Hello,

I am using a codon substitution model that is being imported with variables in it that I set in the hyphy batch script. 

If I set the variable as global and constrain certain values to numerics then everything works fine.  For example, if I do:

global fixed_w := 2;

Then, during optimization the value of fixed_w is properly constrained to the numerical value 2.

On the other hand, if I import a matrix of numbers that look like so:

ws = {{1,0.25} {2,0.5} {3, 0.75} {4, 1}};

If we pretend each of the values in that matrix is associated with a site in a protein.  I want to evaluate each one individually, setting fixed_w to the second value of each one.  It looks like so:

for loop:
global fixed_w := ws[iterator][1];

It appears the value of fixed_w is not set numeric, but rather symbolic causing it to be optimized rather than constrained.  It particular it seems to get set to the name of the iterator variable... which seems very strange to me.

I should add.  Unless I'm totally misguided, I think I'm just looking for a function analogous to the N[] function in Mathematica that forces a numeric value.

Alternatively I could just set a variable constant rather than constrain it, but I'm not sure how to do that either.

Need help!!

Thanks,
Austin

Hi Austin,

Try
Code:

global fixed_w := ws[iterator__][1];
 

Putting the double underscore following a variable name will tell HyPhy to insert the value of the variable in the expression.

You can also go the ExecuteCommands route, but when you build the string buffer (using string_id * something command), follow these three steps:

Code:

some_string = ""; /* this will tell HyPhy that some_string is a string */
some_string * 128; /* this will convert some_string into a buffer with initial size of 128 characters */
some_string * (string expression 1);
...
some_string * (string expression N); /* append strings to the buffer */
some_string * 0; /* close the buffer -- if you don't do this step, there may be garbage at the end because of unused allocated space */
 

You can also use
Code:

string1 = string2+string3+...+stringN;
 

to avoid messing around with string buffers. The '+' operation behaves as expected (concatenation).

Cheers,
Sergei