diff py/cigar.py @ 0:6e75a84e9338 draft

planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/py/cigar.py	Tue May 15 02:39:53 2018 -0400
@@ -0,0 +1,108 @@
+import re
+
+class CigarString:
+	def __init__(self, stringIn=None, listIn=None):
+
+		if stringIn == None and listIn == None:
+			print '\nError: CigarString object not initialized.\n'
+			exit(1)
+
+		self.cigarData = []
+
+		if stringIn != None:
+			self.joinCigar(j_stringIn=stringIn)
+
+		if listIn != None:
+			self.joinCigar(j_listIn=listIn)
+
+
+	def stringToList(self, s):
+
+		cigarDat = []
+		letters = re.split(r"\d+",s)[1:]
+		numbers = [int(n) for n in re.findall(r"\d+",s)]
+		dReserve = 0
+		for i in xrange(len(letters)):
+			if letters[i] == 'D':
+				dReserve = numbers[i]
+			if letters[i] == 'M' or letters[i] == 'I':
+				if dReserve:
+					cigarDat += ['D'*dReserve+letters[i]] + [letters[i]]*(int(numbers[i])-1)
+				else:
+					cigarDat += [letters[i]]*int(numbers[i])
+				dReserve = 0
+		return cigarDat
+
+
+	def listToString(self, l):
+
+		symbols      = ''
+		currentSym   = l[0]
+		currentCount = 1
+		if 'D' in currentSym:
+			currentSym   = currentSym[-1]
+		for k in xrange(1,len(l)):
+			nextSym = l[k]
+			if len(nextSym) == 1 and nextSym == currentSym:
+				currentCount += 1
+			else:
+				symbols += str(currentCount) + currentSym
+				if 'D' in nextSym:
+					symbols += str(nextSym.count('D')) + 'D'
+					currentSym   = nextSym[-1]
+				else:
+					currentSym   = nextSym
+				currentCount = 1
+		symbols += str(currentCount) + currentSym
+		return symbols
+
+	def getList(self):
+
+		return self.cigarData
+
+
+	def getString(self):
+
+		return self.listToString(self.cigarData)
+
+
+	def joinCigar(self, j_stringIn=None, j_listIn=None):
+
+		if j_stringIn == None and j_listIn == None:
+			print '\nError: Invalid join operation in CigarString\n'
+			exit(1)
+
+		if j_stringIn != None:
+			self.cigarData += self.stringToList(j_stringIn)
+
+		if j_listIn != None:
+			self.cigarData += j_listIn
+
+
+	def insertCigarElement(self, pos, i_stringIn=None, i_listIn=None):
+
+		if i_stringIn == None and i_listIn == None:
+			print '\nError: Invalid insertion operation in CigarString\n'
+			exit(1)
+
+		if pos < 0 or pos >= len(self.cigarData):
+			print '\nError: Invalid insertion position in CigarString\n'
+			exit(1)
+
+		if i_stringIn != None:
+			self.cigarData = self.cigarData[:pos] + self.stringToList(i_stringIn) + self.cigarData[pos:]
+
+		if i_listIn != None:
+			self.cigarData = self.cigarData[:pos] + i_listIn + self.cigarData[pos:]
+
+
+if __name__ == '__main__':
+	print 'testing CigarString class...'
+
+	str1 = '50M10D7I23M'
+	str2 = '10I25M'
+	iPos = 20
+	myCigar  = CigarString(stringIn=str1)
+	myCigar.insertCigarElement(iPos,i_stringIn=str2)
+	print str1,'+',str2,'[inserted at position',str(iPos)+']','=',myCigar.getString()
+