE/pandas-1.0.4/setup.py", line 42
f"numpy >= {min_numpy_ver}",
^
看上去是numpy包版本不对，于是手动安装numpy
pip install numpy
然后继续python setup.py install --user时，又有报错：
ERROR: poretools 0.6.0 requires pandas, which is not installed.
ERROR: poretools 0.6.0 requires h5py>=2.2.0, which is not installed.
ERROR: poretools 0.6.0 requires matplotlib, which is not installed.
ERROR: poretools 0.6.0 requires seaborn, which is not installed.
原来是还需要上述四个依赖包，继续手动安装：
pip install seaborn -i https://pypi.doubanio.com/simple/
pip install matplotlib -i https://pypi.doubanio.com/simple/
pip install pandas -i https://pypi.doubanio.com/simple/
pip install h5py -i https://pypi.doubanio.com/simple/
然后继续执行安装命令：
python setup.py install --user
安装完成~
> poretools -h
usage: poretools [-h] [-v]
{combine,fastq,fasta,stats,hist,events,readstats,tabular,nucdist,metadata,index,qualdist,qualpos,winner,squiggle,times,yield_plot,occupancy,organise}
...
optional arguments:
-h, --help show this help message and exit
-v, --version Installed poretools version
[sub-commands]:
{combine,fastq,fasta,stats,hist,events,readstats,tabular,nucdist,metadata,index,qualdist,qualpos,winner,squiggle,times,yield_plot,occupancy,organise}
combine Combine a set of FAST5 files in a TAR achive
fastq Extract FASTQ sequences from a set of FAST5 files
fasta Extract FASTA sequences from a set of FAST5 files
stats Get read size stats for a set of FAST5 files
hist Plot read size histogram for a set of FAST5 files
events Extract each nanopore event for each read.
readstats Extract signal information for each read over time.
tabular Extract the lengths and name/seq/quals from a set of
FAST5 files in TAB delimited format
nucdist Get the nucl. composition of a set of FAST5 files
metadata Return run metadata such as ASIC ID and temperature
from a set of FAST5 files
index Tabulate all file location info and metadata such as
ASIC ID and temperature from a set of FAST5 files
qualdist Get the qual score composition of a set of FAST5 files
qualpos Get the qual score distribution over positions in
reads
winner Get the longest read from a set of FAST5 files
squiggle Plot the observed signals for FAST5 reads.
times Return the start times from a set of FAST5 files in
tabular format
yield_plot Plot the yield over time for a set of FAST5 files
occupancy Inspect pore activity over time for a set of FAST5
files
organise Move FAST5 files into a useful folder hierarchy
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