def file_selected(self):
file = self.file_listbox.curselection()
if len(file) != 1:
sys.stderr.write("No file selected.\n")
else:
file = map(int, file)
fname = self.file_listbox.get(file[0])
file_path = os.path.join(self.dir, fname)
if self.GenePair_instance:
# clean it up
self.GenePair_instance = None
else:
self.GenePair_instance = GenePair(file_path)
gene_ids = self.GenePair_instance.gene_id2expr_array.keys()
gene_ids.sort()
for gene_id in gene_ids:
self.gene_pair_listbox.insert(END, gene_id)
def liststore_gene_fill(self, filename): self.GenePair_instance = GenePair(filename) gene_ids = self.GenePair_instance.gene_id2expr_array.keys() gene_ids.sort() self.liststore = gtk.ListStore(str) # we'll add some data now - for gene_id in gene_ids: self.liststore.append([gene_id]) # set the TreeView mode to be liststore self.treeview1.set_model(self.liststore) # make it searchable self.treeview1.set_search_column(0) # Allow sorting on the column self.tvcolumn.set_sort_column_id(0) # Allow drag and drop reordering of rows self.treeview1.set_reorderable(True) self.treeselection.set_mode(gtk.SELECTION_MULTIPLE)
class GenePairGui:
def __init__(self):
xml = gtk.glade.XML('genepairgui.glade')
xml.signal_autoconnect(self)
self.window1 = xml.get_widget("window1")
self.window1.connect("destroy", self.destroy)
#to get gene_ids input by user
self.textview1 = xml.get_widget("textview1")
#to draw the plot
self.textview2 = xml.get_widget("textview2")
#to get gene_ids input by user
self.treeview1 = xml.get_widget("treeview1")
# create the TreeViewColumn to display the data
self.tvcolumn = gtk.TreeViewColumn('Gene Id')
# add tvcolumn to treeview
self.treeview1.append_column(self.tvcolumn)
# create a CellRendererText to render the data
self.cell = gtk.CellRendererText()
# add the cell to the tvcolumn and allow it to expand
self.tvcolumn.pack_start(self.cell, True)
# set the cell "text" attribute to column 0 - retrieve text
# from that column in liststore
self.tvcolumn.add_attribute(self.cell, 'text', 0)
#setting the selection mode
self.treeselection = self.treeview1.get_selection()
#the backend module, non-initilized
self.GenePair_instance = None
def file_ok_sel(self, w):
filename = self.filew.get_filename()
self.filew.destroy()
self.window1.set_title(filename)
self.liststore_gene_fill(filename)
def liststore_gene_fill(self, filename):
self.GenePair_instance = GenePair(filename)
gene_ids = self.GenePair_instance.gene_id2expr_array.keys()
gene_ids.sort()
self.liststore = gtk.ListStore(str)
# we'll add some data now -
for gene_id in gene_ids:
self.liststore.append([gene_id])
# set the TreeView mode to be liststore
self.treeview1.set_model(self.liststore)
# make it searchable
self.treeview1.set_search_column(0)
# Allow sorting on the column
self.tvcolumn.set_sort_column_id(0)
# Allow drag and drop reordering of rows
self.treeview1.set_reorderable(True)
self.treeselection.set_mode(gtk.SELECTION_MULTIPLE)
def on_button1_clicked(self, button):
self.filew = gtk.FileSelection("File selection")
#self.filew.connect("destroy", self.destroy)
# Connect the ok_button to file_ok_sel method
self.filew.ok_button.connect("clicked", self.file_ok_sel)
# Connect the cancel_button to destroy the widget
self.filew.cancel_button.connect("clicked", lambda w: self.filew.destroy())
# Lets set the filename, as if this were a save dialog,
# and we are giving a default filename
#self.filew.set_filename("penguin.png")
self.filew.show()
def on_button2_clicked(self, button):
'''
gene selected
02-15-06
use --process_gene_id_list()
'''
pathlist = []
gene_id_list = []
self.treeselection.selected_foreach(foreach_cb, pathlist)
if len(pathlist) >0:
for i in range(len(pathlist)):
gene_id_list.append(self.liststore[pathlist[i][0]][0])
self.process_gene_id_list(gene_id_list)
def on_button3_clicked(self, button):
gtk.main_quit()
def on_button4_clicked(self, button):
'''
input gene_ids done
02-15-06
use --process_gene_id_list()
'''
textbuffer = self.textview1.get_buffer()
startiter, enditer = textbuffer.get_bounds()
text = textbuffer.get_text(startiter, enditer)
gene_id_list = text.split("\n")
self.process_gene_id_list(gene_id_list)
def process_gene_id_list(self, gene_id_list):
"""
02-15-06
split from on_button2_clicked() and on_button4_clicked()
"""
if len(gene_id_list) >0:
filename = self.GenePair_instance.gene_pair_analyze(gene_id_list)
scatter_plot_fname = self.GenePair_instance.scatter_plot(gene_id_list) #02-15-06
if filename:
self.show_plot(filename)
if scatter_plot_fname:
self.show_plot(scatter_plot_fname)
else:
sys.stderr.write("Have you selected a dataset?\n")
def show_plot(self, filename):
textbuffer = self.textview2.get_buffer()
im = Image.open(filename)
#r.postscript() gives an image with a strange direction, rotate it back
im = im.rotate(-90)
ar = fromimage(im)
pixbuf = gtk.gdk.pixbuf_new_from_array(ar, gtk.gdk.COLORSPACE_RGB, 8)
startiter = textbuffer.get_start_iter()
textbuffer.insert_pixbuf(startiter, pixbuf)
#cleanup the temporary files and others
del im
del ar
os.remove(filename)
def destroy(self, widget):
gtk.main_quit()
class GenePairGui:
def __init__(self, master, dir):
self.dir = dir
frame = Frame(master)
frame.pack()
self.scrollbar_file = Scrollbar(frame, orient=VERTICAL)
self.scrollbar_gene_pair = Scrollbar(frame, orient=VERTICAL)
self.file_listbox = Listbox(frame, yscrollcommand=self.scrollbar_file.set)
self.gene_pair_listbox = Listbox(frame, selectmode=EXTENDED, yscrollcommand=self.scrollbar_gene_pair.set)
self.button_file = Button(frame, text="select file", command=self.file_selected)
self.button_gene_pair = Button(frame, text="select gene pair", command=self.gene_pair_selected)
self.button_quit = Button(frame, text="QUIT", fg="red", command=frame.quit)
# geometry arrangement
self.scrollbar_file.config(command=self.file_listbox.yview)
self.scrollbar_gene_pair.config(command=self.gene_pair_listbox.yview)
self.scrollbar_file.pack(fill=Y, expand=1)
self.scrollbar_gene_pair.pack(fill=Y, expand=1)
self.file_listbox.grid(row=0, column=0)
self.scrollbar_file.grid(row=0, column=1)
self.gene_pair_listbox.grid(row=0, column=2)
self.scrollbar_gene_pair.grid(row=0, column=3)
self.button_file.grid(row=1, column=0, columnspan=2)
self.button_gene_pair.grid(row=1, column=2, columnspan=2)
self.button_quit.grid(row=2, column=1, columnspan=2)
# fill the list box
self.file_listbox_fill()
# GenePair handler
self.GenePair_instance = None
def file_listbox_fill(self):
files = os.listdir(self.dir)
for item in files:
self.file_listbox.insert(END, item)
def file_selected(self):
file = self.file_listbox.curselection()
if len(file) != 1:
sys.stderr.write("No file selected.\n")
else:
file = map(int, file)
fname = self.file_listbox.get(file[0])
file_path = os.path.join(self.dir, fname)
if self.GenePair_instance:
# clean it up
self.GenePair_instance = None
else:
self.GenePair_instance = GenePair(file_path)
gene_ids = self.GenePair_instance.gene_id2expr_array.keys()
gene_ids.sort()
for gene_id in gene_ids:
self.gene_pair_listbox.insert(END, gene_id)
def gene_pair_selected(self):
gene_pair = self.gene_pair_listbox.curselection()
if len(gene_pair) != 2:
sys.stderr.write("Did you select two genes?\n")
else:
gene_pair = map(int, gene_pair)
gene_id1 = self.gene_pair_listbox.get(gene_pair[0])
gene_id2 = self.gene_pair_listbox.get(gene_pair[1])
print gene_id1
print gene_id2
self.GenePair_instance.gene_pair_analyze(gene_id1, gene_id2)