+============================================+
+ Finding ECEs in .wigFix phyloP files
+============================================+
Usage:
python ECE_finding_phyloP.py -f <filename> [-p <phyloP>] [-m <min_ece_length>] [-o <output_filename>]
Only the input filename (should be wigFix format) is absolutely required.
Type:
python ECE_finding_phyloP.py --help
to see the param defaults and usage.
An example usage is:
python ECE_finding_phyloP.py -f example.wigFix -m 50 -p 3.1 -o example.ece.txt
which finds ECEs with length >= 50 and avg. phyloP score >= 3.1
+=================================+
+ Additional note
+=================================+
The core ECE algorithm is implemented in a pure Python version (findECE_pure.py)
and a Cython version (findECE.pyx). The latter reduces the run time by 50%.
In most cases the Cython module (findECE.so) should be directly usable.
In that case nothing needs to be done for setting up the scripts.
To test that the Cython version works, invoke the python interpreter and type:
>>> import findECE
>>> findECE.test()
However if it looks like it needs to be recompiled, do:
make clean
make
The main ECE script (ECE_finding_phyloP.py) will try to use the Cython version
whenever possible. When it fails, it falls back to pure python version.