erange version 4.0a dev release

[erange.git] / regionBins.py

diff --git a/regionBins.py b/regionBins.py
index 2d1649bd6614066656a0ef72a75aa7a90a4ffffc..d6c858de23c670a8526459bf41ba25dc807ac78d 100755 (executable)
--- a/regionBins.py
+++ b/regionBins.py
@@ -10,14 +10,15 @@ except:
     print 'psyco not running'
 
 import sys
+import ReadDataset
+from commoncode import getMergedRegions, computeRegionBins
+
 print '%s: version 2.0' % sys.argv[0]
 
 if len(sys.argv) < 4:
     print 'usage: python %s regionfile rdsfile outfilename [-bins numbins] [-field fieldNum] [-raw] [-padregion bp] [-mergeregion bp] [-cache]' % sys.argv[0]
     sys.exit(1)
 
-from commoncode import *
-
 regionfilename = sys.argv[1]
 hitfile =  sys.argv[2]
 outfilename = sys.argv[3]
@@ -55,7 +56,7 @@ if '-bins' in sys.argv:
     binfield = sys.argv.index('-bins') + 1
     bins = int(sys.argv[binfield])
 
-hitRDS = readDataset(hitfile, verbose = True, cache=doCache)
+hitRDS = ReadDataset.ReadDataset(hitfile, verbose=True, cache=doCache)
 readlen = hitRDS.getReadSize()
 normalizationFactor = 1.0
 if normalize:
@@ -65,7 +66,7 @@ if normalize:
 chromList = hitRDS.getChromosomes(fullChrom=False)
 chromList.sort()
 
-regionDict = getMergedRegions(regionfilename, maxDist = mergeregion, keepLabel = True, verbose = True, chromField = cField, pad=padregion)
+regionDict = getMergedRegions(regionfilename, maxDist=mergeregion, keepLabel=True, verbose=True, chromField=cField, pad=padregion)
 
 hitDict = hitRDS.getReadsDict(doMulti=True, findallOptimize=True)
 
@@ -76,6 +77,7 @@ for regionID in regionsBins:
     tagCount = 0.
     for binAmount in regionsBins[regionID]:
         tagCount += binAmount
+
     outfile.write('%s\t%s\t%.1f\t%d' % (regionID, regionID, tagCount, Len[gid]))
     for binAmount in gidBins[gid]:
             if normalizeBins: