Compile kent source as dynamic library

To run kent src functions from python, you need to compile the tree with -fPIC. It's easier to deactivate the various libraries:

 cd src/lib
 make USE_SAMTABIX=0 USE_TABIX=0 USE_BAM=0 CFLAGS=-fPIC USE_SSL=0
 gcc -shared -o kent.so *.o font/*.o -lz -lpng

Now you can do this to generate a python stub (wrapper) for any kent source library:

 ctypesgen.py ../inc/psl.h -lkent.so -o psl.py
 

It's probably easier to create a big stub for all functions in the kent source library:

 ctypesgen.py ../inc/*.h -lkent.so -o kent.py
 

And then call kent source functions in your python script:

 import kent
 p = kent.pslLoadAll("test.psl")
 print p.contents.blockCount
 kent.freeMem(p) # remember that all objects we get back have to be freed, these are normal C structs, not python objects

Most functions return pointers to structs, not data directly, so you will usually have to use the .contents attribute to get the data.