coding_dna = Seq(Refseq1, generic_dna)
coding_dna.translate()
str(coding_dna.translate())
seq = ''
for i in range(len(Refseq1)):
seq += Refseq1[i]
typing1 = 'A*23:17'
typing2 = 'A*23:01:01'
HLAtyping = typing1+'_'+typing2
Exons = 'Exon1, Exon2, Exon3, Exon4, Exon5, Exon6, Exon7, Exon8'
IMGTdbIO.checkSynonymMutation(HLAtyping, Exons, db_fp = '../Database/')
##################
## Check Synonymous
#################
out_fp = '../Output/Stats/allLoci_paired_cases/'
Loci_num = 'AllLoci'
for locus in All_loci:
for Allele, Item in AllField_allele_stats[locus].items():
if Item['ARS']
AllField_allele_stats[locus]
TwoField_allele_stats[locus]
AllField_allele_stats[locus][FullField][
'ARS'].append(caseID)
TwoField_allele_stats[locus][TwoField][
'ARS'].append(caseID)
#ExonList = [exn.split('.')[0] for exn in Records[locus][ps]['ARS']]
#ExonList = list(set(ExonList))
#Exons = ''
#for i in range(len(ExonList)):
# if i == 0:
# Exons += ExonList[i]
# else:
# Exons += ', ' + ExonList[i]
if not IMGTdbIO.checkSynonymMutation(
FullField, 'Exon1, Exon2, Exon3',
db_fp): # non-synonymous
AllField_allele_stats[locus][FullField][
'ARS_nonSynonymous'].append(caseID)
TwoField_allele_stats[locus][TwoField][
'ARS_nonSynonymous'].append(caseID)
if len(Records[locus][ps]['non_ARS_exon']) > 0:
AllField_allele_stats[locus][FullField][
'non_ARS_exon'].append(caseID)
TwoField_allele_stats[locus][TwoField][
'non_ARS_exon'].append(caseID)
ExonList = [
exn.split('.')[0] for exn in Records[locus]
[ps]['non_ARS_exon']