def mapStartRangeCheckFunction(val, line):
lineStart = int(line.strip().split('\t')[3])
lineEnd = lineStart + len(line.strip().split('\t')[4])
chrom, strand, start, end = cg.tccSplit(val)
start = int(start)
end = int(end)
if cg.simpleOverlap(start, end, lineStart, lineEnd):
return 0
else:
return -1
def mapStartRangeCheckFunction(val, line):
lineStart = int(line.strip().split('\t')[3])
lineEnd = lineStart + len(line.strip().split('\t')[4])
chrom, strand, start, end = cg.tccSplit(val)
start = int(start)
end = int(end)
if cg.simpleOverlap(start, end, lineStart, lineEnd):
return 0
else:
return -1
def subtractTwoRanges(rangeKeep, rangeOther):
'''rangeKeep is a list of ranges, rangeOther is a list of ranges'''
'''Im not sure if rangeOther can overlap for this to work...should union them first...'''
#take care of empty ranges
if len(rangeKeep) == 1 and not rangeKeep[0]:
return list()
if len(rangeOther) == 1 and not rangeOther[0]:
return rangeKeep
coord_type = {}
#annotate keep
for left, right in rangeKeep:
#overlap with each otherPair
if not rangeOther:
coord_type[left] = 1
coord_type[right] = 5
for oLeft, oRight in rangeOther:
#left
if bioLibCG.simpleOverlap(left, left, oLeft, oRight):
#same as coord
if left == oLeft:
if coord_type.get(left, 0) < 2:
coord_type[left] = 2
elif left == oRight:
if coord_type.get(left, 0) < 2:
coord_type[left] = 3
else:
coord_type[left] = 4
else:
if coord_type.get(left, 0) < 1:
coord_type[left] = 1
#right
if bioLibCG.simpleOverlap(right, right, oLeft, oRight):
#same as coord
if right == oLeft:
if coord_type.get(right, 0) < 2:
coord_type[right] = 2
elif right == oRight:
if coord_type.get(right, 0) < 2:
coord_type[right] = 3
else:
coord_type[right] = 4
else:
if coord_type.get(right, 0) < 1:
coord_type[right] = 5
#annotate other
for left, right in rangeOther:
for kLeft, kRight in rangeKeep:
#left
if left == kLeft or left == kRight:
pass
else:
if bioLibCG.simpleOverlap(left, left, kLeft, kRight):
coord_type[left] = 2
#right
if right == kLeft or right == kRight:
pass
else:
if bioLibCG.simpleOverlap(right, right, kLeft, kRight):
coord_type[right] = 3
returnList = []
#get cut coords
sortedKeys = sorted(coord_type.keys())
#print zip(sortedKeys, [coord_type[x] for x in sortedKeys])
for i, key in enumerate(sortedKeys):
if i == 0: continue
a = coord_type[sortedKeys[i - 1]]
b = coord_type[key]
if (a, b) in [(1, 2), (3, 5), (1, 5), (3, 2)]:
#move by one
left = sortedKeys[i - 1]
right = key
if a == 2:
left = left - 1
elif a == 3:
left = left + 1
if b == 2:
right = right - 1
elif b == 3:
right = right + 1
returnList.append((left, right))
return returnList
def subtractTwoRanges(rangeKeep, rangeOther):
'''rangeKeep is a list of ranges, rangeOther is a list of ranges'''
'''Im not sure if rangeOther can overlap for this to work...should union them first...'''
#take care of empty ranges
if len(rangeKeep) == 1 and not rangeKeep[0]:
return list()
if len(rangeOther) == 1 and not rangeOther[0]:
return rangeKeep
coord_type = {}
#annotate keep
for left, right in rangeKeep:
#overlap with each otherPair
if not rangeOther:
coord_type[left] = 1
coord_type[right] = 5
for oLeft, oRight in rangeOther:
#left
if bioLibCG.simpleOverlap(left, left, oLeft, oRight):
#same as coord
if left == oLeft:
if coord_type.get(left, 0) < 2:
coord_type[left] = 2
elif left == oRight:
if coord_type.get(left, 0) < 2:
coord_type[left] = 3
else:
coord_type[left] = 4
else:
if coord_type.get(left, 0) < 1:
coord_type[left] = 1
#right
if bioLibCG.simpleOverlap(right, right, oLeft, oRight):
#same as coord
if right == oLeft:
if coord_type.get(right, 0) < 2:
coord_type[right] = 2
elif right == oRight:
if coord_type.get(right, 0) < 2:
coord_type[right] = 3
else:
coord_type[right] = 4
else:
if coord_type.get(right, 0) < 1:
coord_type[right] = 5
#annotate other
for left, right in rangeOther:
for kLeft, kRight in rangeKeep:
#left
if left == kLeft or left == kRight:
pass
else:
if bioLibCG.simpleOverlap(left, left, kLeft, kRight):
coord_type[left] = 2
#right
if right == kLeft or right == kRight:
pass
else:
if bioLibCG.simpleOverlap(right, right, kLeft, kRight):
coord_type[right] = 3
returnList = []
#get cut coords
sortedKeys = sorted(coord_type.keys())
#print zip(sortedKeys, [coord_type[x] for x in sortedKeys])
for i, key in enumerate(sortedKeys):
if i == 0: continue
a = coord_type[sortedKeys[i - 1]]
b = coord_type[key]
if (a, b) in [(1,2), (3,5), (1,5), (3,2)]:
#move by one
left = sortedKeys[i-1]
right = key
if a == 2:
left = left - 1
elif a == 3:
left = left + 1
if b == 2:
right = right - 1
elif b == 3:
right = right + 1
returnList.append((left, right))
return returnList
def multiLoopCheck(xMerSeq, hairpinSeq, structure):
fixedseq = xMerSeq.upper() #check U to T
symbols = str(structure)
nucleotides = hairpinSeq
#find position of conserved Kmer
matchObject = re.search(fixedseq, nucleotides) #find all matches of 8mer
startingpt = matchObject.start(0) #returns in 0 format the start position of FIRST match
#get the num/positions of each loop
looppositions=[]
loopcounter = 0 #
matches = re.finditer('[(][.]{1,100}[)]', str(symbols))
for match in matches:
loopcounter += 1
looppositions.append(int(match.start()))
looppositions.append(int(match.end()))
#ex. looppositions=[loop1start, loop1end, loop2start, loop2end, loop3start, loop3end]
#multiple loops?
if loopcounter > 1:
multipleloops = True
else:
multipleloops = False
if not multipleloops:
return True
else:
#count number of parenths to starting point...
a=0
countmatch=0
while a < startingpt:
char=str(symbols[a])
if char=='(':
countmatch +=1
if char==')':
countmatch -=1
a +=1
#finding position of 8mer on the - strand (count backwards)
revpos=len(symbols)-1
revmatch=0
while revmatch < countmatch:
char=str(symbols[revpos])
if char==')':
revmatch +=1
if char=='(':
revmatch -=1
revpos -=1
#checking if the 8mer contains loop
forward8mer=symbols[startingpt:startingpt+8]
if '(' in str(forward8mer) and ')' in str(forward8mer):
return False
#checking if there is a loop directly across from 8mer
reverse8mer=symbols[revpos-7:revpos+1]
if '(' in str(reverse8mer) and ')' in str(reverse8mer):
return False
#if 8mer is on (-) strand, switch the coordinates
if startingpt > revpos:
temp=startingpt
startingpt=revpos
revpos=temp
if (revpos - startingpt) > 60:
loopspast8mer=0
x=0
while x<len(looppositions)-1:
loopstart=int(looppositions[x])
loopend=int(looppositions[x+1])
if ((loopstart > startingpt) and (loopend < revpos)) or cg.simpleOverlap(startingpt, revpos, loopstart, loopend):
loopspast8mer +=1
x+=2
else: #redo range to be 60
spread = (60 - (revpos - startingpt))/2
startingpt -= spread
revpos += spread
loopspast8mer=0
x=0
while x<len(looppositions)-1:
loopstart=int(looppositions[x])
loopend=int(looppositions[x+1])
if ((loopstart > startingpt) and (loopend < revpos)) or cg.simpleOverlap(startingpt, revpos, loopstart, loopend):
loopspast8mer +=1
x+=2
if loopspast8mer < 2:
return True
else:
return False
def createGeneSetEditing(fN):
'''Read transcript info into a gene set from our editing file...'''
file = open(fN, 'r')
file.readline() #header
#collect all transcripts
allTranscripts = []
for line in file:
#parse info
ls = line.strip().split('\t')
tID = ls[0]
chrom = ls[1]
strand = ls[2]
if strand == '+':
strand = '1'
else:
strand = '-1'
tStart = int(ls[3])
tEnd = int(ls[4]) - 1 #0 based
cStart = int(ls[5])
cEnd = int(ls[6]) - 1 #0 based
numExons = int(ls[7])
exonStarts = [int(x) for x in ls[8][:-1].split(',')]
exonEnds = [int(x) - 1 for x in ls[9][:-1].split(',')] # 0 based
geneName = ls[10]
cStartStat = ls[11]
cEndStat = ls[12]
tType = ls[13]
gType = ls[15]
#make transcript
t = transcript()
t.id = tID
t.parent = geneName
t.strand = strand
t.chromosome = chrom
t.tcc = '%s:%s:%s:%s' % (chrom, strand, tStart, tEnd)
t.tType = tType
t.gType = gType
#Exons
for i, eStart in enumerate(exonStarts):
t.exonList.append([eStart, exonEnds[i]])
#Introns
for i, eStart in enumerate(exonStarts):
if i == 0: continue
t.intronList.append([exonEnds[i - 1] + 1, eStart - 1])
#Set UTR stats.
if strand == '1':
if cStart == tStart or cStart == tEnd:
t.cds5Stat = 'INC'
else:
t.cds5Stat = 'COMP'
if cEnd == tEnd or cEnd == tStart:
t.cds3Stat = 'INC'
else:
t.cds3Stat = 'COMP'
else:
if cStart == tStart or cStart == tEnd:
t.cds3Stat = 'INC'
else:
t.cds3Stat = 'COMP'
if cEnd == tEnd or cEnd == tStart:
t.cds5Stat = 'INC'
else:
t.cds5Stat = 'COMP'
#only do UTR if complete!!! Will be empty list if not complete
if (cStart != tStart): #update 3' or 5' depending on which strand...
if strand == '1':
utr = t.utr5
else:
utr = t.utr3
for exon in t.exonList:
if bioLibCG.simpleOverlap(exon[0], exon[1], cStart,
cStart + 1):
utr.append([
exon[0], cStart - 1
]) #-1 because utr ends right before coding begins...
break
else:
utr.append(exon)
if (cEnd != tEnd): #again, based on strand
if strand == '1':
utr = t.utr3
else:
utr = t.utr5
for exon in reversed(
t.exonList): #don't permanently reverse the list...
if bioLibCG.simpleOverlap(exon[0], exon[1], cEnd, cEnd + 1):
utr.append([cEnd + 1, exon[1]])
break
else:
utr.append(exon)
allTranscripts.append(t)
#put transcripts into genes
genes = {}
for t in allTranscripts:
if t.parent in genes:
genes[t.parent].append(t)
else:
genes[t.parent] = [t]
allGenes = []
for gID in genes:
g = gene(gID, genes[gID])
allGenes.append(g)
##print 'testing gene creation', allGenes[0].transcripts, allGenes[0].id
#return a gene set
return geneSet(allGenes)
def createGeneSetEditing(fN):
"""Read transcript info into a gene set from our editing file..."""
file = open(fN, "r")
file.readline() # header
# collect all transcripts
allTranscripts = []
for line in file:
# parse info
ls = line.strip().split("\t")
tID = ls[0]
chrom = ls[1]
strand = ls[2]
if strand == "+":
strand = "1"
else:
strand = "-1"
tStart = int(ls[3])
tEnd = int(ls[4]) - 1 # 0 based
cStart = int(ls[5])
cEnd = int(ls[6]) - 1 # 0 based
numExons = int(ls[7])
exonStarts = [int(x) for x in ls[8][:-1].split(",")]
exonEnds = [int(x) - 1 for x in ls[9][:-1].split(",")] # 0 based
geneName = ls[10]
cStartStat = ls[11]
cEndStat = ls[12]
tType = ls[13]
gType = ls[15]
# make transcript
t = transcript()
t.id = tID
t.parent = geneName
t.strand = strand
t.chromosome = chrom
t.tcc = "%s:%s:%s:%s" % (chrom, strand, tStart, tEnd)
t.tType = tType
t.gType = gType
# Exons
for i, eStart in enumerate(exonStarts):
t.exonList.append([eStart, exonEnds[i]])
# Introns
for i, eStart in enumerate(exonStarts):
if i == 0:
continue
t.intronList.append([exonEnds[i - 1] + 1, eStart - 1])
# Set UTR stats.
if strand == "1":
if cStart == tStart or cStart == tEnd:
t.cds5Stat = "INC"
else:
t.cds5Stat = "COMP"
if cEnd == tEnd or cEnd == tStart:
t.cds3Stat = "INC"
else:
t.cds3Stat = "COMP"
else:
if cStart == tStart or cStart == tEnd:
t.cds3Stat = "INC"
else:
t.cds3Stat = "COMP"
if cEnd == tEnd or cEnd == tStart:
t.cds5Stat = "INC"
else:
t.cds5Stat = "COMP"
# only do UTR if complete!!! Will be empty list if not complete
if cStart != tStart: # update 3' or 5' depending on which strand...
if strand == "1":
utr = t.utr5
else:
utr = t.utr3
for exon in t.exonList:
if bioLibCG.simpleOverlap(exon[0], exon[1], cStart, cStart + 1):
utr.append([exon[0], cStart - 1]) # -1 because utr ends right before coding begins...
break
else:
utr.append(exon)
if cEnd != tEnd: # again, based on strand
if strand == "1":
utr = t.utr3
else:
utr = t.utr5
for exon in reversed(t.exonList): # don't permanently reverse the list...
if bioLibCG.simpleOverlap(exon[0], exon[1], cEnd, cEnd + 1):
utr.append([cEnd + 1, exon[1]])
break
else:
utr.append(exon)
allTranscripts.append(t)
# put transcripts into genes
genes = {}
for t in allTranscripts:
if t.parent in genes:
genes[t.parent].append(t)
else:
genes[t.parent] = [t]
allGenes = []
for gID in genes:
g = gene(gID, genes[gID])
allGenes.append(g)
##print 'testing gene creation', allGenes[0].transcripts, allGenes[0].id
# return a gene set
return geneSet(allGenes)
def multiLoopCheck(xMerSeq, hairpinSeq, structure):
fixedseq = xMerSeq.upper() #check U to T
symbols = str(structure)
nucleotides = hairpinSeq
#find position of conserved Kmer
matchObject = re.search(fixedseq, nucleotides) #find all matches of 8mer
startingpt = matchObject.start(
0) #returns in 0 format the start position of FIRST match
#get the num/positions of each loop
looppositions = []
loopcounter = 0 #
matches = re.finditer('[(][.]{1,100}[)]', str(symbols))
for match in matches:
loopcounter += 1
looppositions.append(int(match.start()))
looppositions.append(int(match.end()))
#ex. looppositions=[loop1start, loop1end, loop2start, loop2end, loop3start, loop3end]
#multiple loops?
if loopcounter > 1:
multipleloops = True
else:
multipleloops = False
if not multipleloops:
return True
else:
#count number of parenths to starting point...
a = 0
countmatch = 0
while a < startingpt:
char = str(symbols[a])
if char == '(':
countmatch += 1
if char == ')':
countmatch -= 1
a += 1
#finding position of 8mer on the - strand (count backwards)
revpos = len(symbols) - 1
revmatch = 0
while revmatch < countmatch:
char = str(symbols[revpos])
if char == ')':
revmatch += 1
if char == '(':
revmatch -= 1
revpos -= 1
#checking if the 8mer contains loop
forward8mer = symbols[startingpt:startingpt + 8]
if '(' in str(forward8mer) and ')' in str(forward8mer):
return False
#checking if there is a loop directly across from 8mer
reverse8mer = symbols[revpos - 7:revpos + 1]
if '(' in str(reverse8mer) and ')' in str(reverse8mer):
return False
#if 8mer is on (-) strand, switch the coordinates
if startingpt > revpos:
temp = startingpt
startingpt = revpos
revpos = temp
if (revpos - startingpt) > 60:
loopspast8mer = 0
x = 0
while x < len(looppositions) - 1:
loopstart = int(looppositions[x])
loopend = int(looppositions[x + 1])
if ((loopstart > startingpt) and
(loopend < revpos)) or cg.simpleOverlap(
startingpt, revpos, loopstart, loopend):
loopspast8mer += 1
x += 2
else: #redo range to be 60
spread = (60 - (revpos - startingpt)) / 2
startingpt -= spread
revpos += spread
loopspast8mer = 0
x = 0
while x < len(looppositions) - 1:
loopstart = int(looppositions[x])
loopend = int(looppositions[x + 1])
if ((loopstart > startingpt) and
(loopend < revpos)) or cg.simpleOverlap(
startingpt, revpos, loopstart, loopend):
loopspast8mer += 1
x += 2
if loopspast8mer < 2:
return True
else:
return False
