def isNonContiguous(lst, isSorted=True):
''' Return True iff Beds are not overlapping or contiguous. Modifies list if sorted is not True '''
if not isSorted:
sortByChromStartEnd(lst)
lstLen = len(lst)
if lstLen <= 1:
return True
for i in xrange(1, lstLen):
prev = lst[i - 1]
curr = lst[i]
if curr.chrom < prev.chrom:
errAbort("Bed list is not sorted.")
elif curr.chrom == prev.chrom:
if (curr.chromStart < prev.chromStart) or (
(curr.chromStart == prev.chromStart) and
(curr.chromEnd < prev.chromEnd)):
errAbort("Bed list is not sorted.")
if curr.chromStart <= prev.chromEnd:
print prev.chrom, prev.chromStart, prev.chromEnd
return False
return True
def codonValue(dna):
'''Return the codon value of the dna string or 'X' if it is not a valid DNA string '''
global codonTable, NON_CODON
if len(dna) != 3:
errAbort("codonValue takes a 3-bp dna string as argument: %s" % dna)
return codonTable.get(dna.upper(), NON_CODON)
def getDNA(chrom, start, end, fn, noMask=False):
''' Return the DNA associated with the BED-style position as a single long string '''
maskFlag = ""
if noMask:
maskFlag = " -noMask"
cmd = ("twoBitToFa %s stdout" % fn) + maskFlag + " -seq="
proc = subprocess.Popen(cmd + "%s:%d-%d" % (chrom, start, end),
shell=True,
stdout=subprocess.PIPE)
dna = str(proc.communicate()[0]).strip()
dna = dna.split('\n')
if len(dna) < 2:
errAbort("Must be at least a header line and one line of DNA.")
tmp = "".join(dna[1:])
return "".join(tmp.split())
def getOverlappingRegionDict(bd1, bd2, debug=True):
''' Return a dictionary of overlapping regions within two dictionaries of Bed regions '''
retval = {}
for chrom, bedList1 in bd1.items():
bedList2 = bd2.get(chrom, [])
if bedList2 == []:
continue
if debug:
if not isNonContiguous(bedList1):
errAbort(
"Calculating overlapping regions must have non-contiguous input elements."
)
if not isNonContiguous(bedList2):
errAbort(
"Calculating overlapping regions must have non-contiguous input elements."
)
b1Len = len(bedList1)
b1Idx = 0
b2Len = len(bedList2)
b2Idx = 0
while (b1Idx < b1Len) and (b2Idx < b2Len):
b1Curr = bedList1[b1Idx]
b2Curr = bedList2[b2Idx]
assert b1Curr.chrom == b2Curr.chrom
maxStart = max(b1Curr.chromStart, b2Curr.chromStart)
minEnd = min(b1Curr.chromEnd, b2Curr.chromEnd)
if maxStart < minEnd:
retval[b1Curr.chrom] = retval.get(b1Curr.chrom, []) + [
Bed.Bed("%s\t%d\t%d" % (b1Curr.chrom, maxStart, minEnd))
]
if b1Curr.chromEnd < b2Curr.chromEnd:
b1Idx += 1
elif b1Curr.chromEnd > b2Curr.chromEnd:
b2Idx += 1
else:
b1Idx += 1
b2Idx += 1
return retval
def exonMutationType(wtDNA, mutantDNA):
''' Return the type of mutation. Assumes both wt and mutant are fully within exons '''
global NON_CODON, SILENT_MUT, MISSENSE_MUT, NONSENSE_MUT, GAIN_MUT, FS_INS, INFRAME_INS, FS_DEL, INFRAME_DEL
wtLen = len(wtDNA.replace('-', ''))
mutantLen = len(mutantDNA.replace('-', ''))
if wtLen < mutantLen:
if (mutantLen - wtLen) % 3 != 0:
return FS_INS
else:
return INFRAME_INS
elif wtLen > mutantLen:
if (wtLen - mutantLen) % 3 != 0:
return FS_DEL
else:
return INFRAME_DEL
else:
wtCodon = codonValue(wtDNA)
mutantCodon = codonValue(mutantDNA)
if (wtCodon == NON_CODON) or (mutantCodon == NON_CODON):
errAbort(
"Invalid DNA codons tested for mutation type. Wt: %s, mutant: %s"
% (wtDNA, mutantDNA))
if not isStopCodon(wtDNA):
if isStopCodon(mutantDNA):
return NONSENSE_MUT
else:
if wtCodon == mutantCodon:
return SILENT_MUT
else:
return MISSENSE_MUT
else:
if isStopCodon(mutantDNA):
return SILENT_MUT
else:
return GAIN_MUT