def SuperSiteAnalyzer(SiteFile1, SiteFile2, SiteFile3, RepeatFile1,
RepeatFile2, RepeatFile3, RepeatFile4):
#==============Constructing Lists of Site data ==========================================
site1 = siteParser(SiteFile1)
site2 = siteParser(SiteFile2)
site3 = siteParser(SiteFile3)
list = [RepeatFile1, RepeatFile2, RepeatFile3, RepeatFile4]
for repeat in list:
repeat = ParserS(repeat, repeat, False) # Constructing Lists of Repeat data
siteAnalyzer(repeat, site1, SiteFile1)
siteAnalyzer(repeat, site2, SiteFile2)
siteAnalyzer(repeat, site3, SiteFile3)
del repeat
def SuperSiteAnalyzer(SiteFile, RepeatFile1, RepeatFile2, RepeatFile3, RepeatFile4,
RepeatFile5, RepeatFile6, RepeatFile7, RepeatFile8, RepeatFile9,
RepeatFile10 , RepeatFile11, RepeatFile12, RepeatFile13, RepeatFile14,
RepeatFile15, RepeatFile16, RepeatFile17, RepeatFile18, RepeatFile19):
#==============Constructing Lists of Site data ==========================================
sites = siteParser(SiteFile)
list = [RepeatFile1, RepeatFile2, RepeatFile3, RepeatFile4, RepeatFile5, RepeatFile6, RepeatFile7, RepeatFile8, RepeatFile9, RepeatFile10 , RepeatFile11, RepeatFile12, RepeatFile13, RepeatFile14,
RepeatFile15, RepeatFile16, RepeatFile17, RepeatFile18, RepeatFile19]
for repeat in list:
repeats = ParserS(repeat, repeat, False) # Constructing Lists of Repeat data
print ' now processing the ', repeat, 'for CpG sites'
siteAnalyzer(repeats, sites, 'CpG')
del repeats
def SuperSiteAnalyzer(SiteFile, RepeatFile1, RepeatFile2, RepeatFile3,
RepeatFile4, RepeatFile5, RepeatFile6, RepeatFile7,
RepeatFile8, RepeatFile9, RepeatFile10, RepeatFile11,
RepeatFile12, RepeatFile13, RepeatFile14, RepeatFile15,
RepeatFile16, RepeatFile17, RepeatFile18, RepeatFile19):
#==============Constructing Lists of Site data ==========================================
sites = siteParser(SiteFile)
list = [
RepeatFile1, RepeatFile2, RepeatFile3, RepeatFile4, RepeatFile5,
RepeatFile6, RepeatFile7, RepeatFile8, RepeatFile9, RepeatFile10,
RepeatFile11, RepeatFile12, RepeatFile13, RepeatFile14, RepeatFile15,
RepeatFile16, RepeatFile17, RepeatFile18, RepeatFile19
]
for repeat in list:
repeats = ParserS(repeat, repeat,
False) # Constructing Lists of Repeat data
print ' now processing the ', repeat, 'for CpG sites'
siteAnalyzer(repeats, sites, 'CpG')
del repeats
def siteAnalyzer(RepeatMaskerData, siteData, suffix):
# ============ Picking the Repeat Element name from the RepeatMaskerData file ==========
data = open(RepeatMaskerData, 'rU')
string = data.readline()
list = string.split()
print 'Analyzing reads for the following repeat element :', list[9]
repFamily = list[9]
data.close()
#==============Constructing Lists of RepeatMasker data and Read data =====================
repeats = ParserS(RepeatMaskerData, repFamily, False) #False is to specify that we are not saving the parser output to any file.
#only the per base scores will be saved.
sites = siteParser(siteData)
#================= getting consensus length of the repeat element =====================
# one line of repeats looks like this :
# 318 23.0 3.8 0.0 chr1 15265 15355 (249235266) C MIR3 SINE/MIR (119) 143 49 5
if repeats[0][0][8] == '+':
length = repeats[0][0][12] + repeats[0][0][13]
else:
length = repeats[0][0][11]+ repeats[0][0][12]
consensus = [0]*(length*2) # consensus length is kept twice of the original length as some repeat elements extend beyond the range of consensus
x = 0
#========================================================================================
#=========== now doing binary search=====================================================
# this calls binaryS() method, which is a recursive implementation of binary search. The method is present in Overlap.py
i = 0
while i < 24:
for read in sites[i]:
max = len(repeats[i]) - 1
min = 0
mid = binaryS(repeats[i], read, min, max)
if mid == -2:
x +=1
else:
readS = read[1]
readE = read[2]
TPS = repeats[i][mid][5]
TPE = repeats[i][mid][6]
if repeats[i][mid][8] == '+':
start = repeats[i][mid][11] - 1
end = repeats[i][mid][12]
else:
start = repeats[i][mid][13] - 1
end = repeats[i][mid][12]
overlap(consensus, start, end, readS, readE, TPS, TPE)
#========= end of for loop =============
i = i+1
Newlength = length + (length/20) # clipping back consensus to its original length
Newconsensus = consensus[:Newlength]
print 'number of unmatched sites is :', x
printScore(Newconsensus, repFamily, suffix) #this method prints the consensus to an output file
graph(Newconsensus, repFamily, True) #this plots the data and saves the figure
