Mercurial > repos > davidvanzessen > shm_csr

annotate igm_naive_mutations.py @ 95:d63eff357515 draft

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planemo upload commit d96a736dcd6da34137f79861fbc6369716c332f1
author rhpvorderman
date Mon, 27 Mar 2023 13:11:53 +0000
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1 #!/usr/bin/env python3
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2
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3 """
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4 Find naive mutations (< 2% mutated) for IGM genes
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5 """
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6
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7 import argparse
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8 import contextlib
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11 def find_naive_mutations(mutation_file, naive_file, naive_memory_file,
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12 percentage_cutoff=0.02):
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13 # A compound with statement throws a syntax error with the included python
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14 # 3.7.1 in the container, so use an exit stack instead.
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15 with contextlib.ExitStack() as stack:
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16 mutations = stack.enter_context(open(mutation_file, "rt"))
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17 naive = stack.enter_context(open(naive_file, "wt"))
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18 naive_memory = stack.enter_context(open(naive_memory_file, "wt"))
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19 header = next(mutations)
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20 naive.write(header)
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21 naive_memory.write(header)
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22 for line in mutations:
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23 sequence_id, best_match, mutation_no, region_length, _ = \
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24 line.strip('\n').split('\t')
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25 if best_match != "IGM":
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26 continue
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27 mutation_no = int(mutation_no)
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28 region_length = int(region_length)
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29 if (mutation_no / region_length) < percentage_cutoff:
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30 naive.write(line)
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31 else:
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32 naive_memory.write(line)
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33
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34
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35 def main():
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36 parser = argparse.ArgumentParser()
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37 parser.add_argument("mutation_file", help="scatter.txt")
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38 parser.add_argument("naive_file")
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39 parser.add_argument("naive_memory_file")
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40 args = parser.parse_args()
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41 find_naive_mutations(args.mutation_file, args.naive_file,
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42 args.naive_memory_file)
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45 if __name__ == "__main__":
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46 main()