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Error reading in tree file (nexus and newick) (Read 5452 times)
Kurt Wollenberg
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Error reading in tree file (nexus and newick)
Mar 23rd, 2011 at 7:59am
 
Hello:

I am having a problem reading in a tree file in both nexus and newick formats. In both cases it appears the error is in the same place in the file. This is from the message log for the nexus file read:

Syntax error in expression:311((GA1_0000_226:1417.6209380711498,?((GA3_0056_333:367.900967542157
56,etc.

Here is the tree specification from the file:
#NEXUS

begin trees;
tree GA_CU_Run3mcc = ((GA1_0000_226:1417.6209380711498,((GA3_0056_333:367.90096754215756,etc.
end;

These are stripped-down maximum clade compatibility trees from BEAST. I'm running HYPHY 2.0020101222beta under Mac OS 10.6.6

Help?
Kurt
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Sergei
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Re: Error reading in tree file (nexus and newick)
Reply #1 - Mar 23rd, 2011 at 7:31pm
 
Hi Kurt,

Would you mind attaching the complete NEXUS file? I can't recreate the error based on the information in the message, sorry. The "311" preceding the opening parenthesis of the Newick string suggests to me that HyPhy is not recognizing the tree string for what it is.
Sergei
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Kurt Wollenberg
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Re: Error reading in tree file (nexus and newick)
Reply #2 - Mar 24th, 2011 at 9:24am
 
Hi Sergei:

Thanks for looking into this. Attached is the nexus file. As a test I ran this through FigTree which worked so the newick formatting seems to be OK. Also, I had to change the file extension to get this to attach. The attachment is a plain text file.

Cheers,
Kurt
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Sergei
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Re: Error reading in tree file (nexus and newick)
Reply #3 - Mar 24th, 2011 at 11:44am
 
Hi Kurt,

Very odd; I am able to open the file you attached with HyPhy version 2 (current build). Are you, perchance, using the three year old 1.00 build?

Sergei
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Kurt Wollenberg
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Re: Error reading in tree file (nexus and newick)
Reply #4 - Mar 24th, 2011 at 11:52am
 
Hi Sergei:

I just thought to try to open the tree file first rather than after opening the data file. Attached is a screen shot of the messages.log from that attempt. Any idea what this means? I am running HYPHY 2.0020101222beta under Mac OS 10.6.7.

Cheers,
Kurt
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Re: Error reading in tree file (nexus and newick)
Reply #5 - Mar 24th, 2011 at 11:55am
 
Hi Kurt,

Your version is fairly current -- that should not be a problem.

The messages are normal for this case (no models etc). Try going to Windows:Object Inspector menu and then double clicking on the tree ID (see attached image) to open it.

Sergei

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Kurt Wollenberg
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Re: Error reading in tree file (nexus and newick)
Reply #6 - Mar 24th, 2011 at 11:57am
 
Ahhhh! Thank you.
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Sergei
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Re: Error reading in tree file (nexus and newick)
Reply #7 - Mar 24th, 2011 at 1:07pm
 
Hi Kurt,

Your experience actually reminded me that HyPhy automatically opens tree viewers for files that have Newick strings, but doesn't do the same for NEXUS. I just added some code to do this (so you don't have to go to the Object Inspector). It'll be available in the next update of the binary

Cheers and thanks for your feedback,
Sergei
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