add test for csv_table and compares

data/data_test/sequences.csv

@@ -0,0 +1,35 @@
+Accession,Release_Date,Species,Length,Geo_Location,Host,Isolation_Source,Collection_Date
+MT292569,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29780,Spain,Homo sapiens,,2020-03-09
+MT292570,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29781,Spain,Homo sapiens,,2020-03-10
+MT292571,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29782,Spain,Homo sapiens,,2020-03-09
+MT292572,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29783,Spain,Homo sapiens,,2020-03-10
+MT292574,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29784,Spain,Homo sapiens,oronasopharynx,2020-03-02
+MT292575,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29785,Spain,Homo sapiens,,2020-03-10
+MT292576,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29786,Spain,Homo sapiens,,2020-03-10
+MT292573,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29787,Spain,Homo sapiens,,2020-03-09
+MT292577,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29788,Spain,Homo sapiens,,2020-03-08
+MT292578,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29789,Spain,Homo sapiens,,2020-03-09
+MT292579,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29790,Spain,Homo sapiens,,2020-03-09
+MT292580,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29791,Spain,Homo sapiens,,2020-02-27
+MT292581,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29792,Spain,Homo sapiens,,2020-02-27
+MT292582,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29792,Spain,Homo sapiens,,2020-03-06
+MT256917,2020-03-30T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29792,Spain: Valencia,Homo sapiens,,2020-03-02
+MT256918,2020-03-30T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29792,Spain: Valencia,Homo sapiens,,2020-03-06
+MT281577,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29903,"China: Anhui, Fuyang",Homo sapiens,feces,2020-03-10
+MT291826,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29807,China: Wuhan,Homo sapiens,lung,2019-12-30
+MT291827,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29858,China: Wuhan,Homo sapiens,lung,2019-12-30
+MT291828,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29858,China: Wuhan,Homo sapiens,lung,2019-12-30
+MT291829,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29774,China: Wuhan,Homo sapiens,lung,2019-12-30
+MT291830,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29807,China: Wuhan,Homo sapiens,lung,2019-12-30
+MT291831,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29872,China: Beijing,Homo sapiens,oronasopharynx,2020-01-24
+MT291832,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29828,China: Beijing,Homo sapiens,oronasopharynx,2020-01-25
+MT291833,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29821,China: Beijing,Homo sapiens,oronasopharynx,2020-01-28
+MT291834,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29865,China: Beijing,Homo sapiens,oronasopharynx,2020-01-28
+MT291835,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29834,China: Beijing,Homo sapiens,oronasopharynx,2020-01-27
+MT291836,2020-04-06T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29860,China: Beijing,Homo sapiens,oronasopharynx,2020-01-29
+MT259226,2020-03-30T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29868,"China: Hubei, Wuhan",Homo sapiens,oronasopharynx,2020-01-10
+MT259227,2020-03-30T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29863,"China: Hubei, Wuhan",Homo sapiens,oronasopharynx,2020-01-26
+MT259228,2020-03-30T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29861,"China: Hubei, Wuhan",Homo sapiens,oronasopharynx,2020-01-26
+MT259229,2020-03-30T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29864,"China: Hubei, Wuhan",Homo sapiens,oronasopharynx,2020-01-26
+MT259230,2020-03-30T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29866,"China: Hubei, Wuhan",Homo sapiens,oronasopharynx,2020-01-25
+MT259231,2020-03-30T00:00:00Z,Severe acute respiratory syndrome-related coronavirus,29865,"China: Hubei, Wuhan",Homo sapiens,oronasopharynx,2020-01-25

src/python/utils/csv_table.py

@@ -3,7 +3,9 @@
 """
 from csv import DictReader
 from typing import List, Union, Dict
+
 from prettytable import PrettyTable
+
 import utils.select
 
 
@@ -34,21 +36,22 @@ class CsvTable:
         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()))
         for row in self:
             pretty_table.add_row(row.values())
         return str(pretty_table)
 
-    def values(self, column: int) -> List:
+    def values(self, column: str) -> List[str]:
         """
         :param column:
         :return List of values for this column:
         """
-        list_values = list()
+        return [row[column] for row in self]
-        for row in self:
-            list_values.append(row[column])
-        return list_values
 
     def group_countries_by_median_length(self):
         """

test/test_csv_table.py

@@ -0,0 +1,42 @@
+from unittest import TestCase
+
+from src.python.utils.csv_table import CsvTable
+
+
+class TestCsvTable(TestCase):
+    def test_values(self):
+        path = "../data/data_test/sequences.csv"
+        accession = ["MT292569", "MT292570", "MT292571", "MT292572", "MT292574",
+                     "MT292575", "MT292576", "MT292573", "MT292577", "MT292578",
+                     "MT292579", "MT292580", "MT292581", "MT292582", "MT256917",
+                     "MT256918", "MT281577", "MT291826", "MT291827", "MT291828",
+                     "MT291829", "MT291830", "MT291831", "MT291832", "MT291833",
+                     "MT291834", "MT291835", "MT291836", "MT259226", "MT259227",
+                     "MT259228", "MT259229", "MT259230", "MT259231"]
+        csv_table = CsvTable(path)
+        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"
+        row_china = {"Accession": "MT259228",
+                     "Release_Date": "2020-03-30T00:00:00Z",
+                     "Species": "Severe acute respiratory syndrome-related coronavirus",
+                     "Length": "29861",
+                     "Geo_Location": "China",
+                     "Host": "Homo sapiens",
+                     "Isolation_Source": "oronasopharynx",
+                     "Collection_Date": "2020-01-26"}
+        row_spain = {"Accession": "MT292577",
+                     "Release_Date": "2020-04-06T00:00:00Z",
+                     "Species": "Severe acute respiratory syndrome-related coronavirus",
+                     "Length": "29788",
+                     "Geo_Location": "Spain",
+                     "Host": "Homo sapiens",
+                     "Isolation_Source": "",
+                     "Collection_Date": "2020-03-08"}
+
+        list_cases = [row_spain, row_china]
+        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))

test/test_fasta_map.py

@@ -0,0 +1,29 @@
+from unittest import TestCase
+
+import src.python.libs.seqalign as sq
+
+
+class TestFastaMap(TestCase):
+
+    def test_sequence_align(self):
+        """
+            Use https://n9.cl/2qcq to
+            check the distance.
+        """
+        seq1 = "AATCG"
+        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
+        self.assertEqual(expected, sq.compare_samples(seq1, seq2))
+