Added number of cores in config.

__init__.py

@@ -62,7 +62,7 @@ def start_cluster(comps, genome, region, cn, pth, sf):
     print "%s.%s: saving sequences to pickle" % (comps, genome)
     rnamotifs2.sequence.save(comps, genome)
 
-    num_worker_threads = 40
+    num_worker_threads = rnamotifs2.config.cores
     q = Queue()
     def worker():
         while True:

bin/rnamotifs2

@@ -5,8 +5,13 @@ import sys
 import os
 import shutil
 import glob
+import argparse
 
-comps = sys.argv[1]
+parser = argparse.ArgumentParser()
+parser.add_argument('-comps', action="store", dest="comps", default=None)
+args = parser.parse_args()
+
+comps = args.comps
 rnamotifs2.data.read_config(comps)
 rnamotifs2.data.read(comps)
 

cluster/__init__.py

@@ -73,7 +73,7 @@ def next_cluster(comps, genome, region, cn, pth=0.5, sf="r"):
                 draw(comps, genome, region, cn, steps=step)
                 return # stop tree construction
 
-        num_worker_threads = 40
+        num_worker_threads = rnamotifs2.config.cores
         q = Queue()
         def worker():
             while True:

config/__init__.py

@@ -1,3 +1,4 @@
 import rnamotifs2
 
+cores = 20 # number of cores to use in parallel computation
 perms = 0