Open heatmap (html) generated with compare proteins tool

[Alexis Varin]

I used compare proteins tool to compare my prot.xml files. The command was successfull and I obtained the compare.xls.d3.html file containing the heatmap. Problem : the html is 80 Mb and nothing seems to be sturdy enough to open it, all browsers, 32 bits or 64 bits (and I really mean all) crash before (the PC has 32 Gb RAM but the browsers crash way before reaching that limit).

What can I use to visualize the data ? I can see the html code fine with EmEditor for example (1.6 million lines) but seeing the heatmap proves difficult.

Thanks for the help

[David Shteynberg]

Can you check the console errors to see if there might be a problem in the html code?

Thanks,

-David

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[Adam R]

I am running into an issue with the generation of the file in order to compare four prot.xml files...the commands are run and say "successful" but no files are generated screenshot attached). Are there any recommended settings to use for a first pass? I am using TPP v5.0.1-7604

Best,

Adam

[David Shteynberg]

Hello Adam,

Was there any other output generated on the webpage from the rest of the commands?

Thanks,

-David

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[Ulrich auf dem Keller]

Hi David

I have the same problem here. Newly installed Windows 10, TPP 5.0.0 full installation. Only .pl scripts are affected, all compiled binaries run normally. Once started in Petunia, commands are passed to ‘runCommands’ but never executed. All output from the daemon is normal (I set ‘debug’ to ‘1’ and checked tpp_web.log for details). Scripts run fine on command line, but from Petunia only a folder ‘%SYSTEMSDRIVE% with ‘Program Data’ etc. is created within the working directory. Setting ENV{SYSTEMSDRIVE} and ENV{PROGRAMDATA} in tpp_config.pl does not help. Seems to be a problem with perl, maybe ‘FindBin’ etc.

Thanks for any help.

Best regards

Ulrich

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<compare_protxml_files_missing.PNG>

[Adam R]

Hi David,

Besides the commands there was nothing else. I re-ran the analysis and have included screenshots of the entire page. 

Best,

Adam

On Wednesday, October 18, 2017 at 1:04:31 PM UTC-5, David Shteynberg wrote:

Hello Adam,

Was there any other output generated on the webpage from the rest of the commands?

Thanks,

-David

On Wed, Oct 18, 2017 at 10:20 AM, Adam R <raba...@gmail.com> wrote:

I am running into an issue with the generation of the file in order to compare four prot.xml files...the commands are run and say "successful" but no files are generated screenshot attached). Are there any recommended settings to use for a first pass? I am using TPP v5.0.1-7604

Best,

Adam

On Monday, October 16, 2017 at 12:47:56 PM UTC-5, Alexis Varin wrote:

I used compare proteins tool to compare my prot.xml files. The command was successfull and I obtained the compare.xls.d3.html file containing the heatmap. Problem : the html is 80 Mb and nothing seems to be sturdy enough to open it, all browsers, 32 bits or 64 bits (and I really mean all) crash before (the PC has 32 Gb RAM but the browsers crash way before reaching that limit).

What can I use to visualize the data ? I can see the html code fine with EmEditor for example (1.6 million lines) but seeing the heatmap proves difficult.

Thanks for the help

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[David Shteynberg]

Hi Adam,

I verified on my system that I can generate a heatmap on some test data.   If you can transfer your protXML files to me I can try to troubleshoot.

-David

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[Adam R]

Hi David,

I have attached the prot.xml files to this post. Thank you for checking this out.

Best,

Adam

[David Shteynberg]

Hello Adam,

I was able to generate a heatmap just running the tool on your files.  I am not sure why this would be broken for you.  Which version are you using at the moment?  Perhaps you can try our latest release candidate.

-David

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[Adam R]

Hi David,

I am using TPP v5.01 Post-Typhoon dev, Build 201706192108-7604 (Windows_NT-x86_64)

Are you using default parameters when running the tool? 

Best,

Adam

[David Shteynberg]

Hi Adam,

That looks like a bug in the older version that has since been corrected.  You can try the following release candidate that should fix the issue:

https://www.dropbox.com/s/581xjz8kzpl4nrn/TPP_Setup_5.1.0-rc1.exe?dl=0

-David

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