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Genometric / MSPC

Using combined evidence from replicates to evaluate ChIP-seq peaks
https://genometric.github.io/MSPC/
GNU General Public License v3.0
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Problem about "Invalid culture info" #192

Closed xiagjt closed 1 year ago

xiagjt commented 1 year ago

Hi! Recently I want to run the MSPC software to merge the peaks generated by MACS2 form DAP-Seq data. However, When I test the program using the demo data, I encountered an issue about wrong Invalid culture info as following: image

I Tried to add a parser configuration using parameter "-p"; image However, it does not work. thus, please help me to figure it out. Thanks.

VJalili commented 1 year ago

Hello, @xiagjt.

Please see this context on the Culture if you are interested in how they impact MSPC.

Could you please try zh-Hans or zh-Hant for Chinese Culture?

From .net docs:

There are two culture names that contradict this rule. The cultures Chinese (Simplified), named zh-Hans, and Chinese (Traditional), named zh-Hant, are neutral cultures. The culture names represent the current standard and should be used unless you have a reason for using the older names zh-CHS and zh-CHT.

Also, I noticed MSPC docs reference an outdated list of cultures for valid values. I updated the documentation to refer to the correct Culture values.

xiagjt commented 1 year ago

Dear sir, thanks for your kind response. I tried the zh-Hans and zh-Hant in the JSON file. However, it also failed with the same error. image image

VJalili commented 1 year ago

Referring to the following part of the screenshot you shared: 

Error: Invalid culture info. (Parameter 'value')
Actual value was zh-CN.

You have this error in both calls of MSPC, even though the JSON file you shared has other Culture info. Could you please make sure you are referencing the correct config.json? You may try giving the absolute/full path of the file (e.g., /home/files/config.json instead of config.json).

xiagjt commented 1 year ago

Hi, I have found the error which was actually due to the mistake in my Linux system. The command "export LANG=zh-Hans-CN" has resolved the problem. Thanks again for your help.

xiagjt commented 1 year ago

Hi. Another question about the option "--multipleIntersections": the lowest p-value refers to the -log10(P) format or just P value?

VJalili commented 1 year ago

Glad the issue was resolved.

Hi. Another question about the option "--multipleIntersections": the lowest p-value refers to the -log10(P) format or just P value?

It is applied to the p-value.

The following lines of the code are when this parameter is applied.

https://github.com/Genometric/MSPC/blob/1f3700b2667f873616a5df34a13d1fd2719f5df3/Core/Functions/Processor.cs#L260-L264

VJalili commented 1 year ago

I hope the above explanation resolves this issue. I am closing this, but please feel free to reopen it if you have a similar question.