More readme updates

python/readme.MD

@@ -2,6 +2,7 @@ MOODS-python 1.9.1
 ==================
 
 Motif Occurrence Detection Suite
+
 https://www.cs.helsinki.fi/group/pssmfind/
 
 
@@ -11,8 +12,10 @@ Getting Started
 Start by compiling the MOODS extensions and optionally installing
 the MOODS module to Python library path. Do one of the following:
 
-(a) If you don't want to install MOODS package right now, you can just
-compile the extensions in place and create a symlink under `scripts/`:
+(a) Compile the extensions in place and create a symlink under `scripts/`
+(if you just want to test things without installing to Python library path,
+or you are simply planning to use the `moods_dna.py` scripts for basic 
+analysis):
 
     python setup.py build_ext --inplace
     cd scripts
@@ -29,6 +32,7 @@ compile the extensions in place and create a symlink under `scripts/`:
 In all cases, you can test MOODS by running the `moods_dna.py` script
 with the example data provided with the package:
 
+    cd scripts/
     python moods_dna.py -m example-data/matrices/*.{pfm,adm} -s example-data/seq/chr1-5k-55k.fa -p 0.0001
     python moods_dna.py --help