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RFCT remove tool attribute from normalizers
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It was never actually used
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luispedro committed Apr 25, 2024
1 parent 3b3e4a9 commit d10424a
Showing 1 changed file with 1 addition and 7 deletions.
8 changes: 1 addition & 7 deletions argnorm/normalizers.py
Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,10 @@

class BaseNormalizer:
"""
Inherit this class and customize subclass methods to implement the normalization of tools.
Inherit this class and customize subclass methods to implement the normalization of new databases/formats.
"""

def __init__(self, database=None, is_hamronized=False) -> None:
self.tool = ''
self.database = database
self.is_hamronized = is_hamronized
self._set_input_gene_col()
Expand Down Expand Up @@ -70,7 +69,6 @@ class ARGSOAPNormalizer(BaseNormalizer):
def __init__(self, database=None, is_hamronized=False) -> None:
database = 'sarg'
super().__init__(database, is_hamronized)
self.tool = 'argsoap'


def _set_input_gene_col(self):
Expand All @@ -90,7 +88,6 @@ class DeepARGNormalizer(BaseNormalizer):
def __init__(self, database=None, is_hamronized=False) -> None:
database = 'deeparg'
super().__init__(database, is_hamronized)
self.tool = 'deeparg'

def _set_input_gene_col(self):
if self.is_hamronized:
Expand All @@ -103,7 +100,6 @@ class ResFinderNormalizer(BaseNormalizer):
def __init__(self, database=None, is_hamronized=False) -> None:
database = 'resfinder'
super().__init__(database, is_hamronized)
self.tool = 'resfinder'

def _set_input_gene_col(self):
if self.is_hamronized:
Expand All @@ -122,7 +118,6 @@ class AMRFinderPlusNormalizer(BaseNormalizer):
def __init__(self, database=None, is_hamronized=False) -> None:
database = 'ncbi'
super().__init__(database, is_hamronized)
self.tool = 'amrfinderplus'

def _set_input_gene_col(self):
if self.is_hamronized:
Expand All @@ -143,7 +138,6 @@ def __init__(self, database=None, is_hamronized=False) -> None:
raise Exception(f'{database} is not a supported database for raw files.')

super().__init__(database, is_hamronized)
self.tool = 'abricate'

def _set_input_gene_col(self):
if self.is_hamronized:
Expand Down

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