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# We will need to create Qt4 items
from PyQt4 import QtCore
from PyQt4.QtGui import QGraphicsRectItem, QColor, QPen, QBrush
from PyQt4.QtGui import QGraphicsSimpleTextItem, QFont
from ete3 import faces, TreeStyle, PhyloTree, TextFace
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"
}
class MySequenceFace(faces.StaticItemFace):
""" Creates a new molecular sequence face object.
:argument seq: Sequence string to be drawn
:argument seqtype: Type of sequence: "nt" or "aa"
:argument fsize: Font size, (default=10)
You can set custom colors for amino-acids or nucleotides:
:argument None codon : a string that corresponds to the reverse translation of the amino-acid sequence
:argument 11 col_w : width of the column (if col_w is lower than font size, letter wont be displayed)
:argument None fg_colors : dictionary of colors for foreground, with as keys each possible character in sequences, and as value the colors
:argument None bg_colors : dictionary of colors for background, with as keys each possible character in sequences, and as value the colors
:argument 3 alt_col_w : works together with special_col option, defines the width of given columns
:argument None special_col : list of lists containing the bounds of columns to be displayed with alt_col_w as width
:argument False interactive : more info can be displayed when mouse over sequence
"""
def __init__(self, seq, seqtype="aa", fsize=10,
fg_colors=None, bg_colors=None,
codon=None, col_w=11, alt_col_w=3,
special_col=None, interactive=False):
self.seq = seq
self.codon = codon
self.fsize = fsize
self.style = seqtype
self.col_w = float(col_w)
self.alt_col_w = float(alt_col_w)
self.special_col = special_col if special_col else []
self.width = 0 # will store the width of the whole sequence
self.interact = interactive
if self.style == "aa":
if not fg_colors:
fg_colors = _aafgcolors
if not bg_colors:
bg_colors = _aabgcolors
else:
if not fg_colors:
fg_colors = _ntfgcolors
if not bg_colors:
bg_colors = _ntbgcolors
self.fg_col = self.__init_col(fg_colors)
self.bg_col = self.__init_col(bg_colors)
# for future?
self.row_h = 13.0
super(MySequenceFace,
self).__init__(QGraphicsRectItem(0, 0, self.width, self.row_h))
def __init_col(self, color_dic):
"""to speed up the drawing of colored rectangles and characters"""
new_color_dic = {}
for car in color_dic:
new_color_dic[car] = QBrush(QColor(color_dic[car]))
return new_color_dic
def update_items(self):
#self.item = QGraphicsRectItem(0,0,self._total_w, self.row_h)
seq_width = 0
nopen = QPen(QtCore.Qt.NoPen)
font = QFont("Courier", self.fsize)
rect_cls = self.InteractiveLetterItem if self.interact else QGraphicsRectItem
for i, letter in enumerate(self.seq):
width = self.col_w
for m in self.special_col:
if m[0] < i <= m[1]:
width = self.alt_col_w
break
#load interactive item if called correspondingly
rectItem = rect_cls(0, 0, width, self.row_h, parent=self.item)
rectItem.setX(seq_width) # to give correct X to children item
rectItem.setBrush(self.bg_col[letter])
rectItem.setPen(nopen)
if self.interact:
if self.codon:
rectItem.codon = '%s, %d: %s' % (self.seq[i], i,
self.codon[i*3:i*3+3])
else:
rectItem.codon = '%s, %d' % (self.seq[i], i)
# write letter if enough space
if width >= self.fsize:
text = QGraphicsSimpleTextItem(letter, parent=rectItem)
text.setFont(font)
text.setBrush(self.fg_col[letter])
# Center text according to rectItem size
tw = text.boundingRect().width()
th = text.boundingRect().height()
text.setPos((width - tw)/2, (self.row_h - th)/2)
seq_width += width
self.width = seq_width
class InteractiveLetterItem(QGraphicsRectItem):
"""This is a class"""
def __init__(self, *arg, **karg):
QGraphicsRectItem.__init__(self, *arg, **karg)
self.codon = None
self.label = None
self.setAcceptsHoverEvents(True)
def hoverEnterEvent (self, e):
""" when mouse is over"""
if not self.label:
self.label = QGraphicsRectItem(parent=self)
#self.label.setY(-18)
self.label.setX(11)
self.label.setBrush(QBrush(QColor("white")))
self.label.text = QGraphicsSimpleTextItem(parent=self.label)
self.setZValue(1)
self.label.text.setText(self.codon)
self.label.setRect(self.label.text.boundingRect())
self.label.setVisible(True)
def hoverLeaveEvent(self, e):
"""when mouse leaves area"""
if self.label:
self.label.setVisible(False)
self.setZValue(0)
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 = MySequenceFace(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 = MySequenceFace(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 = MySequenceFace(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 = MySequenceFace(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 xrange (5000)]) + \
"\n>Chimp\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in xrange (5000)]) + \
"\n>Orangutan\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in xrange (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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