Pymix fix: short note on compiling PyMix on Ubuntu

A fix for users of Python 2.6 or 2.7 when installing PyMix:

	# 3 steps
	# 1) in setup.py
	# change
	from distutils.core import setup, Extension,DistutilsExecError
	#to:
	from distutils.core import setup, Extension
	from distutils.errors import DistutilsExecError
	# 2) in setup.py
	# change
	numpypath = prefix + '/lib/python' +pyvs + '/site-packages/numpy/core/include/numpy' # path to arrayobject.h
	# to
	# (locate arrayobject.h) - for me this path was
	numpypath = '/usr/share/pyshared/numpy/core/include/numpy'
	# Finally
	# 3) in /usr/local/lib/python2.7/dist-packages/AminoAcidPropertyPrior.py
	# change
	as = alpha.pop(0) # (line 170)
	# to
	dummy = alpha.pop(0) # 'as' is a reserved keyword

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How to pass arguments to python programs ...

... the right way (in my opinion). This is the basic template I always use. Not complicated, but the general formula might be useful to someone.

It allows you to pass arguments to a program with the use of flags, so they can be provided in any order. It has a 'help' flag (-h), will raise an error if no arguments are passed.

In this example one of the inputs (-a) is supposed to be a file. If the file is not provided, it uses Tkinter to open a simple 'get file' window dialog.

It then parses the other arguments out. Here I have assumed one argument is a string, one is a float, and one is an integer. If any arguments are not provided, it creates variables based on default variables. It prints everything it's doing to the screen.

	# these are the libraries needed
	import sys, getopt
	from Tkinter import Tk
	from tkFileDialog import askopenfilename
	import numpy as np
	# get list of input arguments and pre-allocate arrays
	argv = sys.argv[1:]
	inputfile = ''; arg2 = ''
	arg3 = ''; arg4 = ''
	# parse inputs to variables
	try:
	opts, args = getopt.getopt(argv,"ha:b:c:d:")
	except getopt.GetoptError:
	print 'my_script.py -a <inputfile> -b <arg2> -c <arg3> -d <arg4>'
	sys.exit(2)
	for opt, arg in opts:
	if opt == '-h': # h is 'help'
	print 'my_script.py -a <inputfile> -b <arg2> -c <arg3> -d <arg4>'
	sys.exit()
	elif opt in ("-a"):
	inputfile = arg
	elif opt in ("-b"):
	arg2 = arg
	elif opt in ("-c"):
	arg3 = arg
	elif opt in ("-d"):
	arg4 = arg
	# prompt user to supply file if no input file given
	if not inputfile:
	print 'An input file is required!!!!!!'
	# we don't want a full GUI, so keep the root window from appearing
	Tk().withdraw()
	# show an "Open" dialog box and return the path to the selected file
	inputfile = askopenfilename(filetypes=[("JPG files","*.jpg")])
	# print given arguments to screen and convert data type where necessary
	# let's assume arg2 is meant to be an integer, arg3 is a float, and arg4 is a string
	# let's further assume arg2 and arg3 are meant to be numpy arrays
	if inputfile:
	print 'Input file is %s' % (inputfile)
	if arg2:
	arg2 = np.asarray(arg2,int)
	print 'Argument 2 is %s' % (str(arg2))
	if arg3:
	arg3 = np.asarray(arg3,float)
	print 'Argument 3 is %s' % (str(arg2))
	if arg4:
	print 'Argument 4 is %s' % (arg4)
	# if arguments not supplied, use defaults
	if not arg2:
	arg2 = 100
	print '[Default] Argument 2 is %s' % (str(arg2))
	if not arg3:
	arg3 = 0.1
	print '[Default] Argument 3 is %s' % (str(arg3))
	if not arg4:
	arg4 = 'hello'
	print '[Default] Argument 4 is %s' % (arg4)

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Kivy python script for capturing displaying webcam

Kivy is very cool. It allows you to make graphical user interfaces for computers, tablets and smart phones ... in Python. Which is great for people like me. And you, I'm sure. And it's open source, of course.

Today was my first foray into programming using Kivy. Here was my first 'app'. It's not very sophisticated, but I find Kivy's documentation rather impenetrable and frustratingly lacking in examples. Therefore I hope more people like me post their code and projects on blogs.

Right, it detects and displays your webcam on the screen, draws a little button in the bottom. When you press that button it takes a screengrab and writes it to an image file. Voila! Maximise the window before you take a screen shot for best effects.

	import kivy
	kivy.require('1.7.2')
	from kivy.app import App
	from kivy.uix.floatlayout import FloatLayout
	from kivy.uix.camera import Camera
	from kivy.uix.button import Button
	from kivy.core.window import Window
	class CamApp(App):
	# Function to take a screenshot
	def screengrab(self,*largs):
	outname = self.fileprefix+'_%(counter)04d.png'
	Window.screenshot(name=outname)
	def build(self):
	# create a floating layout as base
	camlayout = FloatLayout(size=(600, 600))
	cam = Camera() #Get the camera
	cam=Camera(resolution=(1024,1024), size=(300,300))
	cam.play=True #Start the camera
	camlayout.add_widget(cam)
	button=Button(text='Take Picture',size_hint=(0.12,0.12))
	button.bind(on_press=self.screengrab)
	camlayout.add_widget(button) #Add button to Camera Layout
	self.fileprefix = 'snap'
	return camlayout
	if __name__ == '__main__':
	CamApp().run()

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Simple Python script to write a list of coordinates to a .geojson file

This has probably been done better elsewhere, but here's a really simple way to write a geojson file programmatically to display a set of coordinates, without having to bother learning the syntax of yet another python library. Geojson is a cool little format, open source and really easy.

Below, arrays x and y are decimal longitude and latitude respectively. The code would have to be modified to include a description for each coordinate, which could be included easily on line 15 if in the form of an iterable list.

	f = open('points.geojson', 'w')
	f.write('\n')
	f.write('{\n')
	f.write(' "type": "FeatureCollection",\n')
	f.write(' "features": [\n')
	for k in range(len(x)):
	f.write('\n')
	f.write(' {\n')
	f.write(' "type": "Feature",\n')
	f.write(' "geometry": {\n')
	f.write(' "type": "Point",\n')
	f.write(' "coordinates": ['+str(y[k])+', '+str(x[k])+']\n')
	f.write(' },\n')
	f.write(' "properties": {\n')
	f.write(' "'+str(k)+'": "description here"\n')
	f.write(' }\n')
	if k==len(x)-1:
	f.write(' }\n')
	else:
	f.write(' },\n')
	f.write('\n')
	f.write('\n')
	f.write(' ]\n')
	f.write('}\n')
	f.close()

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