Trouble downweighting terminal gaps in v.4

[Ivar]

Attempting analysis with POY v. 4.1.2 (as there seem to be problems running v. 5.1.1 in the environment I’m using), I ran into an error I can’t quite interpret.

transform(tcm:"s50t100i200.mat", ti:(1,1,1,1,0), td:(1,1,1,1,0))

renders the error message
[transform_argument] expected after "," (in [transform])

Despite the manual for v.4 giving the example

transform(tcm:(2,2), ti:(1,1,1,1,0), td:(1,1,1,1,0))

When I remove the ", ti:(1,1,1,1,0), td:(1,1,1,1,0)" -part, it works. I need to ameliorate the effects of variable sequence lengths though (working with ITS2).

Would appreciate a piece of advice,
I.

[Nick Lucaroni]

I think this is a bug in the command parser and I've fixed it in 5+. I can fix the command parser by transplanting those changes from 5 back to 4, are you able to compile the distribution from github, or do you require a binary? If you need a binary I'll try to find time to get one to you, what OS would you need?

What limitations do you have with 5.1.1 ? I think in the latest head of 5 we've removed the trailing-insertion / -deletion commands. Ward, do you recall why? I think we assumed they were used internally.

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nL

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[Ward C Wheeler]

Thanks Nick

I think this is a bug in the command parser and I've fixed it in 5+. I can fix the command parser by transplanting those changes from 5 back to 4, are you able to compile the distribution from github, or do you require a binary? If you need a binary I'll try to find time to get one to you, what OS would you need?

Unfortunately, I don’t.  But that makes sense.

What limitations do you have with 5.1.1 ? I think in the latest head of 5 we've removed the trailing-insertion / -deletion commands. Ward, do you recall why? I think we assumed they were used internally.

W

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nL

On Wed, Mar 9, 2016 at 2:07 PM, Ivar <ikba...@gmail.com> wrote:

Attempting analysis with POY v. 4.1.2 (as there seem to be problems running v. 5.1.1 in the environment I’m using), I ran into an error I can’t quite interpret.

transform(tcm:"s50t100i200.mat", ti:(1,1,1,1,0), td:(1,1,1,1,0))

renders the error message
[transform_argument] expected after "," (in [transform])

Despite the manual for v.4 giving the example

transform(tcm:(2,2), ti:(1,1,1,1,0), td:(1,1,1,1,0))

When I remove the ", ti:(1,1,1,1,0), td:(1,1,1,1,0)" -part, it works. I need to ameliorate the effects of variable sequence lengths though (working with ITS2).

Would appreciate a piece of advice,
I.

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Ward Wheeler
Division of Invertebrate Zoology
American Museum of Natural History
Central Park West at 79th Street
New York, NY 10024-5192
USA
http://www.amnh.org/our-research/staff-directory/ward-wheeler

http://www.amnh.org/our-research/computational-sciences/research/projects/systematic-biology/poy/download

[Ivar]

Thanks for prompt reply. I’m using POY on a cluster and it’s still unclear exactly what the problem is. With the above information from you, admin is now working on finding out with which version this is best solved.
Meanwhile, have a nice weekend,
I.

[Nicholas Lucaroni]

The problem is that the parser, that reads your commands (from a file or interactively), had an error in version 4 that doesn't support what you want. I can make a patch to the application (and it will be done shortly, testing it tonight). I will post it to the github poy4 project[1] and you/admin can download and compile the executable. Is that appropriate for your needs? I can also try and compile a binary, but i'll need to know what OS and version you're using to make the proper binaries. Feel free to forward my email address to your admin if they have any specific questions.

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nL