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Copy pathCurrito3.1_candidates_proportion.py
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Currito3.1_candidates_proportion.py
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import sys, getopt
def main(argv):
Input_File_1 = ""
Input_File_2 = ""
Input_File_3 = ""
Output_File = ""
SeqID_index_1 = 0
SeqID_index_2 = 0
SeqID_index_3 = 0
TargetID = ""
try:
opts, args = getopt.getopt(argv,"i:j:k:o:t:",["Input_File_1=","Input_File_2=","Input_File_3=", "Output_File=", "TargetID="])
except getopt.GetoptError:
print ('candidates_proportion.py -i <Input_File_1> -j <Input_File_2> -k <Input_File_3> -o <Output_File> -t <TargetID>')
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print ('candidates_proportion.py -i <Input_File_1> -j <Input_File_2> -k <Input_File_3> -o <Output_File> -t <TargetID>')
sys.exit()
elif opt in ("-i", "--Input_File_1"):
Input_File_1 = arg
elif opt in ("-j", "--Input_File_2"):
Input_File_2 = arg
elif opt in ("-k", "--Input_File_3"):
Input_File_3 = arg
elif opt in ("-o", "--Output_File"):
Output_File = arg
elif opt in ("-t", "--TargetID"):
TargetID = arg
print ('Input file is :"', Input_File_1)
print ('Input file is : "', Input_File_2)
print ('Input file is : "', Input_File_3)
print ('Output file is :"', Output_File)
PreStatistics_1 = open(Input_File_1)
PreStatistics_2 = open(Input_File_2)
PreStatistics_3 = open(Input_File_3)
OutputFile = open(Output_File, 'w')
BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_1 = set()
BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_2 = set()
BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_3 = set()
tempstring = PreStatistics_1.readline()
tempstring = "temp"
while tempstring:
tempstring = PreStatistics_1.readline()
if tempstring == "":
break
templine = tempstring.splitlines()
x = templine[0]
rowlist = x.split("\t")
SeqID = rowlist[SeqID_index_1]
BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_1.add(SeqID)
Number_of_sequences_hiting_candidate_1 = len(BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_1)
tempstring = PreStatistics_2.readline()
tempstring = "temp"
while tempstring:
tempstring = PreStatistics_2.readline()
if tempstring == "":
break
templine = tempstring.splitlines()
x = templine[0]
rowlist = x.split("\t")
SeqID = rowlist[SeqID_index_2]
BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_2.add(SeqID)
Number_of_sequences_hiting_candidate_2 = len(BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_2)
tempstring = PreStatistics_3.readline()
tempstring = "temp"
while tempstring:
tempstring = PreStatistics_3.readline()
if tempstring == "":
break
templine = tempstring.splitlines()
x = templine[0]
rowlist = x.split("\t")
SeqID = rowlist[SeqID_index_3]
BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_3.add(SeqID)
Number_of_sequences_hiting_candidate_3 = len(BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_3)
INTERSECTION_BETWEEN_1_and_2 = BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_1.intersection(BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_2)
Size_of_Intersection_1_and_2 = len(INTERSECTION_BETWEEN_1_and_2)
INTERSECTION_BETWEEN_2_and_3 = BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_2.intersection(BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_3)
Size_of_Intersection_2_and_3 = len(INTERSECTION_BETWEEN_2_and_3)
INTERSECTION_BETWEEN_1_and_3 = BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_1.intersection(BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_3)
Size_of_Intersection_1_and_3 = len(INTERSECTION_BETWEEN_1_and_3)
UNION_BETWEEN_1_and_2 = BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_1.union(BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_2)
Size_of_union_1_and_2 = len(UNION_BETWEEN_1_and_2)
UNION_BETWEEN_2_and_3 = BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_2.union(BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_3)
Size_of_union_2_and_3 = len(UNION_BETWEEN_2_and_3)
UNION_BETWEEN_1_and_3 = BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_1.union(BLAST_INDEXES_FROM_Genome_8_Pre_statistics_output_3)
Size_of_union_1_and_3 = len(UNION_BETWEEN_1_and_3)
Proportion_in_common_1_and_2 = (Size_of_Intersection_1_and_2/Size_of_union_1_and_2)
Proportion_in_common_2_and_3 = (Size_of_Intersection_2_and_3/Size_of_union_2_and_3)
Proportion_in_common_1_and_3 = (Size_of_Intersection_1_and_3/Size_of_union_1_and_3)
AllHeaders = ("TargetID" + "\t" +
"Size_of_Intersection_1_and_2" + "\t" + "Size_of_Intersection_2_and_3" + "\t" + "Size_of_Intersection_1_and_3" + "\t" +
"Size_of_union_1_and_2" + "\t" + "Size_of_union_2_and_3" + "\t" + "Size_of_union_1_and_3" + "\t" +
"Proportion_in_common_1_and_2" + "\t" + "Proportion_in_common_2_and_3" + "\t" + "Proportion_in_common_1_and_3" + "\n")
OutputFile.write(AllHeaders)
Data = (TargetID + "\t" +
str(Size_of_Intersection_1_and_2) + "\t" + str(Size_of_Intersection_2_and_3) + "\t" + str(Size_of_Intersection_1_and_3) + "\t" +
str(Size_of_union_1_and_2) + "\t" + str(Size_of_union_2_and_3) + "\t" + str(Size_of_union_1_and_3)+ "\t" +
str(Proportion_in_common_1_and_2) + "\t" + str(Proportion_in_common_2_and_3) + "\t" + str(Proportion_in_common_1_and_3) + "\n")
OutputFile.write(Data)
PreStatistics_1.close()
PreStatistics_2.close()
PreStatistics_3.close()
OutputFile.close()
if __name__ == "__main__":
main(sys.argv[1:])