def output_diff(sam1,sam2,reads,diff_1_2,diff_2_1,diff_1_2_reads,diff_2_1_reads):
print("These mappings are only seen in "+sam1+" and not in "+sam2+" : ")
f1 = open(sam1,'r')
line = common.skipAts(f1)
while line != "":
if line in diff_1_2:
print("READ ID : "+line.split()[0])
print("POS ON RED : "+line.split()[3])
print("CIGAR : "+line.split()[5])
line = f1.readline()
f1.close()
print("Now outputting the relevent reads : ")
common.output_selected_reads(diff_1_2,reads)
f2 = open(sam2,'r')
line = common.skipAts(f2)
print("These mappings are only seen in "+sam2+" and not in "+sam1+" : ")
while line != "":
if line in diff_2_1:
print("READ ID : "+line.split()[0])
print("POS ON RED : "+line.split()[3])
print("CIGAR : "+line.split()[5])
line = f2.readline()
f2.close()
print("Now outputting the relevent reads : ")
common.output_selected_reads(diff_2_1,reads)
def output_intersection(sam1,sam2,reads,inter,inter_reads):
print("These are the common mappings between both files : ")
f = open(sam1,'r')
line = common.skipAts(f)
while line != "":
if line in inter:
print("READ ID : "+line.split()[0])
print("POS ON RED : "+line.split()[3])
print("CIGAR : "+line.split()[5])
line = f.readline()
f.close()
print("Now outputting the relevent reads : ")
common.output_selected_reads(inter_reads,reads)
def extractMultiMappings(IOstream):
IOstream.seek(0)
multimappedReads = set()
occurrences = dict()
#We start by skipping the @ lines
line = common.skipAts(IOstream)
while line!='':
readID = line.split()[0]
if readID in occurrences:
if occurrences[readID]==1:
multimappedReads.add(readID)
occurrences[readID]+=1
else:
occurrences[readID]=1
line = IOstream.readline()
return multimappedReads
parser.add_argument("samFile1", help="One of the SAM files to be studied")
parser.add_argument("samFile2", help="The second SAM file to be studied")
parser.add_argument("outfileDifferences1", help="Name of the file where the mappings in file1 but not in file2 will be outputted")
parser.add_argument("outfileDifferences2", help="Name of the file where the mappings in file2 but not in file1 will be outputted")
parser.add_argument("outfileIntersection", help="Name of the file where the intersection will be outputted")
args = parser.parse_args()
o_diff1, o_diff2 , o_inter = open(args.outfileDifferences1,"w+") , open(args.outfileDifferences2,"w+") , open(args.outfileIntersection,"w+")
o_diff1.write("Mappings found in "+args.samFile1+" and not in "+args.samFile2+"\n")
o_diff2.write("Mapping found in "+args.samFile1+" and not in "+args.samFile2+"\n")
o_inter.write("This file will contain the common mappings between both SAM files "+args.samFile1+" and "+args.samFile2+"\n")
f1 , f2 = open(args.samFile1,'r') , open(args.samFile2, 'r')
line1 , line2 = common.skipAts(f1) , common.skipAts(f2)
while line1 !="" or line2 != "":
read1 , read2 = line1.split()[0] , line2.split()[0]
if read1 < read2:
splitted = line1.split()
o_diff1.write("Mappings with read ID"+splitted[0]+" :\n\n")
while line1!="" and splitted[0] == read1:
o_diff1.write("POS ON REF : "+splitted[3]+"\n")
o_diff1.write("CIGAR : "+splitted[5]+"\n")
line1 = f1.readline()
splitted = line1.split()
o_diff1.write("\n\n")
elif read2 < read1:
splitted = line2.split()
o_diff2.write("Mappings with read ID "+read2+" :\n\n")
help="SAM file obtained with the -k option")
parser.add_argument(
"k",
type=int,
help="The value of k used when producing SAMobtainedByK")
parser.add_argument("SAMobtainedByA",
help="SAM file obtained with the -a option")
args = parser.parse_args()
fk, fa = open(args.SAMobtainedByK, 'r'), open(args.SAMobtainedByA, 'r')
occK, occA = common.count_occurences(
args.SAMobtainedByK), common.count_occurences(args.SAMobtainedByA)
ligne_k, ligne_a = common.skipAts(fk), common.skipAts(fa)
while ligne_k != "" and ligne_a != "":
if ligne_a.split()[0] not in occK:
read_a = ligne_a.split()[0]
print("Alignement(s) produit(s) par -a mais pas par -k")
while ligne_a != "" and ligne_a.split()[0] == read_a:
print(ligne_a)
else:
if occK[ligne_k.split()[0]] < occA[ligne_a.split()[0]]:
read_id_k = ligne_k.split()[0]
lignes_set_k = set()
#We add every line from the file obtained with k to the set
while ligne_k.split()[0] == read_id_k and ligne_k != "":