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https://codeberg.org/JasterV/sarscov-hierarchy.git
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refactorizing
This commit is contained in:
JasterV
parent
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4ecbd661c2
6 changed files with 55 additions and 49 deletions
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@ -1,49 +1,47 @@
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graph "Hierarchy Sars-Cov-2" {
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node [shape=plaintext]
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"Japan,Hong Kong" -- Japan
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"Japan,Hong Kong" -- "Hong Kong"
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"Japan,Hong Kong,Brazil" -- "Japan,Hong Kong"
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"Japan,Hong Kong,Brazil" -- Brazil
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"Japan,Hong Kong,Brazil,South Korea" -- "Japan,Hong Kong,Brazil"
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"Japan,Hong Kong,Brazil,South Korea" -- "South Korea"
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"Japan,Hong Kong,Brazil,South Korea,Pakistan" -- "Japan,Hong Kong,Brazil,South Korea"
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"Japan,Hong Kong,Brazil,South Korea,Pakistan" -- Pakistan
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"Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam" -- "Japan,Hong Kong,Brazil,South Korea,Pakistan"
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"Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam" -- "Viet Nam"
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"Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden" -- "Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam"
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"Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden" -- Sweden
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"Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan" -- "Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden"
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"Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan" -- Taiwan
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"South Africa,Greece" -- "South Africa"
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"South Africa,Greece" -- Greece
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"Malaysia,Thailand" -- Malaysia
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"Malaysia,Thailand" -- Thailand
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"South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan" -- "South Africa,Greece"
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"South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan" -- "Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan"
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"South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland" -- "South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan"
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"South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland" -- Finland
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"Hong Kong,Viet Nam" -- "Hong Kong"
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"Hong Kong,Viet Nam" -- "Viet Nam"
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"South Africa,Greece" -- "South Africa"
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"South Africa,Greece" -- Greece
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"South Africa,Greece,Japan" -- "South Africa,Greece"
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"South Africa,Greece,Japan" -- Japan
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"South Africa,Greece,Japan,Brazil" -- "South Africa,Greece,Japan"
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"South Africa,Greece,Japan,Brazil" -- Brazil
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"Spain,Colombia" -- Spain
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"Spain,Colombia" -- Colombia
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"South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France" -- "South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland"
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"South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France" -- France
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"India,Nepal" -- India
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"India,Nepal" -- Nepal
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"South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey" -- "South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France"
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"South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey" -- Turkey
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"South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel" -- "South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey"
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"South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel" -- Israel
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"South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel,Unknown" -- "South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel"
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"South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel,Unknown" -- Unknown
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"India,Nepal,Peru" -- "India,Nepal"
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"India,Nepal,Peru" -- Peru
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"India,Nepal,Peru,China" -- "India,Nepal,Peru"
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"India,Nepal,Peru,China" -- China
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"India,Nepal,Peru,China,South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel,Unknown" -- "India,Nepal,Peru,China"
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"India,Nepal,Peru,China,South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel,Unknown" -- "South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel,Unknown"
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"India,Nepal,Peru,China,South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel,Unknown,USA" -- "India,Nepal,Peru,China,South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel,Unknown"
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"India,Nepal,Peru,China,South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel,Unknown,USA" -- USA
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"India,Nepal,Peru,China,South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel,Unknown,USA,Spain,Colombia" -- "India,Nepal,Peru,China,South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel,Unknown,USA"
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"India,Nepal,Peru,China,South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel,Unknown,USA,Spain,Colombia" -- "Spain,Colombia"
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"Hong Kong,Viet Nam,Sweden" -- "Hong Kong,Viet Nam"
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"Hong Kong,Viet Nam,Sweden" -- Sweden
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"Hong Kong,Viet Nam,Sweden,South Korea" -- "Hong Kong,Viet Nam,Sweden"
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"Hong Kong,Viet Nam,Sweden,South Korea" -- "South Korea"
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"Israel,Taiwan" -- Israel
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"Israel,Taiwan" -- Taiwan
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil" -- "Hong Kong,Viet Nam,Sweden,South Korea"
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil" -- "South Africa,Greece,Japan,Brazil"
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan" -- "Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil"
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan" -- "Israel,Taiwan"
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru" -- "Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan"
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru" -- Peru
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown" -- "Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru"
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown" -- Unknown
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India" -- "Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown"
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India" -- India
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"China,Nepal" -- China
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"China,Nepal" -- Nepal
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"China,Nepal,Turkey" -- "China,Nepal"
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"China,Nepal,Turkey" -- Turkey
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"China,Nepal,Turkey,Finland" -- "China,Nepal,Turkey"
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"China,Nepal,Turkey,Finland" -- Finland
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA" -- "Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India"
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA" -- USA
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA,Pakistan" -- "Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA"
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA,Pakistan" -- Pakistan
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA,Pakistan,China,Nepal,Turkey,Finland" -- "Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA,Pakistan"
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA,Pakistan,China,Nepal,Turkey,Finland" -- "China,Nepal,Turkey,Finland"
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA,Pakistan,China,Nepal,Turkey,Finland,Spain,Colombia" -- "Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA,Pakistan,China,Nepal,Turkey,Finland"
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA,Pakistan,China,Nepal,Turkey,Finland,Spain,Colombia" -- "Spain,Colombia"
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"Nigeria,Australia" -- Nigeria
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"Nigeria,Australia" -- Australia
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"Malaysia,Thailand,Italy" -- "Malaysia,Thailand"
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@ -52,16 +50,18 @@ graph "Hierarchy Sars-Cov-2" {
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"Malaysia,Thailand,Italy,Iran" -- Iran
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"Malaysia,Thailand,Italy,Iran,Philippines" -- "Malaysia,Thailand,Italy,Iran"
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"Malaysia,Thailand,Italy,Iran,Philippines" -- Philippines
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA,Pakistan,China,Nepal,Turkey,Finland,Spain,Colombia,France" -- "Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA,Pakistan,China,Nepal,Turkey,Finland,Spain,Colombia"
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"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA,Pakistan,China,Nepal,Turkey,Finland,Spain,Colombia,France" -- France
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"Nigeria,Australia,Tunisia" -- "Nigeria,Australia"
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"Nigeria,Australia,Tunisia" -- Tunisia
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"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines" -- "Nigeria,Australia,Tunisia"
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"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines" -- "Malaysia,Thailand,Italy,Iran,Philippines"
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"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq" -- "Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines"
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"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq" -- Iraq
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"India,Nepal,Peru,China,South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel,Unknown,USA,Spain,Colombia,Serbia" -- "India,Nepal,Peru,China,South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel,Unknown,USA,Spain,Colombia"
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"India,Nepal,Peru,China,South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel,Unknown,USA,Spain,Colombia,Serbia" -- Serbia
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"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq,Belgium" -- "Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq"
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"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq,Belgium" -- Belgium
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"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq,Belgium,India,Nepal,Peru,China,South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel,Unknown,USA,Spain,Colombia,Serbia" -- "Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq,Belgium"
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"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq,Belgium,India,Nepal,Peru,China,South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel,Unknown,USA,Spain,Colombia,Serbia" -- "India,Nepal,Peru,China,South Africa,Greece,Japan,Hong Kong,Brazil,South Korea,Pakistan,Viet Nam,Sweden,Taiwan,Finland,France,Turkey,Israel,Unknown,USA,Spain,Colombia,Serbia"
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"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq,Belgium,Serbia" -- "Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq,Belgium"
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"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq,Belgium,Serbia" -- Serbia
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"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq,Belgium,Serbia,Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA,Pakistan,China,Nepal,Turkey,Finland,Spain,Colombia,France" -- "Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq,Belgium,Serbia"
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"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq,Belgium,Serbia,Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA,Pakistan,China,Nepal,Turkey,Finland,Spain,Colombia,France" -- "Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA,Pakistan,China,Nepal,Turkey,Finland,Spain,Colombia,France"
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}
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BIN
src/python/hierarchy.pdf
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BIN
src/python/hierarchy.pdf
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Before Width: | Height: | Size: 292 KiB |
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@ -28,6 +28,7 @@ class CsvTable:
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return self._table[index]
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except IndexError:
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print("Index out of range")
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raise IndexError
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def __len__(self):
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return len(self._table)
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@ -47,13 +48,16 @@ class CsvTable:
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:param column:
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:return List of values for this column:
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"""
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return [row[column] for row in self]
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try:
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return [row[column] for row in self]
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except:
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raise KeyError
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def dict_of(self, key, value):
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try:
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return dict(zip(self.values(key), self.values(value)))
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except:
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print("KeyError")
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raise KeyError
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def group_countries_by_median_length(self):
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"""
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@ -75,7 +75,7 @@ class FastaMap:
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sequences = filter(None, fasta.read().split('>'))
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for seq in sequences:
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rna_id, rna = self._get_rna(seq)
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data[rna_id] = rna if len(rna) < 1000 else rna[:1000]
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data[rna_id] = rna
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return data
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def _compare_all_samples(self):
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@ -2,8 +2,8 @@ from graphviz import Graph
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class HierarchyTree:
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def __init__(self, labels):
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self.__dot = Graph("Hierarchy Sars-Cov-2", format='png',
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def __init__(self, labels=None):
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self.__dot = Graph("Hierarchy Sars-Cov-2",
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node_attr={'shape': 'plaintext'})
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self.__labels = labels
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@ -19,4 +19,6 @@ class HierarchyTree:
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def __transform(self, value):
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value = str(value).translate(
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str.maketrans({'(': '', ')': '', "'": ''}))
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if self.__labels == None:
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return value
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return ','.join(map(lambda x: self.__labels[x.strip()], value.split(',')))
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