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#!/usr/bin/python3
# import the HyPhy library
# and standard OS utilities
import os, HyPhy
# first, create a HyPhy interface instance (class _THyPhy)
# the first argument defines the root directory for HyPhy
# and the second - how many threads the computational core
# should spawn
hyphyInstance = HyPhy._THyPhy (os.getcwd(),2)
# the basic interface command is 'ExecuteBF' which
# executes HyPhy batch language commands in HyPhy
# and returns a string representation of the return value
# (if any) from HYPHY
# The returned object is of type _THyPhyString with
# sData and sLength fields
# HyPhy will take care of disposing of the memory needed
# to store the result
hyphyResult = hyphyInstance.ExecuteBF ("return 2+2;");
print("Testing a trivial HyPhy command. 2+2 = ", hyphyResult.sData)
# an optional second argument to ExecuteBF
# can be used to "flush" the current state of the system
# this is the default option for the call of ExecuteBF
# passing the second argument of False or 0 will preserve
# the execution state
print("Consecutive command exection")
hyphyInstance.ExecuteBF ("z:=x+y;",False);
hyphyInstance.ExecuteBF ("x=3;",False);
hyphyInstance.ExecuteBF ("y=5;",False);
hyphyResult = hyphyInstance.ExecuteBF ("return z;",False);
print("The value of z is ", hyphyResult.sData)
print("Resetting the state of the execution erases the value of 'z'")
hyphyResult = hyphyInstance.ExecuteBF ("return z;");
print("The value of z is ", hyphyResult.sData)
# the real utility of the interface is to be able
# to execute prewritten analyses from HBL files
print("Executing the example F81.bf file")
hyphyResult = hyphyInstance.ExecuteBF ("ExecuteAFile(\"../HBL/F81.bf\")");
# retrive the standard output, error and runtime warnings
hyphyOut = hyphyInstance.GetStdout()
#errors will be empty UNLESS there was an exection error
hyphyErrors = hyphyInstance.GetErrors()
hyphyWarnings = hyphyInstance.GetWarnings()
print("Standard out: \n", hyphyOut.sData)
print("Errors: \n", hyphyErrors.sData)
print("Warnings/Log messages: \n", hyphyWarnings.sData)
# these variables can be explicitly deleted when they are no longer needed
# python garbage collection should take care of disposing of disused variables
del hyphyOut
del hyphyErrors
del hyphyWarnings
# A tighter intergration can be achieved by defining a retrieval function
# with the reserved name _THyPhyAskFor in the HBL file; it retrieves data
# by key and returns them in a internal format that can be converted
# to one of the basic return types: number, string or matrix
def retrieveValueByKey (key, returnType,hyphyInstance):
theResult = hyphyInstance.AskFor(key)
# see if HyPhy can retrieve a value with the requested key
if theResult:
canICast = hyphyInstance.CanCast(theResult,returnType)
# see if HyPhy can cast the value to the requested type
if canICast:
# do the casting
theResult = hyphyInstance.CastResult(theResult,returnType)
# the last step is to convert from the basic return type
# to a derived class that we can use in python directly
if (returnType == HyPhy.THYPHY_TYPE_NUMBER):
return theResult.castToNumber()
if (returnType == HyPhy.THYPHY_TYPE_STRING):
return theResult.castToString()
if (returnType == HyPhy.THYPHY_TYPE_MATRIX):
return theResult.castToMatrix()
return null
hyphyResult = hyphyInstance.ExecuteBF ("ExecuteAFile(\"../HBL/HKY85.bf\")");
print("Log-L = ", retrieveValueByKey ("LogL", HyPhy.THYPHY_TYPE_NUMBER, hyphyInstance).nValue);
print("kappa = ", retrieveValueByKey ("kappa", HyPhy.THYPHY_TYPE_NUMBER, hyphyInstance).nValue);
print("tree string = ", retrieveValueByKey ("Tree", HyPhy.THYPHY_TYPE_STRING, hyphyInstance).sData);
bl = retrieveValueByKey ("Branch lengths", HyPhy.THYPHY_TYPE_MATRIX, hyphyInstance);
print("retrieved ", bl.mCols-1, "branch lengths")
for i in range(0,bl.mCols-1):
print("Branch ", i+1, " has length ", bl.MatrixCell(0,i))
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