Class 1 for course: "Programming, data analysis & data visualization in python". A course for the Champlimaud Neuroscience Program.

1. files!
(and reading and writing to them)

2. The plan!
Basics: data types (and operations & calculations)
Basics: conditionals & iteration
Basics: lists, tuples, dictionaries
Basics: writing functions
Reading & writing files: opening, parsing & formats
Working with numbers: numpy & scipy
Making plots: matplotlib & pylab
… if you guys want more after all of that …
Writing better code: functions, pep8, classes
Working with numbers: Numpy & Scipy (advanced)
Other modules: Pandas & Scikit-learn
Interactive notebooks: ipython & jupyter
Advanced topics: virtual environments & version control

3. reading from a file
---- smallfile.txt ----
apple
dog
hammock

4. reading from a file
# lets open and read a small file
file_handle = open("smallfile.txt", "rU")
content = file_handle.read()
print content
# close the file :)
file_handle.close()
---- smallfile.txt ----
apple
dog
hammock
reading a file
handle = open("filename", "rU")
do stuff
handle.close()

5. reading from a file
# lets open and read a small file
file_handle = open("smallfile.txt", "rU")
content = file_handle.read()
print content
# close the file :)
file_handle.close()
# we can only do this once after opening a file
file_handle = open("smallfile.txt", "rU")
content = file_handle.read()
print content
content = file_handle.read()
print content
# close the file :)
file_handle.close()
---- smallfile.txt ----
apple
dog
hammock
reading a file
handle = open("filename", "rU")
do stuff
handle.close()

6. reading from a file
# lets read it line by line
file_handle = open("smallfile.txt", "rU")
for line in file_handle:
print "Line:", line
# close the file :)
file_handle.close()
# them hidden newline characters...
file_handle = open("smallfile.txt", "rU")
for line in file_handle:
print len(line)
# close the file :)
file_handle.close()
Reading a file, line by line
handle = open("filename", "rU")
for line in handle:
do stuff
handle.close()

7. reading from a file
# lets read it line by line
file_handle = open("smallfile.txt", "rU")
for line in file_handle:
print "Line:", line
# close the file :)
file_handle.close()
Reading a file, line by line
handle = open("filename", "rU")
for line in handle:
do stuff
handle.close()

8. reading from a file
# lets read it line by line
file_handle = open("smallfile.txt", "rU")
for line in file_handle:
print "Line:", line
# close the file :)
file_handle.close()
# them hidden newline characters...
file_handle = open("smallfile.txt", "rU")
for line in file_handle:
print len(line)
# close the file :)
file_handle.close()
---- smallfile.txt ----
applen
dogn
hammockn
Reading a file, line by line
handle = open("filename", "rU")
for line in handle:
do stuff
handle.close()

9. reading from a file
# lets read it line by line
file_handle = open("smallfile.txt", "rU")
for line in file_handle:
print "Line:", line
# close the file :)
file_handle.close()
# them hidden newline characters...
file_handle = open("smallfile.txt", "rU")
for line in file_handle:
line_cleaned = line.strip()
print line
# close the file :)
file_handle.close()
---- smallfile.txt ----
applen
dogn
hammockn
Reading a file, line by line
handle = open("filename", "rU")
for line in handle:
line_cleaned = line.strip()
do stuff
handle.close()

10. writing to a file
# lets read it line by line
file_handle = open("myfile.txt", "w")
file_handle.write("My name is Marc")
# close the file :)
file_handle.close()
# we can keep on writing to the file while its open
file_handle = open("myfile.txt", "w")
file_handle.write("My name is Marc.")
file_handle.write("It's a fine day.")
file_handle.write("People open windows..")
# close the file :)
file_handle.close()
removing the "n"
handle = open("filename", "w")
handle.write(some_string)
handle.close()

11. writing to a file
# lets read it line by line
file_handle = open("myfile.txt", "w")
file_handle.write("My name is Marc")
# close the file :)
file_handle.close()
# we can keep on writing to the file while its open
file_handle = open("myfile.txt", "w")
file_handle.write("My name is Marc.n")
file_handle.write("It's a fine day.n")
file_handle.write("People open windows.n")
# close the file :)
file_handle.close()
removing the "n"
handle = open("filename", "w")
handle.write(some_string)
handle.close()

12. writing to a file
# lets read it line by line
file_handle = open("myfile.txt", "w")
file_handle.write("My name is Marc")
# close the file :)
file_handle.close()
# we can keep on writing to the file while its open
file_handle = open("myfile.txt", "w")
file_handle.write("My name is Marc.n")
file_handle.write("It's a fine day.n")
file_handle.write("People open windows.n")
# close the file :)
file_handle.close()
# lastly, we can ONLY write strings:
file_handle = open("myfile.txt", "w")
file_handle.write(10000) # will not work
file_handle.write("10000" + "n") # is better
# close the file :)
file_handle.close()
removing the "n"
handle = open("filename", "w")
handle.write(some_string)
handle.close()

13. exercises!
- Write function that takes three inputs (numbers x, y and z), and produces the
result of : a + b - c. Use return to be able to store and use the value later.
version 2: as above, but if no numbers for b or c are specified, use 5 and 10 as default
values.
---- testfile.txt ----
apple
dog
hammock

14. exercises!
words.txt
- Get the file “words.txt”.
- How many words are there in the file?
- How often does the word “megacycle” occur?
numbers.txt
- Get the file “numbers.txt”.
- How many numbers are there in the file?
- What is the sum of all of the numbers?
mydata.txt
- Create a program that asks a user for the a)
Name, b) favourite color and c) the average
flight speed of a swallow, and saves these to a
text file (see exaple).
---- output.txt ----
Name: Marc
Favourite Color: Orange
Average speed of swallow: 12