Convert Microarray Data to Excel Files
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9.1 KiB

import os
import tkinter as tk
import tkinter.ttk as ttk
from tkinter import filedialog
import pandas
import validators
import inout
APP_STATE_1 = 'no valid files selected'
APP_STATE_2 = 'no valid fields selected'
APP_STATE_3 = 'ok, single files'
APP_STATE_4 = 'ok, multiple files'
class StatusPanel(tk.Frame):
def __init__(self, parent):
tk.Frame.__init__(self, parent.master)
self._parent = parent
self.label = tk.Label(self, bd=1, relief=tk.SUNKEN, anchor=tk.S)
self.label.pack(fill=tk.X)
self.pack(side=tk.BOTTOM, fill=tk.X)
def set_text(self, text):
self.label.config(text=text)
self.label.update_idletasks()
def clear_text(self):
self.set_text('')
class FilePanel(tk.Frame):
def __init__(self, parent):
tk.Frame.__init__(self, parent.master)
self._parent = parent
self.btn_files = tk.Button(self, text="Select Files", command=self._parent.select_files)
self.btn_files.pack(pady=5, padx=5)
self.label = tk.Label(self, anchor=tk.SW)
self.label.pack(fill=tk.X, pady=5, padx=5)
ttk.Separator(self, orient=tk.HORIZONTAL).pack(side=tk.BOTTOM, fill=tk.X)
self.pack(side=tk.TOP, fill=tk.X)
def set_text(self, text):
self.label.config(text=text)
self.label.update_idletasks()
def clear_text(self):
self.set_text('')
class FieldPanel(tk.Frame):
def __init__(self, parent):
tk.Frame.__init__(self, parent.master)
self._parent = parent
self.is_single = tk.BooleanVar()
self.is_single.set(True)
self.rbtn_single = tk.Radiobutton(
self, text='single excel files', variable=self.is_single, value=True, command=self.disable_listbox)
self.rbtn_combine = tk.Radiobutton(
self, text='one combined excel file', variable=self.is_single, value=False, command=self.enable_listbox)
self.rbtn_single.pack(anchor=tk.W)
self.rbtn_combine.pack(anchor=tk.W)
self.listbox = tk.Listbox(self, selectmode=tk.MULTIPLE, activestyle='none', height=19)
self.listbox.pack(fill=tk.X, ipady=5, ipadx=5, )
self.listbox.bind('<<ListboxSelect>>', self._parent.toggle_run_button)
self.pack(side=tk.TOP, fill=tk.X)
def disable_radio_btn(self):
self.rbtn_single.config(state="disabled")
self.rbtn_combine.config(state="disabled")
def disable_listbox(self):
self.listbox.config(state="disabled")
self._parent.toggle_run_button()
def disable(self):
self.disable_listbox()
self.disable_radio_btn()
def enable_radio_btn(self):
self.rbtn_single.config(state="normal")
self.rbtn_combine.config(state="normal")
self.is_single.set(True)
def enable_listbox(self):
self.listbox.config(state="normal")
self._parent.toggle_run_button()
def enable(self):
self.enable_listbox()
self.enable_radio_btn()
def set_listbox_content(self, choices, selection):
self.enable_listbox()
current = self.listbox.size()
self.listbox.selection_clear(0, current)
self.listbox.delete(0,current)
for i, element in enumerate(choices):
self.listbox.insert(tk.END, element)
if element in selection:
self.listbox.selection_set(i)
self.disable_listbox()
class ActionPanel(tk.Frame):
def __init__(self, parent):
tk.Frame.__init__(self, parent.master)
self._parent = parent
self.btn_go = tk.Button(self, text="GO!", command=self._parent.convert_files)
self.btn_go.pack(side=tk.LEFT, pady=5, padx=5)
self.btn_quit = tk.Button(self, text="Quit", command=self._parent.quit)
self.btn_quit.pack(side=tk.RIGHT, pady=5, padx=5)
self.pack(side=tk.BOTTOM, fill=tk.X)
def disable(self):
self.btn_go.config(state='disabled')
def enable(self):
self.btn_go.config(state='active')
class Application(tk.Frame):
def __init__(self, master):
master.minsize(height=330, width=300)
tk.Frame.__init__(self, master)
self._master = master
self.pack(fill=tk.BOTH)
self.file_validator = None
self.validated_files = None
self.status_panel = StatusPanel(self)
self.file_panel = FilePanel(self)
self.field_panel = FieldPanel(self)
self.action_panel = ActionPanel(self)
self.reset()
def reset(self):
self.status_panel.clear_text()
self.field_panel.disable()
self.action_panel.disable()
self.file_validator = None
self.validated_files = None
def select_files(self):
self.reset()
self.file_panel.clear_text()
opts = {
'initialdir': '~/_signalyse test',
'filetypes': [('Signalyse Statistics', '.stx'), ('Signalyse Data', '.dat'), ('Sensovation Data', '.csv')],
'multiple': True}
file_selection = tk.filedialog.askopenfilename(**opts)
if not isinstance(file_selection, tuple) or len(file_selection) == 0:
return
self.file_validator = validators.guess_validator(file_selection)
if self.file_validator is None:
return
self.validated_files = [f for f in validators.validate_files(file_selection, self.file_validator)]
status = '%d of %d valid %s files found' % (len(self.validated_files), len(file_selection), self.file_validator.type)
self.file_panel.set_text(status)
if self._state == APP_STATE_1:
return self.reset()
self.field_panel.enable_radio_btn()
self.field_panel.set_listbox_content(self.file_validator.data_fields, self.file_validator.defaults)
self.toggle_run_button()
def toggle_run_button(self, event=None):
self.action_panel.disable()
if self._state in (APP_STATE_3, APP_STATE_4):
self.action_panel.enable()
def quit(self):
self._master.destroy()
def convert_files(self):
state = self._state
if state not in (APP_STATE_3, APP_STATE_4):
return self.reset()
if state == APP_STATE_3:
text = self._convert_to_separate_files()
else:
text = self._combine_data_files()
self.status_panel.set_text(text + ' Done')
@property
def _state(self):
c = self.field_panel.rbtn_single.config()
if not self.validated_files or c['state'] == 'disabled':
return APP_STATE_1
elif self.field_panel.is_single.get():
return APP_STATE_3
elif self.field_panel.listbox.curselection():
return APP_STATE_4
else:
return APP_STATE_2
def _convert_to_separate_files(self):
total = len(self.validated_files)
text = 'Converting data file %d of %d to separate excel file ...'
all_fields = self.file_validator.id_fields + self.file_validator.data_fields
for i, data_file in enumerate(self.validated_files):
self.status_panel.set_text(text % (i+1, total))
data_frame = inout.read_data_file(data_file, all_fields)
data_frame = data_frame.set_index(data_file.validator.id_fields)
name, ext = os.path.splitext(data_file.path)
path = name + ext.replace('.', '_') + '.xlsx'
inout.write_excel_file(path, data_frame)
return text % (i+1, total)
def _combine_data_files(self):
total = len(self.validated_files)
text = 'Combining data file %d of %d to single excel file ...'
data_fields = [self.file_validator.data_fields[i] for i in self.field_panel.listbox.curselection()]
selected_fields = self.file_validator.id_fields + data_fields
data_frame_list = []
for i, data_file in enumerate(self.validated_files):
self.status_panel.set_text(text % (i + 1, total))
data_frame = inout.read_data_file(data_file, selected_fields)
data_frame['File Name'] = os.path.basename(data_file.path)
data_frame_list.append(data_frame)
master_frame = pandas.concat(data_frame_list, ignore_index=True)
pivoted_df = master_frame.pivot(self.file_validator.id_fields[0],'File Name')
col_grouper = dict()
value_columns = []
for value_col, file_col in pivoted_df.columns:
if value_col not in col_grouper:
col_grouper[value_col] = []
value_columns.append(value_col)
col_grouper[value_col].append(file_col)
sorted_col_names = []
for value_col in value_columns:
sorted_file_cols = sorted(col_grouper[value_col], key=lambda x: inout.natural_sort(x))
sorted_col_names.extend([(value_col, file_col) for file_col in sorted_file_cols])
sorted_df = pivoted_df.reindex_axis(sorted_col_names, axis=1)
first_file = self.validated_files[0]
directory = os.path.dirname(first_file.path)
pseudo_extension = self.file_validator.extension.replace('.', '_')
xls_path = os.path.join(directory, 'combined' + pseudo_extension + '.xlsx')
inout.write_excel_file(xls_path, sorted_df)
return text % (i + 1, total)