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#!/usr/bin/env python
# Copyright 2000 by Thomas Sicheritz-Ponten.
# Copyrigth 2016 by Markus Piotrowski.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
# Created: Sun Dec 3 13:38:52 2000
# thomas@cbs.dtu.dk, http://www.cbs.dtu.dk/thomas
"""Search code for graphical Xbbtools tool."""
import re
import tkinter as tk
import tkinter.ttk as ttk
from tkinter import colorchooser
from Bio.Data.IUPACData import ambiguous_dna_values
from Bio.Seq import reverse_complement
import xbb_widget
class DNAsearch:
"""Class to search a DNA sequence."""
def __init__(self):
"""Set up the alphabet."""
self.init_alphabet()
self.sequence = ""
def init_alphabet(self):
"""Expand alphabet values for ambiguous codes."""
self.alphabet = ambiguous_dna_values
other = "".join(self.alphabet)
self.alphabet["N"] = self.alphabet["N"] + other
for key in self.alphabet:
if key == "N":
continue
if key in self.alphabet[key]:
continue
self.alphabet[key] = self.alphabet[key] + key
def SetSeq(self, seq):
"""Set sequence."""
self.sequence = seq
def SetPattern(self, pattern):
"""Convert search pattern to regular expression."""
self.pattern = pattern
self.rx_pattern = self.IUPAC2regex(pattern)
self.rx = re.compile(self.rx_pattern)
def IUPAC2regex(self, s):
"""Translate search text into pattern."""
rx = ""
for i in s:
r = self.alphabet.get(i, i)
if len(r) > 1:
rx = f"{rx}[{r}]"
else:
rx += r
return rx
def _Search(self, start=0):
"""Search and return MatchObject (PRIVAT)."""
# Only called from SearchAll. Is it used?
pos = self.rx.search(self.sequence, start)
return pos
def Search(self, start=0):
"""Search for query sequence and return position."""
pos = self.rx.search(self.sequence, start)
if pos:
return pos.start()
else:
return -1
def SearchAll(self):
"""Search the whole sequence."""
# Doesn't seem to be used...
pos = -1
positions = []
while True:
m = self._Search(pos + 1)
if not m:
break
pos = m.start()
if pos == -1:
break
positions.append(pos)
return positions
class XDNAsearch(tk.Toplevel, DNAsearch):
"""Graphical tools to perform the DNA search."""
def __init__(self, seq="", master=None, highlight=0):
"""Initialize the search GUI."""
DNAsearch.__init__(self)
self.master = master
self.highlight = highlight
self.colors = []
self.init_graphics()
self.sequence = seq
self.cur_pos = 0
def init_graphics(self):
"""Build the search window."""
tk.Toplevel.__init__(self, self.master)
self.frame = ttk.Frame(self)
self.frame.pack(fill=tk.BOTH, expand=1)
self.search_entry = ttk.Entry(self.frame)
self.search_entry.pack(fill=tk.BOTH, expand=1)
f2 = ttk.Frame(self.frame)
f2.pack(side=tk.TOP, fill=tk.BOTH, expand=1)
f = f2
self.forward = ttk.Button(f, text="Search +", command=self.do_search)
self.forward.pack(side=tk.LEFT)
self.forward = ttk.Button(
f, text="Search -", command=lambda x=self.do_search: x(other_strand=1)
)
self.forward.pack(side=tk.LEFT)
self.cancel = ttk.Button(f, text="Cancel", command=self.exit)
self.cancel.pack(side=tk.LEFT)
self.current_color = "cyan"
self.colorb = ttk.Button(f, text="Color", command=self.change_color)
self.colorb.pack(side=tk.LEFT)
self.config_color(self.current_color)
def config_color(self, color=None):
"""Set color for found sequence tag."""
if not self.highlight:
return
if not color:
color = colorchooser.askcolor()[1]
if not color:
color = "cyan"
self.current_color = color
self.current_tag = f"searched_{self.current_color}"
self.master.tag_config(self.current_tag, background=self.current_color)
self.master.tag_config(
self.current_tag + "R", background=self.current_color, underline=1
)
self.colors.append(color)
def change_color(self):
"""Call back for color button."""
self.config_color()
def get_pattern(self):
"""Retrieve query sequence."""
pattern = self.search_entry.get()
return pattern
def do_search(self, other_strand=0):
"""Start the search."""
pattern = self.get_pattern()
if other_strand:
pattern = reverse_complement(pattern)
self.SetPattern(pattern)
pos = self.Search(self.cur_pos)
self.cur_pos = pos + 1
w = self.master
if pos != -1:
if self.highlight:
start, stop = pos, pos + len(self.pattern)
if other_strand:
w.tag_add(self.current_tag + "R", f"1.{start:d}", f"1.{stop}")
else:
w.tag_add(self.current_tag, f"1.{start:d}", f"1.{stop}")
w.see(f"1.{start:d}")
def exit(self):
"""Clean up on exit."""
for c in self.colors:
self.master.tag_remove(f"searched_{c}", 1.0, tk.END)
self.master.tag_remove(f"searched_{c}R", 1.0, tk.END)
self.destroy()
del self
if __name__ == "__main__":
win = tk.Tk()
xbbtools = xbb_widget.xbb_widget()
seq = "ATGGTGTGTGTGTACGATCGCCCCCCCCAGTCGATCGATGCATCGTA"
xbbtools.insert_sequence(("Test_seq", seq))
xbbtools.search()
win.mainloop()
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