Release version for Erange 4.0a

[erange.git] / makerdsfrombowtie.py

diff --git a/makerdsfrombowtie.py b/makerdsfrombowtie.py
index 14be260cdf0721b0514098a22d3a07423756c41b..eadb66b83d59e140b0402a9ea76dd351219abad0 100755 (executable)
--- a/makerdsfrombowtie.py
+++ b/makerdsfrombowtie.py
@@ -87,29 +87,13 @@ def makerdsfrombowtie(label, filename, outdbname, genedatafilename=None, init=Tr
                       flip=False, verbose=False, stripSpace=False, cachePages=100000,
                       propertyList=[]):
 
-    delimiter = "|"
+    writeLog("%s.log" % outdbname, verstring, string.join(sys.argv[1:]))
 
+    geneDict = {}
     dataType = "DNA"
     if genedatafilename is not None:
         dataType = "RNA"
         genedatafile = open(genedatafilename)
-
-
-    forcePair = False
-    if forceID is not None:
-        forcePair = True
-    else:
-        forceID = 0
-
-    maxBorder = 0
-    index = 0
-    insertSize = 100000
-
-    writeLog("%s.log" % outdbname, verstring, string.join(sys.argv[1:]))
-
-    geneDict = {}
-    mapDict = {}
-    if dataType == "RNA":
         for line in genedatafile:
             fields = line.strip().split("\t")
             blockCount = int(fields[7])
@@ -130,7 +114,6 @@ def makerdsfrombowtie(label, filename, outdbname, genedatafilename=None, init=Tr
                 totalLength += exonLengths[index]
 
             geneDict[uname] = (sense, blockCount, totalLength, chrom, chromstarts, exonLengths)
-            mapDict[uname] = []
 
         genedatafile.close()
 
@@ -164,12 +147,17 @@ def makerdsfrombowtie(label, filename, outdbname, genedatafilename=None, init=Tr
     fields = line.split()
     readsize = len(fields[5])
     pairedTest = fields[0][-2:]
+    forcePair = False
+    if forceID is not None:
+        forcePair = True
+    else:
+        forceID = 0
+
     paired = False
     if pairedTest in ["/1", "/2"] or forcePair:
         print "assuming reads are paired"
         paired = True
 
-
     print "read size: %d bp" % readsize
     if init:
         rds.insertMetadata([("readsize", readsize)])
@@ -184,8 +172,9 @@ def makerdsfrombowtie(label, filename, outdbname, genedatafilename=None, init=Tr
 
     infile.close()
 
-    trim = -4
+    maxBorder = 0
     if dataType == "RNA":
+        trim = -4
         maxBorder = readsize + trim
 
     infile = open(filename, "r")
@@ -195,6 +184,8 @@ def makerdsfrombowtie(label, filename, outdbname, genedatafilename=None, init=Tr
     mInsertList = []
     sInsertList = []
     index = uIndex = mIndex = sIndex = lIndex = 0
+    delimiter = "|"
+    insertSize = 100000
     for line in infile:
         lIndex += 1
         if stripSpace: