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determine_gene_TN1_or_Nipponbare_20220609.py
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determine_gene_TN1_or_Nipponbare_20220609.py
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import os
Nipponbare_gene1=["Nip_gene_A","Nip_gene_B","Nip_gene_C","Nip_gene_D","Nip_gene_E","Nip_gene_F"]
Nipponbare_gene2=["TNG67_gene1","TNG67_gene2","TNG67_gene2","TNG67_gene2","TNG67_gene2","TNG67_gene1"]
Nipponbare_qcov=[85,90,95,98,99,86]
Nipponbare_qaln=[80,90,95,68,95,82]
TNG67_in_Nipponbare_gene1=[]
TNG67_in_Nipponbare_gene2=[]
TNG67_in_Nipponbare_qcov=[]
TNG67_in_Nipponbare_qaln=[]
TN1_gene1=["TN1_gene_A","TN1_gene_B","TN1_gene_C","TN1_gene_D"]
TN1_gene2=["TNG67_gene1","TNG67_gene2","TNG67_gene2","TNG67_gene2"]
TN1_qcov=[55,67,100,90]
TN1_qaln=[60,45,100,70]
TNG67_in_TN1_gene1=[]
TNG67_in_TN1_gene2=[]
TNG67_in_TN1_qcov=[]
TNG67_in_TN1_qaln=[]
index=0
print Nipponbare_gene2
i=0
while i<len(Nipponbare_gene2):
j=0
while j<len(TN1_gene2):
if Nipponbare_gene2[i]==TN1_gene2[j] and Nipponbare_qcov[i]>TN1_qcov[j] and Nipponbare_qaln[i]>TN1_qaln[j]:
if Nipponbare_qcov[i]>50 and Nipponbare_qaln[i]>50:
if Nipponbare_gene2[i] not in TNG67_in_Nipponbare_gene2:
TNG67_in_Nipponbare_gene1.append(Nipponbare_gene1[i])
TNG67_in_Nipponbare_gene2.append(Nipponbare_gene2[i])
TNG67_in_Nipponbare_qcov.append(Nipponbare_qcov[i])
TNG67_in_Nipponbare_qaln.append(Nipponbare_qaln[i])
print "\n"
print "TNG67_in_Nipponbare_gene1:"
print TNG67_in_Nipponbare_gene1
print "TNG67_in_Nipponbare_gene2:"
print TNG67_in_Nipponbare_gene2
print "TNG67_in_Nipponbare_qcov:"
print TNG67_in_Nipponbare_qcov
print "TNG67_in_Nipponbare_qaln:"
print TNG67_in_Nipponbare_qaln
print ("i:%d" % i)
print ("j:%d" % j)
else:
index=TNG67_in_Nipponbare_gene2.index(Nipponbare_gene2[i])
print ("index:%s" % index)
if Nipponbare_qcov[i]>TNG67_in_Nipponbare_qcov[index] and Nipponbare_qaln[i]>TNG67_in_Nipponbare_qaln[index]:
TNG67_in_Nipponbare_gene1[index]=Nipponbare_gene1[i]
TNG67_in_Nipponbare_gene2[index]=Nipponbare_gene2[i]
TNG67_in_Nipponbare_qcov[index]=Nipponbare_qcov[i]
TNG67_in_Nipponbare_qaln[index]=Nipponbare_qaln[i]
elif Nipponbare_qcov[i]>TNG67_in_Nipponbare_qcov[index] and Nipponbare_qaln[i]<TNG67_in_Nipponbare_qaln[index]:
TNG67_in_Nipponbare_gene1[index]=Nipponbare_gene1[i]
TNG67_in_Nipponbare_gene2[index]=Nipponbare_gene2[i]
TNG67_in_Nipponbare_qcov[index]=Nipponbare_qcov[i]
TNG67_in_Nipponbare_qaln[index]=Nipponbare_qaln[i]
print "\n"
print "TNG67_in_Nipponbare_gene1:"
print TNG67_in_Nipponbare_gene1
print "TNG67_in_Nipponbare_gene2:"
print TNG67_in_Nipponbare_gene2
print "TNG67_in_Nipponbare_qcov:"
print TNG67_in_Nipponbare_qcov
print "TNG67_in_Nipponbare_qaln:"
print TNG67_in_Nipponbare_qaln
print ("i:%d" % i)
print ("j:%d" % j)
else:
print "ewan"
elif Nipponbare_gene2[i]==TN1_gene2[j] and TN1_qcov[j]>Nipponbare_qcov[i] and TN1_qaln[j]>Nipponbare_qaln[i]:
if TN1_qcov[j]>50 and TN1_qaln[j]>50:
if TN1_gene2[j] not in TNG67_in_TN1_gene2:
TNG67_in_TN1_gene1.append(TN1_gene1[j])
TNG67_in_TN1_gene2.append(TN1_gene2[j])
TNG67_in_TN1_qcov.append(TN1_qcov[j])
TNG67_in_TN1_qaln.append(TN1_qaln[j])
print "\n"
print "TNG67_in_TN1_gene1:"
print TNG67_in_TN1_gene1
print "TNG67_in_TN1_gene2:"
print TNG67_in_TN1_gene2
print "TNG67_in_TN1_qcov:"
print TNG67_in_TN1_qcov
print "TNG67_in_TN1_qaln:"
print TNG67_in_TN1_qaln
print ("i:%d" % i)
print ("j:%d" % j)
print "ewan"
else:
index=TNG67_in_TN1_gene2.index(TN1_gene2[j])
print ("index:%s" % index)
if TN1_qcov[j]>TNG67_in_TN1_qcov[index] and Nipponbare_qaln[i]>TNG67_in_TN1_qaln[index]:
TNG67_in_TN1_gene1[index]=TN1_gene1[j]
TNG67_in_TN1_gene2[index]=TN1_gene2[j]
TNG67_in_TN1_qcov[index]=TN1_qcov[j]
TNG67_in_TN1_qaln[index]=TN1_qaln[j]
elif TN1_qcov[j]>TNG67_in_TN1_qcov[index] and TN1_qaln[j]<TNG67_in_TN1_qaln[index]:
TNG67_in_TN1_gene1[index]=TN1_gene1[j]
TNG67_in_TN1_gene2[index]=TN1_gene2[j]
TNG67_in_TN1_qcov[index]=TN1_qcov[j]
TNG67_in_TN1_qaln[index]=TN1_qaln[j]
print "\n"
print "TNG67_in_TN1_gene1:"
print TNG67_in_TN1_gene1
print "TNG67_in_TN1_gene2:"
print TNG67_in_TN1_gene2
print "TNG67_in_TN1_qcov:"
print TNG67_in_TN1_qcov
print "TNG67_in_TN1_qaln:"
print TNG67_in_TN1_qaln
print ("i:%d" % i)
print ("j:%d" % j)
print "ewan"
else:
print "ewan"
j=j+1
i=i+1
"""
i=0
while i<len(TNG67_in_Nipponbare_gene2):
j=0
while i<len(TNG67_in_TN1_gene2):
if TN1_qcov[j]>50 and TN1_qaln[j]>50:
if TN1_gene2[j] not in TNG67_in_TN1_gene2:
TNG67_in_TN1_gene1.append(TN1_gene1[j])
TNG67_in_TN1_gene2.append(TN1_gene2[j])
TNG67_in_TN1_qcov.append(TN1_qcov[j])
TNG67_in_TN1_qaln.append(TN1_qaln[j])
"""
"""
index=0
if TNG67_in_TN1_gene2[j] in TNG67_in_Nipponbare_gene2:
index=TNG67_in_TN1_gene2.index(TNG67_in_TN1_gene2[j])
if (TNG67_in_Nipponbare_qcov[i]>TNG67_in_TN1_qcov[j] and TNG67_in_Nipponbare_qaln[i]>TNG67_in_TN1_qaln[j]) or (TNG67_in_Nipponbare_qcov[i]>TNG67_in_TN1_qcov[j] and TNG67_in_Nipponbare_qaln[i]<=TNG67_in_TN1_qaln[j])
TNG67_in_TN1_gene1.pop(TNG67_in_TN1_gene1[index])
TNG67_in_TN1_gene2.pop(TNG67_in_TN1_gene2[index])
TNG67_in_TN1_qcov.pop(TNG67_in_TN1_qcov[index])
TNG67_in_TN1_qaln.pop(TNG67_in_TN1_qaln[index])
elif:
j=j+1
elif TNG67_in_Nipponbare_gene2[j] in TNG67_in_TN1_gene2:
index=TNG67_in_Nipponbare_gene2.index(TNG67_in_Nipponbare_gene2[j])
if (TNG67_in_TN1_qcov[i]>TNG67_in_Nipponbare_qcov[j] and TNG67_in_TN1_qaln[i]>TNG67_in_Nipponbare_qaln[j]) or (TNG67_in_TN1_qcov[i]>TNG67_in_Nipponbare_qcov[j] and TNG67_in_TN1_qaln[i]<=TNG67_in_Nipponbare_qaln[j])
TNG67_in_Nipponbare_gene1.pop(TNG67_in_Nipponbare_gene1[index])
TNG67_in_Nipponbare_gene2.pop(TNG67_in_Nipponbare_gene2[index])
TNG67_in_Nipponbare_qcov.pop(TNG67_in_Nipponbare_qcov[index])
TNG67_in_Nipponbare_qaln.pop(TNG67_in_Nipponbare_qaln[index])
"""
###
print "\n"
print "TNG67_in_Nipponbare_gene1:"
print TNG67_in_Nipponbare_gene1
print "TNG67_in_Nipponbare_gene2:"
print TNG67_in_Nipponbare_gene2
print "TNG67_in_Nipponbare_qcov:"
print TNG67_in_Nipponbare_qcov
print "TNG67_in_Nipponbare_qaln:"
print TNG67_in_Nipponbare_qaln
print "\n"
print "TNG67_in_TN1_gene1:"
print TNG67_in_TN1_gene1
print "TNG67_in_TN1_gene2:"
print TNG67_in_TN1_gene2
print "TNG67_in_TN1_qcov:"
print TNG67_in_TN1_qcov
print "TNG67_in_TN1_qaln:"
print TNG67_in_TN1_qaln