一个可将Accuri C6数据文件转换为标准FCS文件的python库

niwanmao

Accuri2fcs是一个Accuri C6数据文件转换为标准FCS文件的python库，可通过github直接下载源代码，再用python运行，或通过PyPi直接安装已编译版本。
对于初学python者，最好使用python(x,y)套装，这个套装已将所有python相关工具都集成了。打开IPython(sh)命令行工具，运行pip install accuri2fcs即可。如果提示The required version of distribute(>0.6.36) is not available，那么就先运行easy_install -U distribute即可。

python(x,y)

安装完成后，可以直接运行accuri2fcs再加相关参数即可将Accuri C6文件的.c6数据转换为fcs文件。具体命令及其使用方法见下图：

accuri2fcs使用帮助

附作者原帖：

Accuri2fcs, a command line program for the conversion of Accuri .c6 flow cytometry data files to the standard .fcs format, has been released today viagithub and PyPi.

Background

Someone in our lab recently needed to convert a large number of files (>500) and processing each one manually in the c6 software wasn’t going to be much fun. This script is the result of trying to automate that process, and it works. Usage is not exactly straightforward, however it is quite powerful. In it’s standard configuration it will find all .c6 files in the current directory, match every sample name outputting .fcs files named [filename.c6]_[row|column].fcs. This is probably perfectly fine for most uses.

However, it also supports the use of regular expressions to extract data from your.c6 Sample Name fields, and then saving the resulting .fcs into named files and folders built from that data. Have fun!

Download & Installation

You can install accuri2fcs via the PyPi Python package system. You can install via the command line with:

pip install accuri2fcs

Alternatively the code (and issue tracker) is available on github.

Once installed, using is as simple as entering on the command-line:

accuri2fcs

…to convert everything in the current folder. You’ll end up with a folder named fcscontaining the output. For more options type accuri2fcs --help.

License

Accuri2fcs is licensed under a Modified BSD 2 clause (i.e. completely free), my license of choice for interoperability software.

Contributions

This software is not under active development (I don’t do flow cytometry) but anysuggestions or bug reports are still appreciated.

xialin2120

阁下能否再讲得详细点!

xialin2120

演示一下

niwanmao

xialin2120 发表于 2013-8-21 16:08

                               
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演示一下

你给我一个c6数据吧：） 我这边没有现成的数据文件

晴天哇哇00

这个是一个批量转换的工具吧？不知道这个工具事后能不能调节C6的电压范围呢？  
因为C6的检测范围很广， 我用C6检测周期，再用modfit分析的话，数据就很悲剧的被压缩成一小团，根本没法选门。弱弱的问， 不知道modfit能不能调整坐标的参数范围呢？
用flowjo的话，倒是可以调节参数范围，但由于统计模型不同，G1+S+G2的结果做不到100%。 不知道有木有办法解决呢？

niwanmao

晴天哇哇00 发表于 2013-8-28 18:00

                               
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这个是一个批量转换的工具吧？不知道这个工具事后能不能调节C6的电压范围呢？  
因为C6的检测范围很广， 我 ...

你可以试试看。因为C6的原始数据文件我没有，所以一直没试。

tripleflop

能不能详细介绍一下如何操作呢？
目前已经在Python中打开了Accuri2fcs
从-n NANE_REGEXP这里开始就不知道怎么操作了

niwanmao

tripleflop 发表于 2015-10-29 15:13
能不能详细介绍一下如何操作呢？
目前已经在Python中打开了Accuri2fcs
从-n NANE_REGEXP这里开始就不知道怎 ...

accuri2fcs -f 文件名.c6 应该这样就可以了。