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import sys
from ete3 import Tree, SeqMotifFace, TreeStyle, add_face_to_node
seq = ("-----------------------------------------------AQAK---IKGSKKAIKVFSSA---"
"APERLQEYGSIFTDA---GLQRRPRHRIQSK-------ALQEKLKDFPVCVSTKPEPEDDAEEGLGGLPSN"
"ISSVSSLLLFNTTENLYKKYVFLDPLAG----THVMLGAETEEKLFDAPLSISKREQLEQQVPENYFYVPD"
"LGQVPEIDVPSYLPDLPGIANDLMYIADLGPGIAPSAPGTIPELPTFHTEVAEPLKVGELGSGMGAGPGTP"
"AHTPSSLDTPHFVFQTYKMGAPPLPPSTAAPVGQGARQDDSSSSASPSVQGAPREVVDPSGGWATLLESIR"
"QAGGIGKAKLRSMKERKLEKQQQKEQEQVRATSQGGHL--MSDLFNKLVMRRKGISGKGPGAGDGPGGAFA"
"RVSDSIPPLPPPQQPQAEDED----")
mixed_motifs = [
# seq.start, seq.end, shape, width, height, fgcolor, bgcolor
[10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|long text clipped long text clipped"],
[101, 150, "o", None, 10, "blue", "pink", None],
[155, 180, "()", None, 10, "blue", "rgradient:purple", None],
[160, 190, "^", None, 14, "black", "yellow", None],
[191, 200, "<>", None, 12, "black", "rgradient:orange", None],
[201, 250, "o", None, 12, "black", "brown", None],
[351, 370, "v", None, 15, "black", "rgradient:gold", None],
[370, 420, "compactseq", 2, 10, None, None, None],
]
simple_motifs = [
# seq.start, seq.end, shape, width, height, fgcolor, bgcolor
[10, 60, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|long text clipped long text clipped"],
[120, 150, "o", None, 10, "blue", "pink", None],
[200, 300, "()", None, 10, "blue", "red", "arial|8|white|hello"],
]
box_motifs = [
# seq.start, seq.end, shape, width, height, fgcolor, bgcolor
[0, 5, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|10"],
[10, 25, "[]", None, 10, "black", "rgradient:ref", "arial|8|white|10"],
[30, 45, "[]", None, 10, "black", "rgradient:orange", "arial|8|white|20"],
[50, 65, "[]", None, 10, "black", "rgradient:pink", "arial|8|white|20"],
[70, 85, "[]", None, 10, "black", "rgradient:green", "arial|8|white|20"],
[90, 105, "[]", None, 10, "black", "rgradient:brown", "arial|8|white|20"],
[110, 125, "[]", None, 10, "black", "rgradient:yellow", "arial|8|white|20"],
]
def get_example_tree():
# Create a random tree and add to each leaf a random set of motifs
# from the original set
t = Tree("( (A, B, C, D, E, F, G), H, I);")
seqFace = SeqMotifFace(seq, gapcolor="red")
(t & "A").add_face(seqFace, 0, "aligned")
seqFace = SeqMotifFace(seq, seq_format="line", gap_format="blank")
(t & "B").add_face(seqFace, 0, "aligned")
seqFace = SeqMotifFace(seq, seq_format="line")
(t & "C").add_face(seqFace, 0, "aligned")
seqFace = SeqMotifFace(seq, seq_format="()")
(t & "D").add_face(seqFace, 0, "aligned")
seqFace = SeqMotifFace(seq, motifs=simple_motifs, seq_format="-")
(t & "E").add_face(seqFace, 0, "aligned")
seqFace = SeqMotifFace(seq=None, motifs=simple_motifs, gap_format="blank")
(t & "F").add_face(seqFace, 0, "aligned")
seqFace = SeqMotifFace(seq, motifs=mixed_motifs, seq_format="-")
(t & "G").add_face(seqFace, 0, "aligned")
seqFace = SeqMotifFace(seq=None, motifs=box_motifs, gap_format="line")
(t & "H").add_face(seqFace, 0, "aligned")
seqFace = SeqMotifFace(seq[30:60], seq_format="seq")
(t & "I").add_face(seqFace, 0, "aligned")
return t
if __name__ == '__main__':
t = get_example_tree()
ts = TreeStyle()
ts.tree_width = 50
#t.show(tree_style=ts)
t.render("seq_motif_faces.png", tree_style=ts)
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