# Regions for Secondary Structure
regions_SS=[81,95,103,104,109,113,118,120,125,127,136,137,140,155,161,172,178,179,186,188,198,200,209,210,218,231,234,236,244,251,259,261,269,279,284,286,292,300,307,310,317,350,353,355,361,367,377,387,393,397,400,401,408,409,413,418,430,436,448,469]
# Regions for Active Site
regions_AS=[82,117,118,119,150,151,152,155,156,176,177,222,223,224,225,227,228,276,277,278,292,293,294,295,367,368,401,402]
# print csv file with the sequences
for i in range(len(alignRecords)):
mut=""
mut3d=""
for j in range(len(wildtype.seq)):
# if a mutation appears then show that
if wildtype.seq[j] != alignRecords[i].seq[j]:
# record the Accession Number, the mutation and country
j3d=domain_data.notation_3D(j)
notation3d = str(wildtype.seq[j])+j3d+str(alignRecords[i].seq[j]) # notation for 3D structure.
# check what ist the region in the sequence by active site.
if not('-' in notation3d):
# to notation issues j+1 to print.
mut = mut+str(wildtype.seq[j])+str(j+1)+str(alignRecords[i].seq[j])
# Active Site
mutRegion_AS[domain_data.whatRegion_AS(j+1)].append(notation3d)
# Secondary structure
mutRegion_2D[domain_data.whatRegion_2D(j+1)].append(notation3d)
mut3d = mut3d+notation3d
mut = mut+csv_token
mut3d = mut3d+csv_token
line=str(alignRecords[i].description)+csv_token+str(alignRecords[i].id)+csv_token+mut
line3d=str(alignRecords[i].description)+csv_token+str(alignRecords[i].id)+csv_token+mut3d
# if a mutation appears then show that
seq_record=db.lookup(accession=alignRecords[i].id)
alignRecords[i].description=seq_record.description
# if a mutation exist and is not an insertion or deletion
if (wildtype.seq[j] != alignRecords[i].seq[j]) and (alignRecords[i].seq[j]!='-'):
# record the Accession Number, the mutation and country
sleep(1)
country=getCountry_fromGBDescription(alignRecords[i].description)
# add the found mutation to the mutation_list
mutations_list.append(Mutation.Mutation(wildtype.id,alignRecords[i].id,wildtype.seq[j],j,alignRecords[i].seq[j],country))
# write data in csv file in 3D NOTATION
mut_act_pos=len(mutations_list)-1
# Define regions for SS and AS
ss_reg=domain_data.whatRegion(mutations_list[mut_act_pos].position_1D,regions_SS)
as_reg=domain_data.whatRegion(mutations_list[mut_act_pos].position_1D,regions_AS)
csvrow=[mutations_list[mut_act_pos].sequence_AN,mutations_list[mut_act_pos].old_aa,domain_data.notation_3D(mutations_list[mut_act_pos].position_1D),mutations_list[mut_act_pos].new_aa,str(mutations_list[mut_act_pos].country),ss_reg,as_reg]
#print csvrow
dataWriter.writerow(csvrow)
# increase progressbar
pbar.update(i+1)
# finish progressbar
pbar.finish()
sys.stdout.write('\n')
print 20*'-'
print 'Creating country files ...'
# put country_list for accession number mutation
country_list={}
country_csv_files={}
for m in mutations_list:
