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import os
# Once the first phase of the program was run, we test the results
filin = open('results_with_validation_no_coma.txt', 'r') # used to get the bcc numbers only...
no_mapping=0
seen=0
valid_splice_sites=0
GT_AG_non_confirmed=0
GC_AG_non_confirmed=0
ATATC_A_non_confirmed=0
GTATC_AT_non_confirmed=0
GT_AG_confirmed=0
GC_AG_confirmed=0
ATATC_A_confirmed=0
GTATC_AT_confirmed=0
# returns 1 if the couple site_left, site_right is in {GT*** ***AG}|{GC*** ***AG}|{ATATC ****A}|{GTATC ***AT} --> Direct
# returns 2 if the couple site_left, site_right is in {CT*** ***AC}|{CT*** ***GC}|{T**** GATAT}|{AT*** GATAC} --> Reverse
# else returns 0
def is_splicing_event(site_left, site_right, confirmed):
global GT_AG_non_confirmed
global GC_AG_non_confirmed
global ATATC_A_non_confirmed
global GTATC_AT_non_confirmed
global GT_AG_confirmed
global GC_AG_confirmed
global ATATC_A_confirmed
global GTATC_AT_confirmed
# try Direct:
if site_left.startswith("GT") and site_right.endswith("AG"):
if confirmed==1: GT_AG_confirmed+=1
else: GT_AG_non_confirmed+=1
return 1
if site_left.startswith("GC") and site_right.endswith("AG"):
if confirmed==1: GC_AG_confirmed+=1
else: GC_AG_non_confirmed+=1
return 1
if site_left.startswith("ATATC") and site_right.endswith("A"):
if confirmed==1: ATATC_A_confirmed+=1
else: ATATC_A_non_confirmed+=1
return 1
if site_left.startswith("GTATC") and site_right.endswith("AT"):
if confirmed==1: GTATC_AT_confirmed+=1
else: GTATC_AT_non_confirmed+=1
return 1
# try reverse
if site_left.startswith("CT") and site_right.endswith("AC"):
if confirmed==1: GT_AG_confirmed+=1
else: GT_AG_non_confirmed+=1
return 2
if site_left.startswith("CT") and site_right.endswith("GC"):
if confirmed==1: GC_AG_confirmed+=1
else: GC_AG_non_confirmed+=1
return 2
if site_left.startswith("T") and site_right.endswith("GATAT"):
if confirmed==1: ATATC_A_confirmed+=1
else: ATATC_A_non_confirmed+=1
return 2
if site_left.startswith("AT") and site_right.endswith("GATAC"):
if confirmed==1: GTATC_AT_confirmed+=1
else: GTATC_AT_non_confirmed+=1
return 2
# did not find any
return 0
twice_one_block=0
one_block_valid_confirmed=0
one_block_valid_non_confirmed=0
# test if a line contains a succession of {CT AC}|{CT GC}|{ATATC A}|{GTATC AT} --> Direct
# or a successsion of {GT AG}|{GC AG}|{T GATAT}|{AT GATAC} --> Reverse
def test_line (line, confirmed):
global IR_confirmed_valid
global IR_non_confirmed_valid
global IR_confirmed_invalid
global IR_non_confirmed_invalid
global twice_one_block
global one_block_valid_non_confirmed
global one_block_valid_confirmed
array_line=line.split(" ")
if array_line[0]=="\n":
return False
# print array_line
if array_line[0].endswith("IR") and len(array_line) < 3: # INTRON RETENTION# check if its a direct or reverve transcript (or nothing)
# spurious case: as results/bcc_34093_sequences_25_unsorted.fa.toblat.fasta
#chr7 130154452 130154476 1 2 130154452 24 130154452 24 3
twice_one_block+=1
print("BCC: ",bcc,": Twice one mapped block")
return False
# check if its a direct or reverve transcript (or nothing)
direct=is_splicing_event(array_line[1],array_line[2], confirmed)
if direct==0:
return False
# in this case the positions starts on odd indices as the first is stolen by "IR"
for i in range(3,len(array_line)-1,2):
# if is_splicing_event(array_line[i],array_line[i+1], confirmed) == 0:
if is_splicing_event(array_line[i],array_line[i+1], confirmed) != direct: # either the direction changed or this is not a splice site
return False
return True
confirmed=0
valid_confirmed_LAIR=0
confirmed_LAIR=0
valid_confirmed_SM=0
confirmed_SM=0
valid_confirmed_LA=0
confirmed_LA=0
valid_confirmed_SMIR=0
confirmed_SMIR=0
valid_confirmed_others=0
confirmed_others=0
valid_non_confirmed_LAIR=0
non_confirmed_LAIR=0
valid_non_confirmed_SM=0
non_confirmed_SM=0
valid_non_confirmed_LA=0
non_confirmed_LA=0
valid_non_confirmed_SMIR=0
non_confirmed_SMIR=0
valid_non_confirmed_others=0
non_confirmed_others=0
# one_block_small_confirmed=0
# one_block_small_non_confirmed=0
# others_confirmed=0
# others_non_confirmed=0
nb_confirmed=0
nb_confirmed_valid=0
nb_non_confirmed=0
nb_non_confirmed_valid=0
# nb_with_only_small_among_confirmed=0
# nb_with_only_small_among_non_confirmed=0
# others_valid_confirmed=0
# others_valid_non_confirmed=0
for line in filin.readlines():
if line.startswith("results"): # a new result
seen+=1
bcc=line.split("_")[1]
this_bcc_valid=False
this_bcc_only_SM=True
this_bcc_only_SMIR=True
this_bcc_only_LAIR=True
this_bcc_only_LA=True
if os.path.isfile("bcc_"+bcc):
file=open("bcc_"+bcc)
confirmed=0
nb_non_confirmed+=1
elif os.path.isfile("bcc_"+bcc+"_confirmed"):
file=open("bcc_"+bcc+"_confirmed")
confirmed=1
nb_confirmed+=1
else:
no_mapping+=1
continue
for sites in file.readlines():
if test_line(sites.upper(), confirmed):
if this_bcc_valid==False:
valid_splice_sites+=1
this_bcc_valid=True
if sites.startswith("SM ") == False: this_bcc_only_SM=False
if sites.startswith("LA ") == False: this_bcc_only_LA=False
if sites.startswith("SMIR") == False: this_bcc_only_SMIR=False
if sites.startswith("LAIR") == False: this_bcc_only_LAIR=False
# compute the type of bcc:
if confirmed:
if this_bcc_only_SM: confirmed_SM+=1
elif this_bcc_only_LA: confirmed_LA+=1
elif this_bcc_only_SMIR:confirmed_SMIR+=1
elif this_bcc_only_LAIR:confirmed_LAIR+=1
else:confirmed_others+=1
else:
if this_bcc_only_SM:non_confirmed_SM+=1
elif this_bcc_only_LA: non_confirmed_LA+=1
elif this_bcc_only_SMIR:non_confirmed_SMIR+=1
elif this_bcc_only_LAIR:non_confirmed_LAIR+=1
else: non_confirmed_others+=1
# FOR VINCENT: BCC MULTIPLE BLOCKS, NON VALID:
if this_bcc_valid == False and this_bcc_only_LA:
print("BCC, ",bcc, end=' ')
if confirmed: print(" confirmed ", end=' ')
else: print(" non confirmed ")
file.seek(0)
for sites in file.readlines():
print(sites, end=' ')
# compute the type of bcc that are splice site coherent
if this_bcc_valid:
if confirmed:
nb_confirmed_valid+=1
if this_bcc_only_SM: valid_confirmed_SM+=1
elif this_bcc_only_LA: valid_confirmed_LA+=1
elif this_bcc_only_SMIR: valid_confirmed_SMIR+=1
elif this_bcc_only_LAIR:valid_confirmed_LAIR+=1
else: valid_confirmed_others+=1
else:
nb_non_confirmed_valid+=1
if this_bcc_only_SM:valid_non_confirmed_SM+=1
elif this_bcc_only_LA: valid_non_confirmed_LA+=1
elif this_bcc_only_SMIR:valid_non_confirmed_SMIR+=1
elif this_bcc_only_LAIR:valid_non_confirmed_LAIR+=1
else: valid_non_confirmed_others+=1
file.close()
print("\n\n **************** RESULTS *****************")
print(seen,"BCC seen, among which ",no_mapping," are not mapped on genome and there was also ",twice_one_block,"paths having one unique block mapped both upper and lower")
print(valid_splice_sites," are coherent with respect to splice sites.")
total_confirmed=confirmed_SMIR+ confirmed_LAIR+confirmed_SM+confirmed_LA+confirmed_others
total_valid_confirmed=valid_confirmed_SMIR+ valid_confirmed_LAIR+valid_confirmed_SM+valid_confirmed_LA+valid_confirmed_others
total_non_confirmed=non_confirmed_SMIR+ non_confirmed_LAIR+non_confirmed_SM+non_confirmed_LA+non_confirmed_others
total_valid_non_confirmed=valid_non_confirmed_SMIR+ valid_non_confirmed_LAIR+valid_non_confirmed_SM+valid_non_confirmed_LA+valid_non_confirmed_others
print("\n\n******** too sum up : *********")
print("\t\t\t Total \t Slice site coherent \t percentage splice site coherent ")
print(" FP \t\t\t", no_mapping, "\t0 \t0")
print(" **** Among Confirmed ****")
print(" only [1 bloc/small] \t", confirmed_SMIR, "\t", valid_confirmed_SMIR, "\t NIL")#, "\t %.2f"%(valid_confirmed_SMIR*100/confirmed_SMIR)
print(" only [1 bloc/long] \t", confirmed_LAIR, "\t", valid_confirmed_LAIR, "\t %.2f"%(valid_confirmed_LAIR*100/float(confirmed_LAIR)))
print(" only [n blocs/small] \t", confirmed_SM, "\t", valid_confirmed_SM, "\t %.2f"%(valid_confirmed_SM*100/float(confirmed_SM)))
print(" only [n blocs/long] \t", confirmed_LA, "\t", valid_confirmed_LA, "\t %.2f"%(valid_confirmed_LA*100/float(confirmed_LA)))
print(" all others \t\t", confirmed_others, "\t", valid_confirmed_others, "\t %.2f"%(valid_confirmed_others*100/float(confirmed_others)))
print(" total confirmed \t", total_confirmed, "\t", total_valid_confirmed, "\t %.2f"%(total_valid_confirmed*100/float(total_confirmed)))
#print " validation total confirmed \t", nb_confirmed , "\t", nb_confirmed_valid
print(" **** Among Non Confirmed ****")
print(" only [1 bloc/small] \t", non_confirmed_SMIR, "\t", valid_non_confirmed_SMIR, "\t %.2f"%(valid_non_confirmed_SMIR*100/float(non_confirmed_SMIR)))
print(" only [1 bloc/long] \t", non_confirmed_LAIR, "\t", valid_non_confirmed_LAIR, "\t %.2f"%(valid_non_confirmed_LAIR*100/float(non_confirmed_LAIR)))
print(" only [n blocs/small] \t", non_confirmed_SM, "\t", valid_non_confirmed_SM, "\t %.2f"%(valid_non_confirmed_SM*100/float(non_confirmed_SM)))
print(" only [n blocs/long] \t", non_confirmed_LA, "\t", valid_non_confirmed_LA, "\t %.2f"%(valid_non_confirmed_LA*100/float(non_confirmed_LA)))
print(" all others \t\t", non_confirmed_others, "\t", valid_non_confirmed_others, "\t %.2f"%(valid_non_confirmed_others*100/float(non_confirmed_others)))
print(" total non confirmed \t", total_non_confirmed, "\t", total_valid_non_confirmed, "\t %.2f"%(total_valid_non_confirmed*100/float(total_non_confirmed)))
#print " validation total non confirmed \t", nb_non_confirmed , "\t", nb_non_confirmed_valid
print(" **** Grand total (including FP) ****\t")
print(" total \t\t\t", (total_non_confirmed+total_confirmed+no_mapping), "\t", (total_valid_non_confirmed+total_valid_confirmed+no_mapping), "\t %.2f"%(100*(total_valid_non_confirmed+total_valid_confirmed+no_mapping)/float(total_non_confirmed+total_confirmed+no_mapping)))
print("\n\n******** Splice sites repartition: *********")
print("\t\t{GT*** ***AG}\t{GC*** ***AG}\t{ATATC ****A}\t{GTATC ***AT} \t total")
print("total\t\t ",GT_AG_non_confirmed+GT_AG_confirmed ,"\t", GC_AG_non_confirmed+GC_AG_confirmed ,"\t", ATATC_A_non_confirmed+ATATC_A_confirmed ,"\t", GTATC_AT_non_confirmed+GTATC_AT_confirmed ,"\t", GT_AG_non_confirmed+GT_AG_confirmed + GC_AG_non_confirmed+GC_AG_confirmed + ATATC_A_non_confirmed+ATATC_A_confirmed + GTATC_AT_non_confirmed+GTATC_AT_confirmed)
print("Among confirmed\t\t", GT_AG_confirmed ,"\t", GC_AG_confirmed ,"\t", ATATC_A_confirmed ,"\t",GTATC_AT_confirmed ,"\t", GT_AG_confirmed + GC_AG_confirmed + ATATC_A_confirmed + GTATC_AT_confirmed)
print("Among non confirmed\t", GT_AG_non_confirmed ,"\t", GC_AG_non_confirmed ,"\t", ATATC_A_non_confirmed ,"\t",GTATC_AT_non_confirmed ,"\t", GT_AG_non_confirmed + GC_AG_non_confirmed + ATATC_A_non_confirmed + GTATC_AT_non_confirmed)
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