confidence/evalues in confidence attributes of domain architectures

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Daniel Lang

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May 6, 2015, 4:44:03 PM5/6/15
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Hi,

this is Archaeopteryx/phyloxml related question. I'm generating my own phyloxml files to visualize gene families in Archaeopteryx. For these families I'm adding domain_architectures and domains. The information is based on hmmerscan searches and also has confidence (evalues) values, I'd like to add. It works nicely as long as I have positive float values, but some these matches have evalues of 0.00. If I add domains like these:

 <domain_architecture length="369">
                    <domain from="232" to="266" confidence="0">WD40</domain>
                    <domain from="171" to="203" confidence="0">WD40</domain>
</domain_architecture>

I get the error that:
failed to parse: ....
from, to, or confidence attribute not set in:
....

What is the expected input for the confidence attribute? 

Best,
Daniel

Christian Zmasek

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May 6, 2015, 4:49:46 PM5/6/15
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Hi, Daniel:

I just realized this is a very stupid error in forester: it does not allow confidence values of 0.0.
For now, a "workaround" is to use very small values instead of zero (e.g. 1e-250).
I will fix this eventually, though.

-Christian-




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Christian

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May 13, 2015, 11:06:13 PM5/13/15
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Hi, 

I fixed this issue.
You can download the newest version here:

-Christian-
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