def check_ORNA_in_ago(oFN, oFF, agoFN, clippingAmount = 1):
NX = Nexus(oFN, oFF)
NX.load(['sequence', 'geneNames'])
#make truncated sequences
id_sequence = NX.createMap('id', 'sequence')
if clippingAmount > 0:
id_sequence = dict( (i, j[clippingAmount:-clippingAmount]) for i,j in id_sequence.items())
#get fastq sequences
agoF = open(agoFN, 'r')
agoSeqs = []
while True:
fPacket = nextFilePacket(agoF, 4)
if not fPacket: break
agoSeqs.append(fPacket[1])
agoF.close()
#count for each oRNA
id_count = {}
for id, seq in id_sequence.items():
for agoSeq in agoSeqs:
if seq in agoSeq:
id_count[id] = id_count.get(id, 0) + 1
#out
totalCount = 0
for id, count in id_count.items():
NX.id = id
print '%s\t%s\t%s' % (id, count, NX.geneNames)
totalCount += count
print totalCount
def check_ORNA_in_ago(oFN, oFF, agoFN, clippingAmount=1):
NX = Nexus(oFN, oFF)
NX.load(['sequence', 'geneNames'])
#make truncated sequences
id_sequence = NX.createMap('id', 'sequence')
if clippingAmount > 0:
id_sequence = dict((i, j[clippingAmount:-clippingAmount])
for i, j in id_sequence.items())
#get fastq sequences
agoF = open(agoFN, 'r')
agoSeqs = []
while True:
fPacket = nextFilePacket(agoF, 4)
if not fPacket: break
agoSeqs.append(fPacket[1])
agoF.close()
#count for each oRNA
id_count = {}
for id, seq in id_sequence.items():
for agoSeq in agoSeqs:
if seq in agoSeq:
id_count[id] = id_count.get(id, 0) + 1
#out
totalCount = 0
for id, count in id_count.items():
NX.id = id
print '%s\t%s\t%s' % (id, count, NX.geneNames)
totalCount += count
print totalCount
def testMap(fN, fF):
NX = Nexus(fN, fF)
NX.load(['geneName', 'numReads', 'otherIDs'])
geneName_numReads = NX.createMap('otherIDs', 'geneName', False) #not 1to1
for k,v in geneName_numReads.iteritems():
print k, v[:5]
return
def cleanForSNR(dataFN, oFF):
dataNX = Nexus(dataFN, oFF)
dataNX.load(['numUniqueSims', 'numUFBS', 'snrClean', 'siblingSet'])
id_numUFBS = dataNX.createMap('id', 'numUFBS')
id_siblingSet = dataNX.createMap('id', 'siblingSet')
unusedSiblings = []
for id, siblingSet in id_siblingSet.iteritems():
if len(siblingSet) == 1: continue #NOTE: oRNA IDs are in their own sibling set
numUFBS__id = [(id_numUFBS[x], x) for x in siblingSet]
numUFBS__id.sort()
numUFBS__id.pop() #take last one (one we're keeping) out of list
unusedIDs = [x[1] for x in numUFBS__id]
unusedSiblings.extend(unusedIDs)
#tag unclean oRNA
while dataNX.nextID():
if (dataNX.id in unusedSiblings) or (dataNX.numUniqueSims < 10):
dataNX.snrClean = False
else:
dataNX.snrClean = True
dataNX.save()
def updateSimilarSiblings(oFN, oFF, frameLength):
dataNX = Nexus(oFN, oFF)
dataNX.load(['sequence', 'siblingSet'])
oID_sequence = dataNX.createMap('id', 'sequence')
consolidatedSets = getSimilarORNASets(oID_sequence, frameLength)
for cSet in consolidatedSets:
for oID in cSet:
dataNX.id = oID
dataNX.siblingSet = list(cSet)
dataNX.save()
def updateSimilarSiblings(oFN, oFF, frameLength):
dataNX = Nexus(oFN, oFF)
dataNX.load(['sequence', 'siblingSet'])
oID_sequence = dataNX.createMap('id', 'sequence')
consolidatedSets = getSimilarORNASets(oID_sequence, frameLength)
for cSet in consolidatedSets:
for oID in cSet:
dataNX.id = oID
dataNX.siblingSet = list(cSet)
dataNX.save()
def cleanForSNR(dataFN, oFF):
dataNX = Nexus(dataFN, oFF)
dataNX.load(['numUniqueSims', 'numUFBS', 'snrClean', 'siblingSet'])
id_numUFBS = dataNX.createMap('id', 'numUFBS')
id_siblingSet = dataNX.createMap('id', 'siblingSet')
unusedSiblings = []
for id, siblingSet in id_siblingSet.iteritems():
if len(siblingSet) == 1:
continue #NOTE: oRNA IDs are in their own sibling set
numUFBS__id = [(id_numUFBS[x], x) for x in siblingSet]
numUFBS__id.sort()
numUFBS__id.pop() #take last one (one we're keeping) out of list
unusedIDs = [x[1] for x in numUFBS__id]
unusedSiblings.extend(unusedIDs)
#tag unclean oRNA
while dataNX.nextID():
if (dataNX.id in unusedSiblings) or (dataNX.numUniqueSims < 10):
dataNX.snrClean = False
else:
dataNX.snrClean = True
dataNX.save()
def testConsolidation(oFN, oFF, frameLength):
dataNX = Nexus(oFN, oFF)
dataNX.load(['sequence'])
oID_sequence = dataNX.createMap('id', 'sequence')
consolidatedSets = getSimilarORNASets(oID_sequence, frameLength)
#check if all oIDs are in set
allConsolidatedIDs = set()
[allConsolidatedIDs.add(x) for theSet in consolidatedSets for x in theSet]
oIDsSet = set(oID_sequence.keys())
print "DIFFERENCE"
print oIDsSet.symmetric_difference(allConsolidatedIDs)
#check Duplicates
#print out sets to verify that they work
for oIDSet in consolidatedSets:
print
print oIDSet
for oID in oIDSet:
print oID, oID_sequence[oID]
def linkTargetIDs(oFN, oFF, aFN, aFF):
oNX = Nexus(oFN, oFF)
oNX.load(['filteredTargets'])
#just give it some blanks
if os.path.getsize(aFN) == 0:
while oNX.nextID():
oNX.filteredTargets = []
oNX.save()
return
aNX = Nexus(aFN, aFF)
aNX.load(['sID'])
sID_aIDs = aNX.createMap('sID', 'id', False)
for sID, aIDs in sID_aIDs.iteritems():
oNX.id = sID
oNX.filteredTargets = aIDs
oNX.save()
def testConsolidation(oFN, oFF, frameLength):
dataNX = Nexus(oFN, oFF)
dataNX.load(['sequence'])
oID_sequence = dataNX.createMap('id', 'sequence')
consolidatedSets = getSimilarORNASets(oID_sequence, frameLength)
#check if all oIDs are in set
allConsolidatedIDs = set()
[allConsolidatedIDs.add(x) for theSet in consolidatedSets for x in theSet]
oIDsSet = set(oID_sequence.keys())
print "DIFFERENCE"
print oIDsSet.symmetric_difference(allConsolidatedIDs)
#check Duplicates
#print out sets to verify that they work
for oIDSet in consolidatedSets:
print
print oIDSet
for oID in oIDSet:
print oID, oID_sequence[oID]
def linkTargetIDs(oFN, oFF, aFN, aFF):
oNX = Nexus(oFN, oFF)
oNX.load(['filteredTargets'])
#just give it some blanks
if os.path.getsize(aFN) == 0:
while oNX.nextID():
oNX.filteredTargets = []
oNX.save()
return
aNX = Nexus(aFN, aFF)
aNX.load(['sID'])
sID_aIDs = aNX.createMap('sID', 'id', False)
for sID, aIDs in sID_aIDs.iteritems():
oNX.id = sID
oNX.filteredTargets = aIDs
oNX.save()
