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gui_ms2_extractor.py
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import os
from tkinter import *
from tkinter import messagebox, ttk
import sys
from PyQt5.QtWidgets import (QFileDialog, QAbstractItemView, QListView,
QTreeView, QApplication, QDialog)
from path import Path
from ms2_extractor import extract_ms2_file
RAW_CONVERTOR_PATH = Path("ms2_extractor.py")
class SelectFolders(QFileDialog):
def __init__(self, *args):
super(SelectFolders, self).__init__(*args)
self.setOption(self.DontUseNativeDialog, True)
self.setFileMode(self.Directory)
self.setOption(self.ShowDirsOnly, True)
self.findChildren(QListView)[0].setSelectionMode(QAbstractItemView.ExtendedSelection)
self.findChildren(QTreeView)[0].setSelectionMode(QAbstractItemView.ExtendedSelection)
class RawFileTinker(Frame):
def __init__(self):
Frame.__init__(self)
self.raw_folders = None
self.generating_file = False
self._frame_width = 100
self.master.title("RawFileExtractor")
self.master.rowconfigure(5, weight=1)
self.master.columnconfigure(5, weight=1)
self.grid(sticky=W + E + N + S)
self.folder_frame = Frame(self)
self.folder_frame.pack(expand=True)
self.button = Button(self.folder_frame, text="Select D folders", command=self.load_file,
width=int(self._frame_width / 3))
self.button.pack(side=LEFT, expand=True)
self.overwrite_flag = BooleanVar()
self.overwrite_button = ttk.Checkbutton(self.folder_frame,
text='overwrite ms2 files',
variable=self.overwrite_flag,
onvalue=True,
offvalue=False)
self.overwrite_button.pack(side=RIGHT, expand=True)
self.timsscore_flag = BooleanVar()
self.timsscore_button = ttk.Checkbutton(self.folder_frame,
text='timsscore format',
variable=self.timsscore_flag,
onvalue=True,
offvalue=False)
self.timsscore_button.pack(side=RIGHT, expand=True)
self.mobility_spectra_flag = BooleanVar()
self.mobility_spectra_flag_button = ttk.Checkbutton(self.folder_frame,
text='include mobility spectrum',
variable=self.mobility_spectra_flag,
onvalue=True,
offvalue=False)
self.mobility_spectra_flag_button.pack(side=RIGHT, expand=True)
self.d_folder_label = Label(self, text="no file selected", width=self._frame_width, height=2)
self.d_folder_label.pack(expand=True)
self.ms1_frame = Frame(self)
self.ms1_frame.pack(expand=True)
self.button_ms1 = Button(self.ms1_frame, text="Generate Ms1 Files", command=self.generate_ms1,
width=int(self._frame_width / 3), state=DISABLED)
self.button_ms1.pack(side=LEFT, expand=True)
self.percent_done_ms1_text = Label(self.ms1_frame, text="0%", width=int(self._frame_width / 3 * 2), height=2)
self.percent_done_ms1_text.pack(side=RIGHT, expand=True)
self.ms2_frame = Frame(self)
self.ms2_frame.pack(expand=True)
self.button_ms2 = Button(self.ms2_frame, text="Generate Ms2 Files", command=self.generate_ms2s,
width=int(self._frame_width / 3), state=DISABLED)
self.button_ms2.pack(side=LEFT, expand=True)
self.percent_done_ms2_text = Label(self.ms2_frame, text="0%", width=int(self._frame_width / 3 * 2), height=2)
self.percent_done_ms2_text.pack(side=RIGHT, expand=True)
directions = "Directions\n" \
" 1) Use shift/ctrl click to highlight multiple folders.\n" \
" 2) Press either ms1 or ms2 button.\n" \
" 3) Wait :) \n" \
" 4) ms1/ms2 files will be generated in the D folder with the same name as the folder.\n" \
" \n" \
"Note: Ms1 files are very large for timsTof experiments ~50 GB\n" \
" - Made by Patrick Garrett 8/6/2021"
messagebox.showinfo("Version 1.0", directions)
def generate_ms1(self):
self.button_ms1['state'] = DISABLED
self.button_ms2['state'] = DISABLED
self.button['state'] = DISABLED
for i, folder in enumerate(self.raw_folders):
percent_done = round((i + 1) / len(self.raw_folders) * 100)
self.percent_done_ms2_text['text'] = f'processing: {os.path.basename(folder)}'
self.master.title(f"RawFileExtractor {percent_done}%")
self.update()
ms1_file_path = os.path.join(folder, os.path.basename(folder) + ".ms1")
contains_file = os.path.exists(ms1_file_path)
if contains_file and not self.overwrite_flag.get():
print(f"Ms1 file exists: {ms1_file_path} skipping...")
else:
os.system(f'python {RAW_CONVERTOR_PATH} {folder}')
self.button_ms1['state'] = NORMAL
self.button_ms2['state'] = NORMAL
self.button['state'] = NORMAL
def generate_ms2s(self):
self.button_ms2['state'] = DISABLED
self.button_ms1['state'] = DISABLED
self.button['state'] = DISABLED
for i, folder in enumerate(self.raw_folders):
percent_done = round((i + 1) / len(self.raw_folders) * 100)
self.percent_done_ms2_text['text'] = f'processing: {os.path.basename(folder)}'
self.master.title(f"RawFileExtractor {percent_done}%")
self.update()
ms2_file_path = os.path.join(folder, os.path.basename(folder) + ".ms2")
contains_file = os.path.exists(ms2_file_path)
if contains_file and not self.overwrite_flag.get():
print(f"Ms2 file exists: {ms2_file_path} skipping...")
else:
extract_ms2_file(analysis_dir=folder,
output_file=None,
include_mobility_spectra=self.mobility_spectra_flag.get(),
ppm=15,
skip_spectra=False
)
self.button_ms1['state'] = NORMAL
self.button_ms2['state'] = NORMAL
self.button['state'] = NORMAL
def load_file(self):
_ = QApplication(sys.argv)
dlg = SelectFolders()
if dlg.exec_() == QDialog.Accepted:
self.raw_folders = dlg.selectedFiles()
number_files_selected = 0
if self.raw_folders:
number_files_selected = len(self.raw_folders)
self.d_folder_label['text'] = f'Files selected: {number_files_selected}'
self.button_ms1['state'] = NORMAL
self.button_ms2['state'] = NORMAL
if __name__ == "__main__":
RawFileTinker().mainloop()