Release version for Erange 4.0a

[erange.git] / makerdsfromeland2.py

diff --git a/makerdsfromeland2.py b/makerdsfromeland2.py
index 66209eef973f36072ba964aac73f8579685aed99..b11848d7a93e3968d7b76b286fa415d04ffa078d 100755 (executable)
--- a/makerdsfromeland2.py
+++ b/makerdsfromeland2.py
@@ -106,8 +106,6 @@ def makeRDSFromEland2(label, filename, outdbname, doIndex=False, delimiter="|",
     insertSize = 100000
 
     geneDict = {}
-    mapDict = {}
-    seenSpliceList = []
     if dataType == 'RNA':
         genedatafile = open(geneDataFileName)
         for line in genedatafile:
@@ -120,17 +118,11 @@ def makeRDSFromEland2(label, filename, outdbname, doIndex=False, delimiter="|",
             chrom = fields[1]
             sense = fields[2]
             chromstarts = fields[8][:-1].split(',')
-            chromstops = fields[9][:-1].split(',')
-            exonLengths = []
-            totalLength = 0
             for index in range(blockCount):
                 chromstarts[index] = int(chromstarts[index])
-                chromstops[index] = int(chromstops[index])
-                exonLengths.append(chromstops[index] - chromstarts[index])
-                totalLength += exonLengths[index]
 
-            geneDict[uname] = (sense, blockCount, totalLength, chrom, chromstarts, exonLengths)
-            mapDict[uname] = []
+            geneDict[uname] = (sense, blockCount, chrom, chromstarts)
+
         genedatafile.close()
 
     rds = ReadDataset.ReadDataset(outdbname, init, dataType, verbose=True)
@@ -322,6 +314,7 @@ def makeRDSFromEland2(label, filename, outdbname, doIndex=False, delimiter="|",
     print '%d unique reads' % index
     infile.close()
 
+    seenSpliceList = []
     if dataType == 'RNA':
         print 'mapping splices...'
         index = 0
@@ -441,7 +434,7 @@ def makeRDSFromEland2(label, filename, outdbname, doIndex=False, delimiter="|",
                     print fields
                     continue
 
-                (sense, blockCount, transLength, chrom, chromstarts, blockSizes) = geneDict[model]
+                (sense, blockCount, chrom, chromstarts) = geneDict[model]
                 if extended:
                     if 'F' in thepos:
                         rsense = '+'