How to refer to the text entry widget`s input in a subprocess.call() in Python GTK? - pygtk

Question

How to refer to the text entry widget`s input in a subprocess.call() in Python GTK? App for calling bioinformatics tool from PyGTK:
#!/usr/bin/env python
import pygtk
pygtk.require('2.0')
import gtk
import subprocess
class EntryExample:
def enter_callback(self, widget, entry):
entry_text = entry.get_text()
print "Entry contents: %s\n" % entry_text
def entry_toggle_editable(self, checkbutton, entry):
entry.set_editable(checkbutton.get_active())
def entry_toggle_visibility(self, checkbutton, entry):
entry.set_visibility(checkbutton.get_active())
def __init__(self):
# create a new window
window = gtk.Window(gtk.WINDOW_TOPLEVEL)
window.set_size_request(200, 100)
window.set_title("GTK Entry")
window.connect("delete_event", lambda w,e: gtk.main_quit())
vbox = gtk.VBox(False, 0)
window.add(vbox)
vbox.show()
entry = gtk.Entry()
entry.set_max_length(50)
entry.connect("activate", self.enter_callback, entry)
entry.set_text("Insert")
entry.insert_text(" SRA accession number", len(entry.get_text()))
entry.select_region(0, len(entry.get_text()))
vbox.pack_start(entry, True, True, 0)
entry.show()
hbox = gtk.HBox(False, 0)
vbox.add(hbox)
hbox.show()
# Create a new button for running Linux Shell script
buttonscript = gtk.Button(label="Download", stock=None)
# Connect the "clicked" signal of the button to the function
buttonscript.connect("clicked", runlinuxshell )
vbox.pack_start(buttonscript, True, True, 0)
buttonscript.set_flags(gtk.CAN_DEFAULT)
buttonscript.grab_default()
buttonscript.show()
button = gtk.Button(stock=gtk.STOCK_CLOSE)
button.connect("clicked", lambda w: gtk.main_quit())
vbox.pack_start(button, True, True, 0)
button.set_flags(gtk.CAN_DEFAULT)
button.grab_default()
button.show()
window.show()
def runlinuxshell ():
subprocess.call('$i=len(entry.get_text()) # Error is here
echo $i
./fastq-dump --split-files $i -v')
def main():
gtk.main()
return 0
if __name__ == "__main__":
EntryExample()
main()
How to pass text input from a widget into the suprocess.call()?
Is there any good example on how to call bioinformatics linux tools in PyGTK?

Answer 1

disclaimer: the sample uses pygobject with introspection and not pygtk which is deprecated for years and should not be used in new code.
disclaimer 2: the sample can be greatly improved to say the least, it's just an adaption of your original script.
You probably would do some like the following:
import gi
from gi.repository import Gtk
import subprocess
class EntryExample:
def __init__(self):
window = Gtk.Window()
window.set_size_request(200, 100)
window.set_title("GTK Entry")
window.connect("delete_event", Gtk.main_quit)
vbox = Gtk.VBox(False, 0)
window.add(vbox)
self.entry = Gtk.Entry()
self.entry.set_max_length(50)
self.entry.set_text("SRA accession number")
vbox.pack_start(self.entry, True, True, 0)
buttonscript = Gtk.Button(label="Download", stock=None)
buttonscript.connect("clicked", self.runlinuxshell)
vbox.pack_start(buttonscript, True, True, 0)
button = Gtk.Button(stock=Gtk.STOCK_CLOSE)
button.connect("clicked", Gtk.main_quit)
vbox.pack_start(button, True, True, 0)
window.show_all()
def runlinuxshell (self, widget):
mylen = len(self.entry.get_text())
# Here you will execute your subprocess with mylen
def main(self):
Gtk.main()
if __name__ == "__main__":
sub = EntryExample()
sub.main()