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1 import re
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2
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3 mutationMatcher = re.compile("^([nactg])(\d+).([nactg]),?[ ]?([A-Z])?(\d+)?[>]?([A-Z;])?(.*)?")
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4
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5 with open("7_V-REGION-mutation-and-AA-change-table.txt", 'r') as file_handle:
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6 first = True
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7 fr3_index = -1
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8 for i, line in enumerate(file_handle):
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9 line_split = line.split("\t")
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10 if first:
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11 fr3_index = line_split.index("FR3-IMGT")
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12 first = False
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13 continue
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14
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15 if len(line_split) < fr3_index:
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16 continue
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17
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18 fr3_data = line_split[fr3_index]
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19 if len(fr3_data) > 5:
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20 try:
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21 test = [mutationMatcher.match(x).groups() for x in fr3_data.split("|") if x]
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22 except:
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23 print(line_split[1])
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24 print("Something went wrong at line {line} with:".format(line=line_split[0]))
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25 #print([x for x in fr3_data.split("|") if not mutationMatcher.match(x)])
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26 if i % 100000 == 0:
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27 print(i)
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