/Scripts/xbbtools/xbb_search.py

#!/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()