def scanSequence(seqList, dirName): '''Given list of sequences --> get all reads that have sequence ''' fileNames = cg.recurseDir(dirName, end = '.sequence') if len(fileNames) > 1: print fileNames print 'there is more than one sequence file in this directory' return 1 else: fN = fileNames[0] #for seq in seqList: seq = seqList fIndex = cgIndex.lineIndex(fN, header = False) fIndex.passCheckFunction(cgIndex.mapSequenceCheckFunction) fIndex.binarySearch(seq) #places file pointer at beginning of sequence line #extend and report fIndex.extendUp(seq) finalReads = [] for line in fIndex.file: if fIndex.checkFunction(seq, line) == 0: finalReads.append(line.strip()) else: return finalReads
def scanVectorsFile(fN, tccList):
'''Given tcc list --> scan wig files and return coord:value...
'''
timer = cg.cgTimer()
timer.start()
coordDict = {} # tcc: [list values]
for tcc in tccList:
chrom, strand, tccStart, tccEnd = cg.tccSplit(tcc)
#goto correct line in index
fIndex = cgIndex.lineIndex(fN, header = True) #!!!there actually is a header...have to deal with this...
fIndex.passCheckFunction(cgIndex.wigCheckFunction)
fIndex.binarySearch(tcc) #places file pointer at beginning of tcc as beginning
stop = False
for line in fIndex.file:
#print 'Line:', line.strip()
lBeg = int(cg.ss(line)[1])
lEnd = int(cg.ss(line)[2])
lValue = int(cg.ss(line)[3].split('.')[0])
if tccStart > lBeg:
lBeg = tccStart
if tccEnd < lEnd:
lEnd = tccEnd
stop = True
#print timer.split()
for i in range(lBeg, lEnd):
coordDict[i] = lValue
if stop: break
#fIndex.close()
return coordDict
def scanSequence(seqList, dirName):
'''Given list of sequences --> get all reads that have sequence
'''
fileNames = cg.recurseDir(dirName, end='.sequence')
if len(fileNames) > 1:
print fileNames
print 'there is more than one sequence file in this directory'
return 1
else:
fN = fileNames[0]
#for seq in seqList:
seq = seqList
fIndex = cgIndex.lineIndex(fN, header=False)
fIndex.passCheckFunction(cgIndex.mapSequenceCheckFunction)
fIndex.binarySearch(
seq) #places file pointer at beginning of sequence line
#extend and report
fIndex.extendUp(seq)
finalReads = []
for line in fIndex.file:
if fIndex.checkFunction(seq, line) == 0:
finalReads.append(line.strip())
else:
return finalReads
def scanVectorsFile(fN, tccList):
'''Given tcc list --> scan wig files and return coord:value...
'''
timer = cg.cgTimer()
timer.start()
coordDict = {} # tcc: [list values]
for tcc in tccList:
chrom, strand, tccStart, tccEnd = cg.tccSplit(tcc)
#goto correct line in index
fIndex = cgIndex.lineIndex(fN, header = True) #!!!there actually is a header...have to deal with this...
fIndex.passCheckFunction(cgIndex.wigCheckFunction)
fIndex.binarySearch(tcc) #places file pointer at beginning of tcc as beginning
stop = False
for line in fIndex.file:
#print 'Line:', line.strip()
lBeg = int(cg.ss(line)[1])
lEnd = int(cg.ss(line)[2])
lValue = int(cg.ss(line)[3].split('.')[0])
if tccStart > lBeg:
lBeg = tccStart
if tccEnd < lEnd:
lEnd = tccEnd
stop = True
#print timer.split()
for i in range(lBeg, lEnd):
coordDict[i] = lValue
if stop: break
#fIndex.close()
return coordDict
def svCoord(tccList, config = None):
'''Given tcc list --> scan Organism wig files and coord:value...
'''
#init
config = c.getConfig(config)
org = config.conf['organism']
wigDir = config.conf['wigSetDir']
wigSetName = config.conf['wigSetName']
splitIntoChroms = config.conf['wigChromSplit']
if splitIntoChroms == 'True':
splitIntoChroms = True
else:
splitIntoChroms = False
coordDict = {} # tcc: [list values]
for tcc in tccList:
chrom, strand, tccStart, tccEnd = cg.tccSplit(tcc)
if splitIntoChroms:
fN = wigDir + '/%s.%s.%s.wig' % (wigSetName, chrom, strand)
else:
fN = wigDir + '/Merge.%s.%s.wig' % (org.lower(), strand)
fIndex = cgIndex.lineIndex(fN, header = True)
fIndex.passCheckFunction(cgIndex.wigCheckFunction)
fIndex.binarySearch(tcc) #places file pointer at beginning of tcc as beginning
stop = False
for line in fIndex.file:
#print 'Line:', line.strip()
lBeg = int(cg.ss(line)[1]) + 1
#print 'lBeg', lBeg
lEnd = int(cg.ss(line)[2])
#print 'lEnd', lEnd
#print '--'
lValue = int(cg.ss(line)[3].split('.')[0])
if tccStart > lBeg:
lBeg = tccStart
if tccEnd < lEnd:
lEnd = tccEnd
stop = True
#print timer.split()
for i in range(lBeg, lEnd + 1):
coordDict[i] = lValue
if stop: break
fIndex.close() #close the file and the index after use...
return coordDict
def save(self, outFN=None):
if outFN == None: outFN = self._dataFileName
if self._rangeSpecified:
outFN += '.range.%s.%s' % (self._rangeSpecified[0],
self._rangeSpecified[1])
#skip to start of specified range
if self._rangeSpecified:
fIndex = cgIndex.lineIndex(self._dataFileName)
fIndex.passCheckFunction(cgIndex.primaryIDCheckFunction)
fIndex.binarySearch(self._rangeSpecified[0])
f = fIndex.file
else:
f = open(self._dataFileName, 'r')
#create new file contents
newLines = []
for line in f:
ls = line.strip().split('\t')
id = int(ls[0])
#skip those that weren't selected and in range
''' #I'm not sure I want to only write the ones with conditions...
if self._conditions:
if id not in self._selectedIDs: continue
'''
#stop checking for ids once out of range
if self._rangeSpecified:
if id > self._rangeSpecified[1]: break
#save the rest
for attName in self._selectedAttNames:
newVal = self._attName_casteToFxn[attName](
self._attName_id_value[attName][id])
ls = lineUpdate(ls, newVal,
self._attName_columnPosition[attName])
newLines.append('%s\n' % '\t'.join(ls))
f.close()
#output file
f = open(outFN, 'w')
f.writelines(newLines)
f.close()
#exit signal for parallel processes
if self._rangeSpecified:
f = open(outFN + '.exitSignal', 'w')
f.write('DONE')
f.close()
def save(self, outFN = None):
if outFN == None: outFN = self._dataFileName
if self._rangeSpecified:
outFN += '.range.%s.%s' % (self._rangeSpecified[0], self._rangeSpecified[1])
#skip to start of specified range
if self._rangeSpecified:
fIndex = cgIndex.lineIndex(self._dataFileName)
fIndex.passCheckFunction(cgIndex.primaryIDCheckFunction)
fIndex.binarySearch(self._rangeSpecified[0])
f = fIndex.file
else:
f = open(self._dataFileName, 'r')
#create new file contents
newLines = []
for line in f:
ls = line.strip().split('\t')
id = int(ls[0])
#skip those that weren't selected and in range
''' #I'm not sure I want to only write the ones with conditions...
if self._conditions:
if id not in self._selectedIDs: continue
'''
#stop checking for ids once out of range
if self._rangeSpecified:
if id > self._rangeSpecified[1]: break
#save the rest
for attName in self._selectedAttNames:
newVal = self._attName_casteToFxn[attName](self._attName_id_value[attName][id])
ls = lineUpdate(ls, newVal, self._attName_columnPosition[attName])
newLines.append('%s\n' % '\t'.join(ls))
f.close()
#output file
f = open(outFN, 'w')
f.writelines(newLines)
f.close()
#exit signal for parallel processes
if self._rangeSpecified:
f = open(outFN + '.exitSignal', 'w')
f.write('DONE')
f.close()
def scanVectorsOrganism(tccList, config=None):
'''Given tcc list --> scan Organism wig files and coord:value...
'''
config = c.getConfig(config)
coordDict = {} # tcc: [list values]
for tcc in tccList:
chrom, strand, tccStart, tccEnd = cg.tccSplit(tcc)
#print 'Checking Tcc'
org = config.conf['organism']
mConf = c.getConfig('Main.conf')
wigDir = mConf.conf['wig%s' % org]
fN = wigDir + '/Merge.%s.%s.wig.%s.wig' % (org.lower(), strand, chrom)
#print 'Checking Index'
#goto correct line in index
fIndex = cgIndex.lineIndex(
fN, header=True
) #!!!there actually is a header...have to deal with this...
fIndex.passCheckFunction(cgIndex.wigCheckFunction)
fIndex.binarySearch(
tcc) #places file pointer at beginning of tcc as beginning
stop = False
for line in fIndex.file:
#print 'Line:', line.strip()
lBeg = int(cg.ss(line)[1])
lEnd = int(cg.ss(line)[2])
lValue = int(cg.ss(line)[3].split('.')[0])
if tccStart > lBeg:
lBeg = tccStart
if tccEnd < lEnd:
lEnd = tccEnd
stop = True
#print timer.split()
for i in range(lBeg, lEnd):
coordDict[i] = lValue
if stop: break
return coordDict
def scanVectorsOrganism(tccList, config = None):
'''Given tcc list --> scan Organism wig files and coord:value...
'''
config = c.getConfig(config)
coordDict = {} # tcc: [list values]
for tcc in tccList:
chrom, strand, tccStart, tccEnd = cg.tccSplit(tcc)
#print 'Checking Tcc'
org = config.conf['organism']
mConf = c.getConfig('Main.conf')
wigDir = mConf.conf['wig%s' % org]
fN = wigDir + '/Merge.%s.%s.wig.%s.wig' % (org.lower(),strand,chrom)
#print 'Checking Index'
#goto correct line in index
fIndex = cgIndex.lineIndex(fN, header = True) #!!!there actually is a header...have to deal with this...
fIndex.passCheckFunction(cgIndex.wigCheckFunction)
fIndex.binarySearch(tcc) #places file pointer at beginning of tcc as beginning
stop = False
for line in fIndex.file:
#print 'Line:', line.strip()
lBeg = int(cg.ss(line)[1])
lEnd = int(cg.ss(line)[2])
lValue = int(cg.ss(line)[3].split('.')[0])
if tccStart > lBeg:
lBeg = tccStart
if tccEnd < lEnd:
lEnd = tccEnd
stop = True
#print timer.split()
for i in range(lBeg, lEnd):
coordDict[i] = lValue
if stop: break
return coordDict
def scanCoord(tcc, dirName):
fileNames = cg.recurseDir(dirName, end='.starts')
#get name of file for index
chrom, strand, start, end = cg.tccSplit(tcc)
nameCheck = '%s.%s' % (chrom, strand)
fN = 'None'
for fileName in fileNames:
if nameCheck in fileName: fN = fileName
if fN == 'None':
print 'No Index file for', nameCheck
return 0
fIndex = cgIndex.lineIndex(fN, header=False)
fIndex.passCheckFunction(cgIndex.mapStartCheckFunction)
fIndex.binarySearch(
tcc, skipEnd=True) #places file pointer at beginning of sequence line
#Check if you need to move down one line
checkLine = fIndex.getLineFromByte(fIndex.currentByte)
fIndex.passCheckFunction(
cgIndex.mapStartRangeCheckFunction
) #Note i'm passing now, but it is also used in extending
if fIndex.checkFunction(tcc, checkLine) != 0:
fIndex.file.readline()
fIndex.currentByte = fIndex.file.tell()
#Now extend up until in range, down until in range --> return reads.
fIndex.extendUp(tcc)
finalReads = []
for line in fIndex.file:
if fIndex.checkFunction(tcc, line) == 0:
finalReads.append(line.strip())
else:
return finalReads
def scanCoord(tcc, dirName):
fileNames = cg.recurseDir(dirName, end = '.starts')
#get name of file for index
chrom, strand, start, end = cg.tccSplit(tcc)
nameCheck = '%s.%s' % (chrom, strand)
fN = 'None'
for fileName in fileNames:
if nameCheck in fileName: fN = fileName
if fN == 'None':
print 'No Index file for', nameCheck
return 0
fIndex = cgIndex.lineIndex(fN, header = False)
fIndex.passCheckFunction(cgIndex.mapStartCheckFunction)
fIndex.binarySearch(tcc, skipEnd = True) #places file pointer at beginning of sequence line
#Check if you need to move down one line
checkLine = fIndex.getLineFromByte(fIndex.currentByte)
fIndex.passCheckFunction(cgIndex.mapStartRangeCheckFunction) #Note i'm passing now, but it is also used in extending
if fIndex.checkFunction(tcc, checkLine) != 0:
fIndex.file.readline()
fIndex.currentByte = fIndex.file.tell()
#Now extend up until in range, down until in range --> return reads.
fIndex.extendUp(tcc)
finalReads = []
for line in fIndex.file:
if fIndex.checkFunction(tcc, line) == 0:
finalReads.append(line.strip())
else:
return finalReads
def load(self, attNames, paraInfo = [None, None], idRange = [], conditions = {}):
'''paraInfo is [runNumber, numberOfRuns]. First parallel is checked, and then idRange'''
self._conditions = conditions
#if running a parallel job, split it into the right ids...
if paraInfo != [None, None]:
idRange = getIDRange(paraInfo, self._dataFileName)
#if running parallel or specific range, mark range info
self._selectedAttNames = attNames
if idRange:
self._rangeSpecified = [idRange[0], idRange[-1]]
#get casting and column info
self.loadTranscriptionInfo(attNames)
#initialize master dict
for attName in attNames:
self._attName_id_value[attName] = {}
#get number of slots
f = open(self._dataFileName, 'r')
numSlots = len(f.readline().split('\t'))
f.close()
loadTime = 0.0
stripTime = 0.0
idTime = 0.0
tranTime = 0.0
conditionTime = 0.0
#skip to start of specified range
if self._rangeSpecified:
fIndex = cgIndex.lineIndex(self._dataFileName)
fIndex.passCheckFunction(cgIndex.primaryIDCheckFunction)
fIndex.binarySearch(self._rangeSpecified[0])
f = fIndex.file
else:
f = open(self._dataFileName, 'r')
#transcribe values
for line in f:
ls = line.strip().split('\t')
id = int(ls[0]) #id is always first slot
#only transcribe selected range!
if idRange:
if id > idRange[1]:
break
#transcribe
for attName in attNames:
if self._attName_columnPosition[attName] < numSlots:
if ls[self._attName_columnPosition[attName]] != '.':
self._attName_id_value[attName][id] = self._attName_casteFromFxn[attName](ls[self._attName_columnPosition[attName]])
else:
self._attName_id_value[attName][id] = copy(self._attName_defaultValue[attName])
else:
self._attName_id_value[attName][id] = copy(self._attName_defaultValue[attName])
#do conditions
if conditions:
for attName in conditions:
if attName == 'ID':
if conditions['ID'](id):
self._selectedIDs.add(id)
else:
for aName in attNames:
del self._attName_id_value[aName][id]
else:
if conditions[attName](self._attName_id_value[attName][id]):
self._selectedIDs.add(id)
else:
for aName in attNames:
del self._attName_id_value[aName][id]
f.close()
#bind attribute names to dictionaries
for attName in attNames:
self.bindAttribute(attName)
def load(self, attNames, paraInfo=[None, None], idRange=[], conditions={}):
'''paraInfo is [runNumber, numberOfRuns]. First parallel is checked, and then idRange'''
self._conditions = conditions
#if running a parallel job, split it into the right ids...
if paraInfo != [None, None]:
idRange = getIDRange(paraInfo, self._dataFileName)
#if running parallel or specific range, mark range info
self._selectedAttNames = attNames
if idRange:
self._rangeSpecified = [idRange[0], idRange[-1]]
#get casting and column info
self.loadTranscriptionInfo(attNames)
#initialize master dict
for attName in attNames:
self._attName_id_value[attName] = {}
#get number of slots
f = open(self._dataFileName, 'r')
numSlots = len(f.readline().split('\t'))
f.close()
loadTime = 0.0
stripTime = 0.0
idTime = 0.0
tranTime = 0.0
conditionTime = 0.0
#skip to start of specified range
if self._rangeSpecified:
fIndex = cgIndex.lineIndex(self._dataFileName)
fIndex.passCheckFunction(cgIndex.primaryIDCheckFunction)
fIndex.binarySearch(self._rangeSpecified[0])
f = fIndex.file
else:
f = open(self._dataFileName, 'r')
#transcribe values
for line in f:
ls = line.strip().split('\t')
id = int(ls[0]) #id is always first slot
#only transcribe selected range!
if idRange:
if id > idRange[1]:
break
#transcribe
for attName in attNames:
if self._attName_columnPosition[attName] < numSlots:
if ls[self._attName_columnPosition[attName]] != '.':
self._attName_id_value[attName][
id] = self._attName_casteFromFxn[attName](
ls[self._attName_columnPosition[attName]])
else:
self._attName_id_value[attName][id] = copy(
self._attName_defaultValue[attName])
else:
self._attName_id_value[attName][id] = copy(
self._attName_defaultValue[attName])
#do conditions
if conditions:
for attName in conditions:
if attName == 'ID':
if conditions['ID'](id):
self._selectedIDs.add(id)
else:
for aName in attNames:
del self._attName_id_value[aName][id]
else:
if conditions[attName](
self._attName_id_value[attName][id]):
self._selectedIDs.add(id)
else:
for aName in attNames:
del self._attName_id_value[aName][id]
f.close()
#bind attribute names to dictionaries
for attName in attNames:
self.bindAttribute(attName)
import sys import cgIndex fIndex = cgIndex.lineIndex(sys.argv[1]) fIndex.passCheckFunction(cgIndex.primaryIDCheckFunction) fIndex.binarySearch(4000000) print fIndex.file.readline()
