HyPhy message board - Individual substitutions on branches?

Sarah YaBB Newbies Offline Posts: 47	Individual substitutions on branches? Sep 10^th, 2006 at 1:18pm Is there any way for HyPhy to list inferred the amino acid substitutions on tree branches? I could export trees to PAUP and rerun ML analysis there, but it would be nice to stick with one program. Thanks, Sarah
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Art Poon

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Re: Individual substitutions on branches?
Reply #1 - Sep 11^th, 2006 at 5:56pm

Dear Sarah,

As a matter of fact, I need to generate a batch file to do just this thing for my own research. Theoretically, one could use ReconstructAncestors(lf) to infer the sequences at internal nodes and traverse the tree to assign substitutions to branches, but that would be assuming no more than one substitution per branch. I'm planning to implement a recently published method that allows for more than one substitution.

After optimizing your likelihood function with the HyPhy GUI, you can select Analysis > Results > Ancestral Sequences to save the reconstructed sequences to a flat-formatted file. In the batch language, you can use:

DataSet ancseq = ReconstructAncestors(lf)

where lf identifies the likelihood function that you just optimized. I'll need to look over some notes to figure out how to write a batch file to do the next step, i.e. assign substitutions to branches given the intervening nodes. I'll post something up here as soon as I do.

As far as I know, however, there isn't an existing batch file to do what I think you're asking for exactly (i.e. the strictly correct way), not yet. If it's okay to assume single substitutions, however, then it's straight-forward (says the post-doc who's going to spend some time now figuring out exactly how to write this into a HYPHY BF).
- Art.

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Re: Individual substitutions on branches?
Reply #2 - Sep 11^th, 2006 at 6:53pm

Dear Sarah,

I poked around a little more and realized that there's some batch files in the UserAddins directory that may be of some use to you. You might want to try CodonMutationToTreeMapper.bf, which will take your likelihood function (has to be called "lf" and generate a PostScript file depicting the inferred tree with the branch or branches highlighted with codon substitutions.

Sorry if you've already tried this out already =) I'm going through the batch file to see how I can adapt it.
- Art.

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: Individual substitutions on branches? Reply #3 - Sep 13^th, 2006 at 9:00am Dear Sarah, As Art pointed out, there are some existing scripts which can report (graphically), inferred substitutions for a given site. If you give me an idea of what kind of output you wanted, I can modify them quite easily. Cheers, Sergei
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Sarah

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Re: Individual substitutions on branches?
Reply #4 - Sep 14^th, 2006 at 6:43pm

Thanks, Art & Sergei.

I had missed CodonMutationToTreeMapper.bf. It looks good.

I have an embarrassing question. Working from the GUI, once I build a likelihood and optimize it under some model, how do I save the likelihood function? I thought I had saved it using File > Save > lf (as data file) in the console after I had optimized my MG94-REV_3x4_DualRV_GDD model. I put copies in both the UserAddins and general HyPhy directories. CodonMutation...bf gives me an initialization error. Am I really saving the likelihood function (= param + seq + tree)? I can see it as an object in Object Explorer but cannot save from there.

I've been rereading the HyPhy manual and GUI examples and am making slow progress.

Thanks for your help.

Sarah

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Art Poon

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Re: Individual substitutions on branches?
Reply #5 - Sep 15^th, 2006 at 1:11pm

Dear Sarah,

To export your likelihood function to a file from the HyPhy GUI, you need to select the menu option Analysis > Results > Save Results, which will bring up a "Likelihood Function Display" dialog window. Select the last option "Export Analysis" and hit OK, which will bring up a file directory window in which you can specify a filename and save.

For importing your likelihood function into CodonMutationToTreeMapper.bf, you need to ensure that your likelihood function identifier is "lf". If your likelihood function takes some other name (you can check this via Object Inspector), you will need to open the file that you've exported your LF to, and find the line that looks like this (it should be near the bottom):

LikelihoodFunction yourLF = (yourDataFilter,yourTree);

and change the identifier (i.e. "yourLF") to "lf". Then open the exported LF file as a batch file. Now "lf" should appear in your Object Inspector. Run CodonMutationToTreeMapper.bf .

I'm working on writing documentation for CodonMutationToTreeMapper.bf, and will try to get it to accept any LF identifier.

- Art.

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Re: Individual substitutions on branches?
Reply #6 - Sep 15^th, 2006 at 2:10pm

Dear Art,

Here's a way to select a likelihood function identifier:

Code:

tIndex = -1;
avLFCount = Rows ("LikelihoodFunction");
if (avLFCount>1)
{
	choices = {avLFCount,2};
	for (k=0; k<avLFCount;k=k+1)
	{
		GetString (tName, LikelihoodFunction, k);
		choices[k][0] = tName;
		choices[k][1] = "Function "+tName;
	}

	ChoiceList (tIndex,"Simulate from this likelihood function:",1,SKIP_NONE,choices);
}
else
{
    tIndex = avLFCount - 1;
}

if (tIndex>=0)
{
	 GetString (tName, LikelihoodFunction, tIndex);
}
else
{
/* no lf's defined */
return 0;
}

/* now tName has the ID of the LF */

Cheers,
Sergei

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Art Poon Global Moderator Offline Feed your monkey! Posts: 0	Re: Individual substitutions on branches? Reply #7 - Sep 15^th, 2006 at 2:55pm Thanks, Sergei! I had gotten stuck on that part. - Art.
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Sarah

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Re: Individual substitutions on branches?
Reply #8 - Sep 19^th, 2006 at 1:33pm

Thanks. I'm still missing something, though. Embarrassed

I can now save, modify, and open the lf just fine. When I try opening CodonMutationToTreeMapper.bf, I get:

Quote:

Likelihood Functionlf has not been initialized
Current BL Command:Reconstruct Ancestors into ancestralSeqs from the likelihood function lf Current Task has been terminated. Would you like to see the remaining error messages, if there are any?

Clicking 'yes':

Quote:

Problem occurred in line:setupMapToTree(0)
Current BL Command:setupMapToTree(0) Current Task has been terminated....

On my second attempt, I opened the object explorer and to view the lf, thinking that might somehow initialize it. I also tried 'recalculate.' After trying to open CodonMutation...bf I got:

Quote:

DataSet/DataSetFilter filteredData has not been initialized
Current BL Command:Harvest Frequencies into matrix observedCEFV from DataSet filteredData with unit size = 3 with atom size = 3 with position specific flag = 0 Partition: Current Task has been terminated. Would you like to see the remaining error messages, if there are any?

Clicking 'yes,' I get the same second message as before.

Am I missing something obvious?

For this analysis I'm working with HyPhy on Windows.

Sarah

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Sarah

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Re: Individual substitutions on branches?
Reply #9 - Sep 19^th, 2006 at 2:05pm

I'm also unable to open the saved lf file on my intel mac. I've tried playing with the extensions (.bf, nothing) and have also checked to confirm that the file opens fine in Windows. The error I get is

Quote:

[Dead end] An error occured:
Node names should begin with a letter, a number, or an underscore....

Sarah

update: I restarted my computer. Now HyPhy on my intel imac can't open any sequence files (including the included example files) without crashing. I get crashes when I try to load a file under 'New Analysis' and when I use Open > Data file. update2: it will open p51.nex if i try to run a basic analysis.

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Re: Individual substitutions on branches?
Reply #10 - Sep 19^th, 2006 at 4:46pm

Dear Sarah,
Have you tried selecting "Show All Files" from the topmost drop-down menu in the file open dialog? This usually allows you to select any file to open.

Sorry for the crashes; I am at a loss why this would happen (Universal Binary Builds work fine on my G5 and Intel iMac).
Could you perhaps paste in the crash log? You can open Applications->Utilities->Console program, open the Log drawer, look under ~/Library/Logs/ then CrashReporter then HYPHY.crash.log and paste in whatever the system wrote out when the program crashed.

Thanks!
Sergei

P.S. Could you also e-mail me the lf fit file which was giving you error messages?

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Sarah

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Re: Individual substitutions on branches?
Reply #11 - Sep 21^st, 2006 at 3:29pm

I was thinking that the error message might come from the way Windows handles carriage returns. I didn't modify the exported likelihood function in any way (except to rename the function itself as Art showed) after saving it in Windows and opening it on my Mac.

The interesting news now is that after building and optimizing a likelihood function in my newly reinstalled HyPhy (on my Mac), I am unable to save results. Analysis > Results is gray. I think I might try uninstalling and reinstalling and working with sample files only to pinpoint the problems.

Sarah

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: Individual substitutions on branches? Reply #12 - Sep 21^st, 2006 at 4:24pm Dear Sarah, Carriage returns should not matter; HyPhy should automatically handle all 3 types (UNIX/Mac/Windows). That the 'Results' menu is grayed out is odd - it usually happens only if HyPhy can't find the TemplateBatchFiles directory. Cheers, Sergei
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Sarah

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Re: Individual substitutions on branches?
Reply #13 - Sep 21^st, 2006 at 5:12pm

How can I check if/how HyPhy recognizes the Template Batch Files directory? It looks like it's there. This is the install from today (universal binary uploaded 9/14). I can run a standard analysis (AnalyzeCodonData.bf) with no problem. I run into problems when I do the following:

Open data file
Create partition
Define partition type as codon
Select tree from file (tree looks good in window)
Define substitution model type
Set parameters to local
Analysis > Build function
Analysis > Optimize

The optimization appears good (messages log and console report no problems); I can see a tree and LF. Analysis > Results remains gray. I repeated this procedure with three different data sets and encountered the same problem.

Maybe there's something wrong with my computer... I'm sorry for all these troubles... thought they might be useful for the record.

Sarah

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Sergei

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Re: Individual substitutions on branches?
Reply #14 - Sep 21^st, 2006 at 5:33pm

Dear Sarah,

The Analysis->Results menu is usually enabled after you run one of the standard (non-GUI) analyses. For your setting (running things via the interface), please use the little gears button in the bottom right of the console window, and choose 'ExportLikelihoodFunction' from the list.

Sorry for the confusion.

Cheers,
Sergei

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