jasterv/sarscov-hierarchy
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some refactoring

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JasterV 2020-05-21 18:28:36 +02:00
parent 7fe5805b03
commit cf25c31291
1 changed files with 18 additions and 18 deletions
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36
src/python/utils/fasta_map.py
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@ -46,6 +46,23 @@ class FastaMap:
"""
return FastaMap(filter(function, self))
def build_hierarchy(self) -> List[Union[Tuple[Any, ...], list]]:
"""
The function that is in charge of the comparison and the hierarchy of the samples
:param threads_option:
:return:
"""
comparisons = self._compare_all_samples()
table = self._to_dict(comparisons)
tree = HierarchyTree("Hierarchy Sars-Cov-2")
while len(table) > 1:
closest_pair = self.__find_closest_pair(table)
tree.add_relation(closest_pair)
new_relation = self.__build_relation(closest_pair, table)
table = self.__refactor_table(closest_pair, new_relation, table)
tree.show()
def _read(self, file_path: str) -> Dict[str, str]:
"""
Reads a fasta file and returns a dict where the keys are the accessions
@ -60,7 +77,7 @@ class FastaMap:
rna_id, rna = self._get_rna(seq)
data[rna_id] = rna
return data
def _compare_all_samples(self):
# Calculate the number of threads that can be
# used in order to speed up the comparisons
@ -79,23 +96,6 @@ class FastaMap:
f"Comparisons performed in {time.time() - start_time:.3f} seconds!")
return comparisons
def build_hierarchy(self) -> List[Union[Tuple[Any, ...], list]]:
"""
The function that is in charge of the comparison and the hierarchy of the samples
:param threads_option:
:return:
"""
comparisons = self._compare_all_samples()
table = self._to_dict(comparisons)
tree = HierarchyTree("Hierarchy Sars-Cov-2")
while len(table) > 1:
closest_pair = self.__find_closest_pair(table)
tree.add_relation(closest_pair)
new_relation = self.__build_relation(closest_pair, table)
table = self.__refactor_table(closest_pair, new_relation, table)
tree.show()
@staticmethod
def __build_relation(pair, table):
relation = dict()