some refactors

.gitignore

@@ -2,7 +2,7 @@
 __pycache__/
 *.py[cod]
 *$py.class
-
+.env
 .vscode
 
 # Distribution / packaging

src/python/sarscovhierarchy.py

@@ -5,33 +5,23 @@ from sys import argv
 
 from utils.csv_table import CsvTable
 from utils.fasta_map import FastaMap
-from utils.process_info import ProcessInfo
 
 signal.signal(signal.SIGTSTP, signal.SIG_IGN)
 
 
-def calculate_max_threads(max_length, num_samples):
-    piu = ProcessInfo(num_samples, max_length)
-    return piu.max_threads if piu.max_threads <= 3 else 3
-
-
 def main():
     data_dir = argv[1]
     csv_path = join(data_dir, "sequences.csv")
     fasta_path = join(data_dir, "sequences.fasta")
 
-    print("Reading and processing files...")
+    print("\nReading and processing files...")
     csv_table = CsvTable(csv_path).group_countries_by_median_length()
     ids = csv_table.values('Accession')
     fasta_map = FastaMap(fasta_path).filter(lambda item: item[0] in ids)
     print("Files processing finished!")
 
-    max_length = max(map(int, csv_table.values("Length")))
+    print("\nBuilding hierarchy...")
-    num_samples = len(fasta_map)
+    fasta_map.build_hierarchy()
-    max_threads_to_use = calculate_max_threads(max_length, num_samples)
-
-    print("Building hierarchy...")
-    fasta_map.build_hierarchy(max_threads_to_use)
     print("Done!")
 
 

src/python/utils/csv_table.py

@@ -6,7 +6,7 @@ from typing import List, Union, Dict
 
 from prettytable import PrettyTable
 
-import utils.select
+import utils.select as sel
 
 
 class CsvTable:
@@ -17,31 +17,27 @@ class CsvTable:
 
     def __init__(self, arg: Union[str, List[Dict]]):
         if isinstance(arg, str):
-            self.__table = self.__read(arg)
+            self._table = self.__read(arg)
         elif isinstance(arg, list):
-            self.__table = arg
+            self._table = arg
         else:
             raise TypeError("Invalid Argument")
 
     def __getitem__(self, index):
         try:
-            return self.__table[index]
+            return self._table[index]
         except:
             raise IndexError("Index out of range")
 
     def __len__(self):
-        return len(self.__table)
+        return len(self._table)
 
     def __iter__(self):
-        for row in self.__table:
+        for row in self._table:
             yield row
 
-    @property
-    def table(self):
-        return self.__table
-
     def __str__(self):
-        pretty_table = PrettyTable(list(self.__table[0].keys()))
+        pretty_table = PrettyTable(list(self._table[0].keys()))
         for row in self:
             pretty_table.add_row(row.values())
         return str(pretty_table)
@@ -68,7 +64,7 @@ class CsvTable:
         return CsvTable(filtered_data)
 
     def __get_average_row(self, values: list) -> Union[dict, List[dict]]:
-        median_value = utils.select.quick_select_median(values, index=1)
+        median_value = sel.quick_select_median(values, index=1)
         row = self[median_value[0]]
         geo_location = row['Geo_Location']
         row['Geo_Location'] = geo_location.split(":")[0] \

src/python/utils/fasta_map.py

@@ -7,6 +7,7 @@
 import collections
 import time
 from typing import Tuple, Dict, List, Callable, Union, Any
+from utils.process_info import ProcessInfo
 
 import libs.seqalign as sq
 
@@ -59,7 +60,13 @@ class FastaMap:
                 data[rna_id] = rna
         return data
 
-    def _compare_all_samples(self, threads):
+    def _compare_all_samples(self):
+        # Calculate the number of threads that can be
+        # used in order to speed up the comparisons
+        max_length = max(map(len, self.__data.values()))
+        num_samples = len(self.__data)
+        threads = ProcessInfo(num_samples, max_length).max_threads
+        # Start the comparisons
         print("Performing comparisons...")
         start_time = time.time()
         ids = list(self.__data.keys())
@@ -67,16 +74,17 @@ class FastaMap:
                       for i in range(len(ids) - 1)
                       for j in range(i + 1, len(ids))]
         comparisons = sq.par_compare(to_compare, self.__data, str(threads))
-        print(f"Comparisons performed in {time.time() - start_time:.3f} seconds!")
+        print(
+            f"Comparisons performed in {time.time() - start_time:.3f} seconds!")
         return comparisons
 
-    def build_hierarchy(self, threads) -> List[Union[Tuple[Any, ...], list]]:
+    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(threads)
+        comparisons = self._compare_all_samples()
         table = self._to_dict(comparisons)
         levels = [tuple(table.keys())]
 

src/python/utils/process_info.py

@@ -12,7 +12,7 @@ import psutil
 
 class ProcessInfo:
     """
-        informer and delimiter of system resources.
+        Calculates system resources.
     """
 
     def __init__(self, num_samples, max_length):
@@ -40,7 +40,7 @@ class ProcessInfo:
 
     @property
     def max_threads(self):
-        threads_available = self.num_logic_cores
+        threads_available = self.num_logic_cores if self.num_logic_cores <= 3 else 3
         threads = math.floor(self.mem_available / self.max_mem_per_comparison)
         max_threads = threads if threads <= threads_available else threads_available
-        return max_threads if max_threads >= 1 else 1
+        return max_threads if max_threads >= 1 else 1

test/test_csv_table.py

@@ -1,11 +1,11 @@
 from unittest import TestCase
 
-from src.python.utils.csv_table import CsvTable
+from utils.csv_table import CsvTable
 
 
 class TestCsvTable(TestCase):
     def test_values(self):
-        path = "../data/data_test/sequences.csv"
+        path = "data/data_test/sequences.csv"
         accession = ["MT292569", "MT292570", "MT292571", "MT292572", "MT292574",
                      "MT292575", "MT292576", "MT292573", "MT292577", "MT292578",
                      "MT292579", "MT292580", "MT292581", "MT292582", "MT256917",
@@ -17,7 +17,7 @@ class TestCsvTable(TestCase):
         self.assertTrue(all([x in accession for x in csv_table.values("Accession")]))
 
     def test_group_countries_by_median_length(self):
-        path = "../data/data_test/sequences.csv"
+        path = "data/data_test/sequences.csv"
         row_china = {"Accession": "MT259228",
                      "Release_Date": "2020-03-30T00:00:00Z",
                      "Species": "Severe acute respiratory syndrome-related coronavirus",
@@ -39,4 +39,5 @@ class TestCsvTable(TestCase):
         list_cases_test = CsvTable(list_cases)
         csv_table = CsvTable(path)
         list_csv = csv_table.group_countries_by_median_length()
-        self.assertTrue(all(x in list_csv.table for x in list_cases_test.table))
+        self.assertTrue(all(x in list_csv._table for x in list_cases_test._table))
+

test/test_fasta_map.py

@@ -1,6 +1,6 @@
 from unittest import TestCase
 
-import src.python.libs.seqalign as sq
+import libs.seqalign as sq
 
 
 class TestFastaMap(TestCase):
@@ -14,14 +14,17 @@ class TestFastaMap(TestCase):
         seq2 = "AACG"
         expected = 2
         self.assertEqual(expected, sq.compare_samples(seq1, seq2))
+
         seq1 = "JDSLFA"
         seq2 = "JALFDSA"
         expected = 6
         self.assertEqual(expected, sq.compare_samples(seq1, seq2))
+        
         seq1 = "DSAJKJFHJAKHDIOUZVJCXMVCZIOIUOWUQRIEUWQIPIDSFSDKZXV"
         seq2 = "FKSJAFKJIOTIGHLKJVMCXXZCMVLJASIRUWQOIUTPQWURIIPOQ"
         expected = 46
         self.assertEqual(expected, sq.compare_samples(seq1, seq2))
+        
         seq1 = "KFDSKAJFJPOTIPWQUIMXZMVMZXBVM"
         seq2 = "FKDSPOIQTUITYSKZMV"
         expected = 31