Mercurial > repos > dcouvin > resfinder
view resfinder/cge/phenotype2genotype/dbhit.py @ 0:a16d245332d6 draft default tip
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author | dcouvin |
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date | Wed, 08 Dec 2021 01:46:07 +0000 |
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#!/usr/bin/env python3 class DBHit(object): """ A DBHit describes an alignment of a feature to a reference/template. The db variable should be used to describe which database the alignment in question was done against. For example 'resfinder' The match_category variable stores one of the integers: 1: Match < 100% identity AND match_length < ref_length 2: Match < 100% identity AND match_length == ref_length 3: Match == 100% identity AND match_length == ref_length """ def __init__(self, name, identity, match_length, ref_length, start_ref, end_ref, acc, depth=None, db=None): self.name = name self.identity = float(identity) if(match_length == "NA"): self.match_length = None else: self.match_length = int(match_length) self.ref_length = int(ref_length) self.start_ref = int(start_ref) self.end_ref = int(end_ref) self.acc = acc self.depth = depth self.db = db if(self.match_length is not None and self.ref_length != self.match_length): self.match_category = 1 elif(self.identity < 100.0): self.match_category = 2 else: self.match_category = 3