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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy bugs >> Error reading in tree file (nexus and newick) http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1300892382 Message started by krwollen on Mar 23^rd, 2011 at 7:59am

Title: Error reading in tree file (nexus and newick)
Post by krwollen on Mar 23^rd, 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_333:367.90096754215756,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

Title: Re: Error reading in tree file (nexus and newick)
Post by Sergei on Mar 23^rd, 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

Title: Re: Error reading in tree file (nexus and newick)
Post by krwollen on Mar 24^th, 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

GA_CU_Run3MCCnex_tree.png (6 KB | )

Title: Re: Error reading in tree file (nexus and newick)
Post by Sergei on Mar 24^th, 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

Title: Re: Error reading in tree file (nexus and newick)
Post by krwollen on Mar 24^th, 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

HyPhy2_TreeReadError1.png (173 KB | )

Title: Re: Error reading in tree file (nexus and newick)
Post by Sergei on Mar 24^th, 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

Screen_shot_2011-03-24_at_11_55_39_AM.png (51 KB | )

Title: Re: Error reading in tree file (nexus and newick)
Post by krwollen on Mar 24^th, 2011 at 11:57am

Ahhhh! Thank you.

Title: Re: Error reading in tree file (nexus and newick)
Post by Sergei on Mar 24^th, 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