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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 DBHit(object):
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5 """ A DBHit describes an alignment of a feature to a reference/template.
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6 The db variable should be used to describe which database the alignment
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7 in question was done against. For example 'resfinder'
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8
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9 The match_category variable stores one of the integers:
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10 1: Match < 100% identity AND match_length < ref_length
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11 2: Match < 100% identity AND match_length == ref_length
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12 3: Match == 100% identity AND match_length == ref_length
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13 """
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14 def __init__(self, name, identity, match_length, ref_length, start_ref,
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15 end_ref, acc, depth=None, db=None):
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16 self.name = name
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17 self.identity = float(identity)
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18 if(match_length == "NA"):
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19 self.match_length = None
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20 else:
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21 self.match_length = int(match_length)
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22 self.ref_length = int(ref_length)
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23 self.start_ref = int(start_ref)
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24 self.end_ref = int(end_ref)
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25 self.acc = acc
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26 self.depth = depth
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27 self.db = db
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28
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29 if(self.match_length is not None
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30 and self.ref_length != self.match_length):
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31 self.match_category = 1
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32 elif(self.identity < 100.0):
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33 self.match_category = 2
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34 else:
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35 self.match_category = 3
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