Release version for Erange 4.0a

[erange.git] / altSpliceCounts.py

diff --git a/altSpliceCounts.py b/altSpliceCounts.py
index 12077c1ec7d9d7e3ba499c67c99734a8a9a54157..c59dc9249b6c82ded0466f872e98a9900e702c46 100755 (executable)
--- a/altSpliceCounts.py
+++ b/altSpliceCounts.py
@@ -2,7 +2,7 @@ try:
     import psyco
     psyco.full()
 except:
-    print 'psyco not running'
+    print "psyco not running"
 
 print "altSpliceCounts: version 3.7"
 
@@ -56,13 +56,13 @@ def altSpliceCounts(hitfile, outfilename, doCache=False, cachePages=100000):
     stopDict = {}
     resultDict = {}
 
-    hitRDS = ReadDataset.ReadDataset(hitfile, verbose = True, cache=doCache)
+    hitRDS = ReadDataset.ReadDataset(hitfile, verbose=True, cache=doCache)
     if cachePages > hitRDS.getDefaultCacheSize():
         hitRDS.setDBcache(cachePages)
 
     readlen = hitRDS.getReadSize()
     hitDict = hitRDS.getSplicesDict(noSense=True)
-    outfile = open(outfilename,'w')
+    outfile = open(outfilename, "w")
 
     for chrom in hitDict:
         startDict[chrom] = []
@@ -155,7 +155,7 @@ def altSpliceCounts(hitfile, outfilename, doCache=False, cachePages=100000):
 
         resultDict[chrom].sort()
         for line in resultDict[chrom]:
-            outfile.write('alt%d' % alternative + '\tchr%s\t%d\t%d\tchr%s\t%d\t%d\n'  % line)
+            outfile.write("alt%d" % alternative + "\tchr%s\t%d\t%d\tchr%s\t%d\t%d\n"  % line)
             alternative += 1
 
         print chrom, maxIndex, spliceEvent, altSpliceEvent