jasterv/sarscov-hierarchy
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JasterV 2020-05-22 02:22:32 +02:00
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output/hierarchy_med.pdf Normal file
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src/python/hierarchy.pdf → output/hierarchy_min.pdf
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src/python/hierarchy
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@ -1,67 +0,0 @@
graph "Hierarchy Sars-Cov-2" {
node [shape=plaintext]
"Malaysia,Thailand" -- Malaysia
"Malaysia,Thailand" -- Thailand
"Hong Kong,Viet Nam" -- "Hong Kong"
"Hong Kong,Viet Nam" -- "Viet Nam"
"South Africa,Greece" -- "South Africa"
"South Africa,Greece" -- Greece
"South Africa,Greece,Japan" -- "South Africa,Greece"
"South Africa,Greece,Japan" -- Japan
"South Africa,Greece,Japan,Brazil" -- "South Africa,Greece,Japan"
"South Africa,Greece,Japan,Brazil" -- Brazil
"Spain,Colombia" -- Spain
"Spain,Colombia" -- Colombia
"Hong Kong,Viet Nam,Sweden" -- "Hong Kong,Viet Nam"
"Hong Kong,Viet Nam,Sweden" -- Sweden
"Hong Kong,Viet Nam,Sweden,South Korea" -- "Hong Kong,Viet Nam,Sweden"
"Hong Kong,Viet Nam,Sweden,South Korea" -- "South Korea"
"Israel,Taiwan" -- Israel
"Israel,Taiwan" -- Taiwan
"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil" -- "Hong Kong,Viet Nam,Sweden,South Korea"
"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil" -- "South Africa,Greece,Japan,Brazil"
"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"
"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan" -- "Israel,Taiwan"
"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"
"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru" -- Peru
"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"
"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown" -- Unknown
"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"
"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India" -- India
"China,Nepal" -- China
"China,Nepal" -- Nepal
"China,Nepal,Turkey" -- "China,Nepal"
"China,Nepal,Turkey" -- Turkey
"China,Nepal,Turkey,Finland" -- "China,Nepal,Turkey"
"China,Nepal,Turkey,Finland" -- Finland
"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"
"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA" -- USA
"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"
"Hong Kong,Viet Nam,Sweden,South Korea,South Africa,Greece,Japan,Brazil,Israel,Taiwan,Peru,Unknown,India,USA,Pakistan" -- Pakistan
"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"
"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"
"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"
"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"
"Nigeria,Australia" -- Nigeria
"Nigeria,Australia" -- Australia
"Malaysia,Thailand,Italy" -- "Malaysia,Thailand"
"Malaysia,Thailand,Italy" -- Italy
"Malaysia,Thailand,Italy,Iran" -- "Malaysia,Thailand,Italy"
"Malaysia,Thailand,Italy,Iran" -- Iran
"Malaysia,Thailand,Italy,Iran,Philippines" -- "Malaysia,Thailand,Italy,Iran"
"Malaysia,Thailand,Italy,Iran,Philippines" -- Philippines
"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"
"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
"Nigeria,Australia,Tunisia" -- "Nigeria,Australia"
"Nigeria,Australia,Tunisia" -- Tunisia
"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines" -- "Nigeria,Australia,Tunisia"
"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines" -- "Malaysia,Thailand,Italy,Iran,Philippines"
"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq" -- "Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines"
"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq" -- Iraq
"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq,Belgium" -- "Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq"
"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq,Belgium" -- Belgium
"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq,Belgium,Serbia" -- "Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq,Belgium"
"Nigeria,Australia,Tunisia,Malaysia,Thailand,Italy,Iran,Philippines,Iraq,Belgium,Serbia" -- Serbia
"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"
"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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src/python/sarscovhierarchy.py
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@ -20,9 +20,7 @@ def main():
ids = csv_table.values('Accession')
fasta_map = FastaMap(fasta_path).filter(lambda item: item[0] in ids)
print("Files processing finished!")
labels = csv_table.dict_of('Accession', 'Geo_Location')
print("\nBuilding hierarchy...")
distances_table = fasta_map.compare_all_samples()
tree = HierarchyTree(distances_table, labels)

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src/python/utils/tree.py
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@ -18,7 +18,7 @@ class HierarchyTree:
closest_pair, new_relation, hierarchy_table)
def show(self):
self.__dot.render("hierarchy")
self.__dot.render("../../output/hierarchy")
def _add_relation(self, pair):
node1, node2 = tuple(map(self.__transform, pair))