Ejemplo n.º 1
0
def testContract():
    import taxa2image
    E = [(0,7),(7,8),(8,9),(1,9),(9,11),(2,10),(3,10),(10,11),(11,14),(13,14),(13,6),(12,13),(4,12),(5,12)]
    A = edgeListToAdjMap(E)

    labels = {}
    for u in A: labels[u] = u
    taxa2image.graphToImage("test.ps", E, labels)

    T = contractNonJunctions(A)
    T = adjMapToEdgeList(T)
    labels = {}
    for u in A: labels[u] = u
    taxa2image.graphToImage("test2.ps", T, labels)
Ejemplo n.º 2
0
def testNewickToTree():
    print "=== testNewickToTree() ==="
    s = "(uma,((cne,dpch),(spo,((((ure,cim),(aor,(ani,afm))),(((mgr,ncr),fgr),ssl)),(yli,(((pgu,dha),(ctp,cal)),((cgr,sce),(kla,ago))))))));"
    s = "(uma,((cne,dpch),(spo,(((aor,(ani,afm)),((mgr,ncr),fgr)),(yli,((dha),((cgr,sce),(kla,ago))))))));"
    s = "(uma,((cne,dpch),(spo,(((aor,(ani,afm)),((mgr,ncr),fgr)),(yli,(dha,((cgr,sce),(kla,ago))))))));"

    A = newickToTree(s)
    E = adjMapToEdgeList(A)
    #print A
    #print E
    import taxa2image
    labels = {}
    for u in A:
        labels[u] = u
    taxa2image.graphToImage("test1.ps", E, labels)
    print "Check test1.ps"
Ejemplo n.º 3
0
def testNewickToTree():
    print "=== testNewickToTree() ==="
    s = "(uma,((cne,dpch),(spo,((((ure,cim),(aor,(ani,afm))),(((mgr,ncr),fgr),ssl)),(yli,(((pgu,dha),(ctp,cal)),((cgr,sce),(kla,ago))))))));"
    s = "(uma,((cne,dpch),(spo,(((aor,(ani,afm)),((mgr,ncr),fgr)),(yli,((dha),((cgr,sce),(kla,ago))))))));"
    s = "(uma,((cne,dpch),(spo,(((aor,(ani,afm)),((mgr,ncr),fgr)),(yli,(dha,((cgr,sce),(kla,ago))))))));"

    A = newickToTree(s)
    E = adjMapToEdgeList(A)
    #print A
    #print E
    import taxa2image
    labels = {}
    for u in A:
        labels[u] = u
    taxa2image.graphToImage("test1.ps", E, labels)
    print "Check test1.ps"
Ejemplo n.º 4
0
def testContract():
    import taxa2image
    E = [(0, 7), (7, 8), (8, 9), (1, 9), (9, 11), (2, 10), (3, 10), (10, 11),
         (11, 14), (13, 14), (13, 6), (12, 13), (4, 12), (5, 12)]
    A = edgeListToAdjMap(E)

    labels = {}
    for u in A:
        labels[u] = u
    taxa2image.graphToImage("test.ps", E, labels)

    T = contractNonJunctions(A)
    T = adjMapToEdgeList(T)
    labels = {}
    for u in A:
        labels[u] = u
    taxa2image.graphToImage("test2.ps", T, labels)
Ejemplo n.º 5
0
def testExpandShoots():
    import taxa2image
    labels = {}
    E = [(1,3),(2,3),(3,4),(4,5),(4,6),(6,8),(6,7)]
    A = edgeListToAdjMap(E)
    nodes = set([4,3])
    T = adjMapToEdgeList(expandShoots(A, nodes))
    for u in A:
        labels[u] = u
    print T
    taxa2image.graphToImage("test1.ps", T, labels)

    nodes = set([3,4,6])
    E = [(1,3),(2,3),(3,4),(4,5),(4,6),(6,8),(6,7),(4,9),(9,10),(9,11),(6,12),(12,13),(12,14)]
    E = [(1,3),(2,3),(3,4),(4,5),(4,6),(6,8),(6,7)]
    A = edgeListToAdjMap(E)
    T = adjMapToEdgeList(expandShoots(A, nodes))
    labels = {}
    for u in A:
        labels[u] = u
    print T
    taxa2image.graphToImage("test2.ps", T, labels)

    nodes = set([3,4,6,9,10,12])
    E = [(1,3),(2,3),(3,4),(4,5),(4,6),(6,8),(6,7),(4,9),(9,10),(9,11),(6,12),(12,13),(12,14)]
    A = edgeListToAdjMap(E)
    T = adjMapToEdgeList(expandShoots(A, nodes))
    labels = {}
    for u in A:
        labels[u] = u
    print T
    taxa2image.graphToImage("test3.ps", T, labels)
Ejemplo n.º 6
0
def testExpandShoots():
    import taxa2image
    labels = {}
    E = [(1, 3), (2, 3), (3, 4), (4, 5), (4, 6), (6, 8), (6, 7)]
    A = edgeListToAdjMap(E)
    nodes = set([4, 3])
    T = adjMapToEdgeList(expandShoots(A, nodes))
    for u in A:
        labels[u] = u
    print T
    taxa2image.graphToImage("test1.ps", T, labels)

    nodes = set([3, 4, 6])
    E = [(1, 3), (2, 3), (3, 4), (4, 5), (4, 6), (6, 8), (6, 7), (4, 9),
         (9, 10), (9, 11), (6, 12), (12, 13), (12, 14)]
    E = [(1, 3), (2, 3), (3, 4), (4, 5), (4, 6), (6, 8), (6, 7)]
    A = edgeListToAdjMap(E)
    T = adjMapToEdgeList(expandShoots(A, nodes))
    labels = {}
    for u in A:
        labels[u] = u
    print T
    taxa2image.graphToImage("test2.ps", T, labels)

    nodes = set([3, 4, 6, 9, 10, 12])
    E = [(1, 3), (2, 3), (3, 4), (4, 5), (4, 6), (6, 8), (6, 7), (4, 9),
         (9, 10), (9, 11), (6, 12), (12, 13), (12, 14)]
    A = edgeListToAdjMap(E)
    T = adjMapToEdgeList(expandShoots(A, nodes))
    labels = {}
    for u in A:
        labels[u] = u
    print T
    taxa2image.graphToImage("test3.ps", T, labels)