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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=[]):
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)
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])
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)
totalLength += exonLengths[index]
geneDict[uname] = (sense, blockCount, totalLength, chrom, chromstarts, exonLengths)
- mapDict[uname] = []
genedatafile.close()
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:]
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
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)])
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()
infile.close()
- trim = -4
+ maxBorder = 0
if dataType == "RNA":
if dataType == "RNA":
+ trim = -4
maxBorder = readsize + trim
infile = open(filename, "r")
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
mInsertList = []
sInsertList = []
index = uIndex = mIndex = sIndex = lIndex = 0
+ delimiter = "|"
+ insertSize = 100000
for line in infile:
lIndex += 1
if stripSpace:
for line in infile:
lIndex += 1
if stripSpace: