[Primeusers] syntax and tree input problems

[Erik Sjölund]

on 07/30/2012 06:59 PM A.Malhotra wrote:
>
> 2. Syntax. By deleting various options and trying again I have narrowed
> it down to a problem with the -Su option. I am writing it like this:
> -Su DNA Pi=0.254 0.283 0.234 0.229 R=0.1087 0.2980 0.0784 0.1029 0.3372
> 0.0747
>
> But this produces "Unknown Beep option" (or similar)
>
> If I replace this string with -Sm JC69 it seems fine.

I looked into the source code 
(src/cxx/applications/primeDLRS/primeDLRS.cc and 
src/cxx/libraries/prime/BeepOption.cc)  and my best guess is that it 
might work if you remove "Pi=" and "R=". In other words

-Su DNA 0.254 0.283 0.234 0.229 0.1087 0.2980 0.0784 0.1029 0.3372

But this is just a guess. I am not too familiar with how PrIME works.

Let us take a look at the help output of the command primeDLRS:

$ primeDLRS -h 2>&1 | grep -A 1 DNA
   -Su <'DNA'/'AminoAcid'/'Codon'> <Pi=float1 float2 ... floatn> 
<R=float1 float2 ...float(n*(n-1)/2)>
       User-defined substitution model. The size of Pi and R must fit 
data type
       (DNA: n=4, AminoAcid: n=20, Codon: n=62). R is given as a flattened
       upper triangular matrix. Don't use both option -Su and -Sm.


I see the text "Pi=" mentioned, but my guess is that it shouldn't be 
written on the command line.

cheers,
Erik Sjölund