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Copy pathCurrito3.1_preparation_for_statistics.py
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Currito3.1_preparation_for_statistics.py
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import sys, getopt
#HERE
import math
def main(argv):
InputBLASTfiltered = ""
Output_preparingBLAST_data_path = ""
Candidate = ""
TargetID = ""
output_preCIRCOS_path = ""
circos_program_path = ""
try:
opts, args = getopt.getopt(argv,"i:o:c:t:w:y:",["InputBLASTfiltered=","Output_preparingBLAST_data_path=", "Candidate=", "TargetID=", "output_preCIRCOS_path=", "circos_program_path="])
except getopt.GetoptError:
print ('statistics.py -i <InputBLASTfiltered> -o <Output_preparingBLAST_data_path> -c <Candidate> -t <TargetID> -w <output_preCIRCOS_path> -y <circos_program_path>')
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print ('statistics.py -i <InputBLASTfiltered> -o <Output_preparingBLAST_data_path> -c <Candidate> -t <TargetID> -w <output_preCIRCOS_path>')
sys.exit()
elif opt in ("-i", "--InputBLASTfiltered"):
InputBLASTfiltered = arg
elif opt in ("-o", "--Output_preparingBLAST_data_path"):
Output_preparingBLAST_data_path = arg
elif opt in ("-c", "--Candidate"):
Candidate = arg
elif opt in ("-t", "--TargetID"):
TargetID = arg
elif opt in ("-w", "--output_preCIRCOS_path"):
output_preCIRCOS_path = arg
elif opt in ("-y", "--circos_program_path"):
circos_program_path = arg
print ('Input file is the InputBLASTfiltered : ', InputBLASTfiltered)
print ('Output_preparingBLAST_data_path : ', Output_preparingBLAST_data_path)
print ('Input for candidate : ', Candidate)
print ('TargetID : ', TargetID)
print ('output_preCIRCOS_path : ', output_preCIRCOS_path)
print ('Circus program PATH for etc = ', circos_program_path)
inputFileToArrange = open(InputBLASTfiltered)
OutputFile = open(Output_preparingBLAST_data_path, 'a')
highlights_sequences = output_preCIRCOS_path + "highlights_sequences.txt"
pident = output_preCIRCOS_path + "pident.txt"
subjectAcc = ""
outputHighLights = open(highlights_sequences, 'a')
outputPident = open(pident, 'a')
karyotype = output_preCIRCOS_path + "karyotype.txt"
outputkaryotype = open(karyotype, 'a')
sLength = ""
ImageLabelNumber = ""
if Candidate == "first_candidate":
ImageLabelNumber = "a)"
elif Candidate == "second_candidate":
ImageLabelNumber = "b)"
elif Candidate == "third_candidate":
ImageLabelNumber = "c)"
highlights = output_preCIRCOS_path + "highlights.txt"
outputHighL = open(highlights,'a')
ticks = output_preCIRCOS_path + "ticks.txt"
outputTicks = open(ticks, 'a')
conf = output_preCIRCOS_path + "conf.txt"
outputConf = open(conf,'a')
VariableForTargetID = ""
NumberOfHeaders = 18
blastIndexColumn = 0
subjectAccColumn = 1
subjectTitleColumn = 2
QseqColumn = 3
SseqColumn = 4
nIdentColumn = 5
nMismatchColumn = 6
PidentColumn = 7
lengthColumn = 8
evalueColumn = 9
bitscoreColumn = 10
qStartColumn = 11
qEndColumn = 12
sStartColumn = 13
sEndColumn = 14
gapOpenColumn = 15
gapsColumn = 16
qLengthColumn = 17
numHitsWithinRefColumn = 18
sStartConverted = 19
sEndConverted = 20
headerTemp = inputFileToArrange.readline()
headerLine = headerTemp.splitlines()
y = headerLine[0]
OutputFile.write(y + '\t' + "sStartConverted" + '\t' + "sEndConverted" + '\t' + "NucleotideSubstitution" + '\t' + "GlobalNucleotideSubstitution" +'\n') #HERE
OutputRowsList = list() #HERE
SumOf_nIdent_I = 0.0 #HERE
SumOf_nMismatch_fv = 0.0 #HERE
SumOf_gapOpen_G = 0.0 #HERE
tempstring = "temp"
while tempstring:
tempstring = inputFileToArrange.readline()
if tempstring == "":
break
templine = tempstring.splitlines()
x = templine[0]
rowlist = x.split('\t')
blastIndex = rowlist[0]
subjectAcc = rowlist[1]
subjectTitle = rowlist[2]
Qseq = rowlist[3]
Sseq = rowlist[4]
nIdent = rowlist[5] #I HERE
nMismatch = rowlist[6] #fv HERE
Pident = rowlist[7]
length = rowlist[8]
evalue = rowlist[9]
bitscore = rowlist[10]
qStart = rowlist[11]
qEnd = rowlist[12]
sStart = rowlist[13]
sEnd = rowlist[14]
gapOpen = rowlist[15] #G HERE
gaps = rowlist[16]
qLength = rowlist[17]
sLength = rowlist[18]
numHitsWithinRef = rowlist[19]
sStartConverted = ""
sEndConverted = ""
SstartNumber = int(sStart)
SendNumber = int(sEnd)
if SstartNumber > SendNumber:
sStartConverted = sEnd
sEndConverted = sStart
else:
sStartConverted = sStart
sEndConverted = sEnd
nIdentFLOAT = float(nIdent)
nMismatchFLOAT = float(nMismatch)
gapOpenFLOAT = float(gapOpen)
SumOf_nIdent_I += nIdentFLOAT
SumOf_nMismatch_fv += nMismatchFLOAT
SumOf_gapOpen_G += gapOpenFLOAT
NucleotideSubstitution = ""
T = (nIdentFLOAT + nMismatchFLOAT + gapOpenFLOAT)
dAB = (-0.75 * math.log(1-0.75 * (nMismatchFLOAT / (nIdentFLOAT+nMismatchFLOAT))) * (1 - (gapOpenFLOAT / T)) + (gapOpenFLOAT / T))
NucleotideSubstitution = str(dAB)
OutputRows = (blastIndex + '\t' + subjectAcc + '\t' + subjectTitle + '\t' + Qseq + '\t' + Sseq + '\t' +
nIdent + '\t' + nMismatch + '\t' + Pident + '\t' + length + '\t' + evalue + '\t' + bitscore + '\t' +
qStart + '\t' + qEnd + '\t' + sStart + '\t' + sEnd + '\t' + gapOpen + '\t' + gaps + '\t' + qLength + '\t' +
sLength + '\t' + numHitsWithinRef + '\t' + sStartConverted + '\t' + sEndConverted + '\t' + NucleotideSubstitution + '\t') #HERE
OutputRowsList.append(OutputRows) #HERE
OutputRowsHighlights = (TargetID + "_vs_" + Candidate + " " + sStartConverted + " " + sEndConverted + '\n')
outputHighLights.write(OutputRowsHighlights)
IntPident = float(Pident)
NewPident = (IntPident / 100 ) - 0.5
NewPident = round(NewPident, 4)
string = str(NewPident)
OutputRowsPident = (TargetID + "_vs_" + Candidate + " " + sStartConverted + " " + sEndConverted + " " + string + '\n')
outputPident.write(OutputRowsPident)
Global_T = (SumOf_nIdent_I + SumOf_nMismatch_fv + SumOf_gapOpen_G)
Global_dAB = (-0.75 * math.log(1-0.75 * (SumOf_nMismatch_fv / (SumOf_nIdent_I+SumOf_nMismatch_fv))) * (1 - (SumOf_gapOpen_G / Global_T)) + (SumOf_gapOpen_G / Global_T))
print("Global_dAB")
print(Global_dAB)
for OutputRow in OutputRowsList:
OutputRow += (str(Global_dAB) + '\n')
OutputFile.write(OutputRow)
OutputRowsKaryotype = ("chr - " + TargetID + "_vs_" + Candidate + " " + ImageLabelNumber + "_" + TargetID + "_vs_" + Candidate + " 0 " + sLength + " " +
"black" + '\n' + "band " + TargetID + "_vs_" + Candidate + " band1 band1 0 " + sLength + " " + "black" + '\n')
outputkaryotype.write(OutputRowsKaryotype)
OutputRowsHighlightsNonSequences = ("<highlights>" + '\n' + "<highlight>" + '\n' + "init_counter = highlight:1" + '\n' +
"file = " + highlights_sequences + '\n' + "fill_color = blue" + '\n' + "r1 = 0.97r" + '\n' +
"r0 = 0.67r" + '\n' + "</highlight>" + '\n' + "</highlights>" + '\n')
outputHighL.write(OutputRowsHighlightsNonSequences)
OutputRowsTicks = ("show_ticks = yes" + '\n' +
"show_tick_labels = yes" + '\n' +
"<ticks>" + '\n' +
"radius = dims(ideogram,radius_outer)" + '\n' +
"multiplier = 1e-6" + '\n' +
"label_offset = 5p" + '\n' +
"thickness = 3p" + '\n' +
"size = 20p" + '\n' +
"label_separation = 10p" + '\n' +
"<tick>" + '\n' +
"spacing = 0.5u" + '\n' +
"color = red" + '\n' +
"thickness = 2p" + '\n' +
"show_label = yes" + '\n' +
"label_size = 30p" + '\n' +
"label_font = bold" + '\n' +
"label_offset = 0p" + '\n' +
"format = %.1f" + '\n' +
"</tick>" + '\n' +
"<tick>" + '\n' +
"spacing = 1u" + '\n' +
"color = red" + '\n' +
"thickness = 2p" + '\n' +
"show_label = yes" + '\n' +
"label_size = 30p" + '\n' +
"label_font = bold" + '\n' +
"label_offset = 0p" + '\n' +
"format = %d" + '\n' +
"</tick>" + '\n' +
"<tick>" + '\n' +
"spacing = 0.1u" + '\n' +
"color = dgrey" + '\n' +
"thickness = 2p" + '\n' +
"show_label = yes" + '\n' +
"label_size = 20p" + '\n' +
"label_font = bold" + '\n' +
"label_offset = 0p" + '\n' +
"format = %.1f" + '\n' +
"</tick>" + '\n' +
"</ticks>" + '\n')
outputTicks.write(OutputRowsTicks)
OutputRowsConf = ("karyotype = " + karyotype + '\n' + "chromosomes_units = 1000000" + '\n' + "chromosomes_display_defaults = yes" + '\n' +
"<<include " + highlights + ">>" + '\n' +
"<ideogram>" + '\n' +
"<spacing>" + '\n' + "default = 0u" + '\n' + "break = 0u" + '\n' +
"</spacing>" + '\n' + "thickness = 20p" + '\n' +
"radius = 0.70r" + '\n' + "show_label = yes" + '\n' + "label_font = bold" + '\n' + "label_with_tag = yes" + '\n' + "label_radius = dims(ideogram,radius) + 0.28r" + '\n' +
"label_size = 30" + '\n' + "label_parallel = yes" + '\n' + "stroke_thickness = 3" + '\n' + "stroke_color = gray" + '\n' + "fill = yes" + '\n' + "show_bands = yes" + '\n' +
"fill_bands = yes" + '\n' +
"</ideogram>" + '\n' +
"<<include " + ticks + ">>" + '\n' +
"<plots>" + '\n' +
"<plot>" + '\n' + "type = histogram" + '\n' +
"file = " + pident + '\n' +
"r1 = 0.62r" + '\n' + "r0 = 0.27r" + '\n' + "thickness = 3" + '\n' + "max = 1.0" + '\n' + "min = 0" + '\n' + "extend_bin = no" + '\n' + "color = green" + '\n' + "orientation = in" + '\n' +
"<rules>" + '\n' + "<rule>" + '\n' + "condition = var(value) < 0.45" + '\n' + "color = red" + '\n' + "</rule>" + '\n' + "</rules>" + '\n' +
"</plot>" + '\n' + "</plots>" + '\n' +
"<image>" + '\n' + "#TO DO - CHANGE THESE PATHS BECAUSE THEY ARE HARCODED" + '\n' +
"<<include etc/image.conf>>" + '\n' + "radius* = 750p" + '\n' + "</image>" + '\n' +
"<<include etc/colors_fonts_patterns.conf>>" + '\n' +
"<<include etc/housekeeping.conf>>" + '\n')
outputConf.write(OutputRowsConf)
inputFileToArrange.close()
OutputFile.close()
outputHighLights.close()
outputPident.close()
outputkaryotype.close()
outputHighL.close()
outputConf.close()
outputTicks.close()
if __name__ == "__main__":
main(sys.argv[1:])