Mercurial > repos > davidvanzessen > shm_csr

annotate mutation_column_checker.py @ 91:f387cc1580c6 draft

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"planemo upload commit 6f5bdb4189fcc9028c90365d8edf8d1d7c1cf690"
author rhpvorderman
date Wed, 02 Feb 2022 10:57:36 +0000
parents 729738462297
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
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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):
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
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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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rhpvorderman
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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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rhpvorderman
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18 fr3_data = line_split[fr3_index]
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
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19 if len(fr3_data) > 5:
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rhpvorderman
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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)