verstring = "makerdsfromblat: version 3.10"
print verstring
+NUM_HEADER_LINES = 5
+
+
def main(argv=None):
if not argv:
argv = sys.argv
verbose=False, cachePages=100000, geneDataFileName="",
propertyList=[]):
- delimiter = "|"
- minIntron = 10
- maxBorder = 0
- index = 0
- insertSize = 100000
-
+ writeLog(outdbname + ".log", verstring, string.join(sys.argv[1:]))
if forceRNA:
print "forcing datatype to RNA"
dataType = "RNA"
- if dataType == "RNA":
- genedatafile = open(geneDataFileName)
-
- writeLog(outdbname + ".log", verstring, string.join(sys.argv[1:]))
-
geneDict = {}
mapDict = {}
if dataType == "RNA" and not forceRNA:
+ genedatafile = open(geneDataFileName)
for line in genedatafile:
fields = line.strip().split("\t")
blockCount = int(fields[7])
# make some assumptions based on first read
infile = open(filename, "r")
- for arg in range(6):
+ for arg in range(NUM_HEADER_LINES):
line = infile.readline()
+ line = infile.readline()
fields = line.split()
readsize = int(fields[10])
pairedTest = fields[9][-2:]
rds.insertMetadata([("blat_mapped", "True")])
minReadScore = readsize - readsize/25 - 1
- trim = -4
+ maxBorder = 0
if dataType == "RNA":
+ trim = -4
maxBorder = readsize + trim
infile = open(filename, "r")
index = uIndex = mIndex = sIndex = lIndex = 0
bestScore = 0
# skip headers
- for arg in range(5):
+ for arg in range(NUM_HEADER_LINES):
line = infile.readline()
+ insertSize = 100000
+ delimiter = "|"
+ minIntron = 10
for line in infile:
lIndex += 1
fields = line.strip().split()