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1 #!/usr/bin/env python3
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2
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3
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4 class Phenotype():
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5 """ A Phenotype object describes the antibiotics a feature/gene causes
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6 resistance and susceptibility against.
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7 unique_id: the id is used to locate the specified phenotype.
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8 phenotype: Tuple of antibiotics that gene causes resistance toward.
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9 ab_class: Class of resistance (e.g. Beta-Lactamase).
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10 pub_phenotype: Tuple of published resistance (antibiotics).
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11 pmid: Tuple of PubMed IDs of publications presenting resistance and
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12 susceptibility.
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13 susceptibility: Tuple of antibiotics that the gene is known to be
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14 susceptibil towards.
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15 gene_class: resistance gene class (e.g. class D)
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16 notes: String containing other information on the resistance gene.
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17 species: Species exceptions, where resistance is not observed. NOTE:
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18 This information is not yet used for anything.
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19 """
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20 def __init__(self, unique_id, phenotype, ab_class, sug_phenotype,
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21 pub_phenotype, pmid, susceptibile=(), gene_class=None,
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22 notes="", species=None, res_mechanics=None):
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23 self.unique_id = unique_id
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24 self.phenotype = phenotype
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25 self.ab_class = ab_class
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26
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27 self.sug_phenotype = sug_phenotype
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28 self.pub_phenotype = pub_phenotype
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29 self.pmid = pmid
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30 self.susceptibile = susceptibile
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31 self.gene_class = gene_class
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32 self.notes = notes
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33 self.species = species
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