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# We will need to create Qt4 items
from ...treeview.qt import QtCore
from ...treeview.qt import QGraphicsRectItem, QColor, QPen, QBrush
from ...treeview.qt import QGraphicsSimpleTextItem, QFont
from ... import faces, TreeStyle, PhyloTree, TextFace, SequenceFace
from random import random
_aafgcolors = {
'A':"#000000" ,
'R':"#000000" ,
'N':"#000000" ,
'D':"#000000" ,
'C':"#000000" ,
'Q':"#000000" ,
'E':"#000000" ,
'G':"#000000" ,
'H':"#000000" ,
'I':"#000000" ,
'L':"#000000" ,
'K':"#000000" ,
'M':"#000000" ,
'F':"#000000" ,
'P':"#000000" ,
'S':"#000000" ,
'T':"#000000" ,
'W':"#000000" ,
'Y':"#000000" ,
'V':"#000000" ,
'B':"#000000" ,
'Z':"#000000" ,
'X':"#000000",
'.':"#000000",
'-':"#000000",
}
_aabgcolors = {
'A':"#C8C8C8" ,
'R':"#145AFF" ,
'N':"#00DCDC" ,
'D':"#E60A0A" ,
'C':"#E6E600" ,
'Q':"#00DCDC" ,
'E':"#E60A0A" ,
'G':"#EBEBEB" ,
'H':"#8282D2" ,
'I':"#0F820F" ,
'L':"#0F820F" ,
'K':"#145AFF" ,
'M':"#E6E600" ,
'F':"#3232AA" ,
'P':"#DC9682" ,
'S':"#FA9600" ,
'T':"#FA9600" ,
'W':"#B45AB4" ,
'Y':"#3232AA" ,
'V':"#0F820F" ,
'B':"#FF69B4" ,
'Z':"#FF69B4" ,
'X':"#BEA06E",
'.':"#FFFFFF",
'-':"#FFFFFF",
}
_ntfgcolors = {
'A':'#000000',
'G':'#000000',
'I':'#000000',
'C':'#000000',
'T':'#000000',
'U':'#000000',
'.':"#000000",
'-':"#000000",
' ':"#000000"
}
_ntbgcolors = {
'A':'#A0A0FF',
'G':'#FF7070',
'I':'#80FFFF',
'C':'#FF8C4B',
'T':'#A0FFA0',
'U':'#FF8080',
'.':"#FFFFFF",
'-':"#FFFFFF",
' ':"#FFFFFF"
}
def test_layout_evol(node):
'''
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"]= False
if node.is_leaf():
if hasattr (node, "sequence"):
seqface = SequenceFace(node.sequence, "aa",
codon=node.nt_sequence, fsize=10,
col_w=11, interactive=True)
faces.add_face_to_node(seqface, node, 1, aligned=True)
def test_layout_phylo_aa(node):
'''
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"]= False
if node.is_leaf():
if hasattr (node, "sequence"):
seqface = SequenceFace(node.sequence, "aa",
fsize=10,
col_w=11, interactive=False)
faces.add_face_to_node(seqface, node, 1, aligned=True)
def test_layout_phylo_aa_motif(node):
'''
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"]= False
special_col = [[10,100],[150,1000],[1000,2000],[3000,4990]]
if node.is_leaf():
if hasattr (node, "sequence"):
seqface = SequenceFace(node.sequence, "aa",
fsize=10,special_col=special_col,
alt_col_w=3,
col_w=11, interactive=True)
faces.add_face_to_node(seqface, node, 1, aligned=True)
def test_layout_phylo_nt(node):
'''
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"]= False
if node.is_leaf():
if hasattr (node, "sequence"):
seqface = SequenceFace(node.sequence, "nt",
fsize=10,
col_w=11, interactive=True)
faces.add_face_to_node(seqface, node, 1, aligned=True)
if __name__ == "__main__":
tree = PhyloTree('(Orangutan,Human,Chimp);')
tree.link_to_alignment("""
>Chimp
HARWLNEKLRCELRTLKKLGLDGYKAVSQYVKGRA
>Orangutan
DARWINEKLRCVSRTLKKLGLDGYKGVSQYVKGRP
>Human
DARWHNVKLRCELRTLKKLGLVGFKAVSQFVIRRA
""")
nt_sequences = {"Human" : "GACGCACGGTGGCACAACGTAAAATTAAGATGTGAATTGAGAACTCTGAAAAAATTGGGACTGGTCGGCTTCAAGGCAGTAAGTCAATTCGTAATACGTCGTGCG",
"Chimp" : "CACGCCCGATGGCTCAACGAAAAGTTAAGATGCGAATTGAGAACTCTGAAAAAATTGGGACTGGACGGCTACAAGGCAGTAAGTCAGTACGTTAAAGGTCGTGCG",
"Orangutan": "GATGCACGCTGGATCAACGAAAAGTTAAGATGCGTATCGAGAACTCTGAAAAAATTGGGACTGGACGGCTACAAGGGAGTAAGTCAATACGTTAAAGGTCGTCCG"
}
for l in nt_sequences:
(tree & l).nt_sequence = nt_sequences[l]
tree.dist = 0
ts = TreeStyle()
ts.title.add_face(TextFace("Example for nucleotides...", fsize=15), column=0)
ts.layout_fn = test_layout_evol
tree.show(tree_style=ts)
# Show very large algs
tree = PhyloTree('(Orangutan,Human,Chimp);')
tree.link_to_alignment(">Human\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in range(5000)]) + \
"\n>Chimp\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in range(5000)]) + \
"\n>Orangutan\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in range(5000)]))
tree.dist = 0
ts = TreeStyle()
ts.title.add_face(TextFace("better not set interactivity if alg is very large", fsize=15), column=0)
ts.layout_fn = test_layout_phylo_aa
tree.show(tree_style=ts)
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