Mercurial > repos > rhpvorderman > shm_csr

annotate mutation_column_checker.py @ 3:dced6d52d218 draft

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"planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
author rhpvorderman
date Mon, 15 Nov 2021 11:35:18 +0000
parents 64d74ba01a7c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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1 import re
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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2
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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3 mutationMatcher = re.compile("^([nactg])(\d+).([nactg]),?[ ]?([A-Z])?(\d+)?[>]?([A-Z;])?(.*)?")
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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4
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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5 with open("7_V-REGION-mutation-and-AA-change-table.txt", 'r') as file_handle:
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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6 first = True
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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7 fr3_index = -1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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8 for i, line in enumerate(file_handle):
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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9 line_split = line.split("\t")
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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10 if first:
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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11 fr3_index = line_split.index("FR3-IMGT")
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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12 first = False
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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13 continue
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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14
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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15 if len(line_split) < fr3_index:
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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16 continue
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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17
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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18 fr3_data = line_split[fr3_index]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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19 if len(fr3_data) > 5:
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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20 try:
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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21 test = [mutationMatcher.match(x).groups() for x in fr3_data.split("|") if x]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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22 except:
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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23 print((line_split[1]))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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24 print(("Something went wrong at line {line} with:".format(line=line_split[0])))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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25 #print([x for x in fr3_data.split("|") if not mutationMatcher.match(x)])
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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26 if i % 100000 == 0:
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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27 print(i)