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annotate.py
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annotate.py
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import operator
def annotate(initialAlignment):
#print initialAlignment
#x = initialAlignment[0]
print str(initialAlignment)
return initialAlignment
# def annotate():
# blastnResultsFile = open("results")
# blastnResults = blastnResultsFile.read()
# qseqid = 0
# sseqid = 1
# pident = 2
# length = 3
# mismatch = 4
# gapopen = 5
# qstart = 6
# qend = 7
# sstart = 8
# send = 9
# evalue = 10
# bitscore = 11
# result = ""
# for blastnResult in blastnResults.split('\n'):
# print blastnResult.split('\t')
# if (blastnResult != "") and (int(blastnResult.split('\t')[length]) > 10000):
# result = result + blastnResult + '\n'
#
# result = result + '\n'
# print result[:-1]
# return result[:-1]
# pgaResultsFile = open("result")
# pgaResults = pgaResultsFile.read()
# qseqid = 0
# sseqid = 1
# pident = 2
# length = 3
# mismatch = 4
# gapopen = 5
# qstart = 6
# qend = 7
# sstart = 8
# send = 9
# evalue = 10
# bitscore = 11
#
# pgaMacStartIndex = 4
# pgaMacEndIndex = 5
# pgaMic1StartIndex = 6
# pgaMic1EndIndex = 7
# pgaMic2StartIndex = 8
# pgaMic2EndIndex = 9
# pgaMic1DirectionIndex = 10
# pgaMic2DirectionIndex = 11
# #listOfBreakpoints = []
# pgaMacStart = []
# pgaMacEnd = []
# pgaMic1Start = []
# pgaMic1End = []
# pgaMic2Start = []
# pgaMic2End = []
# pgaMic1Direction = []
# pgaMic2Direction = []
#
# for pgaResult in pgaResults.split("\n"):
# splitPgaResult = pgaResult.split(" ")
# if splitPgaResult != ['']:
# pgaMacStart.append(splitPgaResult[pgaMacStartIndex])
# pgaMacEnd.append(splitPgaResult[pgaMacEndIndex])
# pgaMic1Start.append(int(splitPgaResult[pgaMic1StartIndex]))
# pgaMic1End.append(int(splitPgaResult[pgaMic1EndIndex]))
# pgaMic2Start.append(int(splitPgaResult[pgaMic2StartIndex]))
# pgaMic2End.append(int(splitPgaResult[pgaMic2EndIndex]))
# pgaMic1Direction.append(splitPgaResult[pgaMic1DirectionIndex])
# pgaMic2Direction.append(splitPgaResult[pgaMic2DirectionIndex])
# #listOfBreakpoints.append([pgaMic1Start, pgaMic1End, pgaMic2Start, pgaMic2End, pgaMic1Direction, pgaMic2Direction])
# #print splitPgaResult[pgaMic1Start], " ", splitPgaResult[pgaMic1End]
#
# micStartLoci = {}
# micEndLoci = {}
# for i in range(len(pgaMic1Start)):
# micStartLoci[pgaMic1Start[i]] = i
# micStartLoci[pgaMic2Start[i]] = i
# micEndLoci[pgaMic1End[i]] = i
# micEndLoci[pgaMic2End[i]] = i
#
# #print micStartLoci
# #sorted_micStartLoci = sorted(micStartLoci.iteritems(), key=operator.itemgetter(0))
# #print sorted_micStartLoci
#
# lastSeenDirection = ""
# constructingMds = True
# MDSs = []
# IESs = []
# lastSeenStart = 0;
# lastSeenEnd = 0;
#
# #print pgaMic1Direction[0]
# for start in sorted(micStartLoci.keys()):
#
# index = micStartLoci[start]
# print start
# print pgaMic1Direction[index]
# print pgaMic2Direction[index]
# #print lastSeenDirection
#
# if (lastSeenDirection == ""):
# if pgaMic1Start[index] == start:
# if pgaMic1Direction[index] == "L":
# #print 1
# MDSs.append(("?", pgaMic1End[index]))
# else:
# #print 2
# pass
# lastSeenStart = pgaMic1Start[index]
# lastSeenEnd = pgaMic1End[index]
# lastSeenDirection = pgaMic1Direction[index]
# continue
# elif pgaMic2Start[index] == start:
# if pgaMic2Direction[index] == "L":
# #print 3
# MDSs.append(("?", pgaMic2End[index]))
# else:
# #print 4
# pass
# lastSeenStart = pgaMic2Start[index]
# lastSeenEnd = pgaMic2End[index]
# lastSeenDirection = pgaMic2Direction[index]
# continue
# else:
# print "Error"
#
# if (pgaMic1Start[index] == start):
# if lastSeenDirection == "R":
# if pgaMic1Direction[index] == "R":
# #print 1
# MDSs.append((lastSeenStart, "?"))
# lastSeenDirection = "R"
# #continue
# else:
# MDSs.append((lastSeenStart, pgaMic1End[index]))
# #print 2
# lastSeenDirection = "L"
# #continue
# elif lastSeenDirection == "L":
# if pgaMic1Direction[index] == "R":
# #print 3
# IESs.append((lastSeenEnd, pgaMic1Start[index]))
# lastSeenDirection = "R"
# #continue
# else:
# #print 4
# MDSs.append(("?", pgaMic1End[index]))
# IESs.append((lastSeenEnd, "?"))
# lastSeenDirection = "L"
# #continue
# lastSeenStart = pgaMic1Start[index]
# lastSeenEnd = pgaMic1End[index]
# elif (pgaMic2Start[index] == start):
# if lastSeenDirection == "R":
# if pgaMic2Direction[index] == "R":
# MDSs.append((lastSeenStart, "?"))
# IESs.append(("?", pgaMic2Start[index]))
# lastSeenDirection = "R"
# #continue
# else:
# MDSs.append((lastSeenStart, pgaMic2End[index]))
# lastSeenDirection = "L"
# #continue
# elif lastSeenDirection == "L":
# if pgaMic2Direction[index] == "R":
# IESs.append((lastSeenEnd, pgaMic2End[index]))
# lastSeenDirection = "R"
# #continue
# else:
# MDSs.append(("?", pgaMic2End[index]))
# IESs.append((lastSeenEnd, "?"))
# lastSeenDirection = "L"
# #continue
# lastSeenStart = pgaMic2Start[index]
# lastSeenEnd = pgaMic2End[index]
# else:
# print "Error"
# #if (lastSeenDirection == ):
# # print ""
#
# result = ""
# for mds in MDSs:
# #print mds
# mdsStart = mds[0]
# mdsEnd = mds[1]
# if mdsStart != "?":
# index1 = micStartLoci[mdsStart]
# index2 = micEndLoci[mdsEnd]
#
# if(pgaMacStart[index1] < pgaMacEnd[index2]):
# macStart = pgaMacStart[index1]
# macEnd = pgaMacEnd[index2]
# else:
# macStart = pgaMacStart[index2]
# macEnd = pgaMacEnd[index1]
# result = result + "MAC\t" + "MIC\t" + "100\t" + str(mdsEnd - mdsStart) + "\t"+"0\t" + "0\t" + str(macStart) + "\t" + str(macEnd) + "\t" + str(mdsStart) + "\t" + str(mdsEnd) + "\t" + "0\t" + "100" + "\n"
# print result
# return result