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Data columns

Reading data from a table and writing data to a table

After this module you can:

  • Read a list of numbers from a text file to a list
  • Calculate the average value of a list of numbers
  • Calculate the average value of the numbers of a table's column
  • Write a list of numbers to a text file

slot

We will use the file neuron_data.txt containing data on dendrites lengths:

16.38
139.90
441.46
29.03
40.93
202.07
142.30
346.00
300.00

and the file neuron_data-2.txt that contains the same data plus an extra column with the indication 1 for primary neurons and 2 for secondary neurons:

1         16.38
2         139.90
2         441.46
1         29.03
1         40.93
2         202.07
1         142.30
2         346.00
2         300.00

What do we have to do?

  • Read data columns from files
  • Store data columns to data structures (lists)
  • Convert text into numbers
  • Convert numbers into text
  • Write text to data columns (i.e. with appropriate format)

Our Goal is to beat Excel at its own game!

Some useful built-in functions

  • split() Stores elements from different columns to a list
  • unpack() Stores elements from different columns to a list using a given format
  • join() Concatenates objects from a list
  • strip() Removes blank spaces and newline characters
  • int() Converts a string into an integer
  • float() Converts a string into a floating point number
  • str() Converts an object into a string
  • repr() Converts an object into a string

Challenge #1

Write a program that reads the file with neuron lengths (neuron_data.txt) and stores neuron lengths as floating point numbers into a list.

See the solution to challenge #1

Challenge #2

Extend the program so that it read data form neuron_data-2.txt and stores primary and secondary neuron lengths to different lists.

See the solution to challenge #2

Manipulating data in the columns

  • Calculate max and min length
  • Calculate their average length
  • Calculate the standard deviation

slot

Challenge #3

Extend program 2 so that it calculates the neuron length average separately for primary and secondary neurons. Print the two averages: which neurons are on average longer?

See the solution to challenge #3

Challenge #4

Extend program 3 so that it calculates the standard deviation of the neuron length.

See the solution to challenge #4

How to write data to columns

This implies that data needs to be nicely formatted and written to a file

  • String concatenation
  • String formatting

The argument of the write() function MUST be a string

>>> out = open('data_out.txt', 'w')
>>> out.write(3)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
TypeError: expected a character buffer object
>>>

>>> out = open('data_out.txt', 'w')
>>> out.write(str(3))
>>>

An example of string concatenation using + :

out = open('data_out.txt', 'w')
out.write(str(1) + '\t' + str(16.38) + '\n')
out.close()

Challenge #5

Use two lists with data from neuron_data-2.txt to write a table identical to neuron_data-2.txt. Do it using string concatenation.

See the solution to challenge #5

String formatting

Nice output can be generated by formatting characters:

print '%d'%(77)
print '%s'%('text')
print '%4.1f'%(2.1111)

print 'The square root of %5.2f is %5.2f'%(a, math.sqrt(a))

print 'The square root of %10.2f is %5.2f'%(a, math.sqrt(a))

print "%i%s%f%s"%(1, '\t', 2.5, '\n')

import math
A = 25
S = 'The square root of {0} is  {1}'
print  S.format (a,  math.sqrt(a))

Challenge #6

Use two lists with data from neuron_data-2.txt to write a table identical to neuron_data-2.txt. Do it using string formatting.

See the solution to challenge #6

Reading and writing tables

  • Read each table column into a different list
  • Use a for loop running over the length of the list to write the elements of the lists to a file (using string concatenation or formatting)
  • You can write the columns in a different order

Match the formatting expressions and their result

slot

Challenge #7

Write a program that reads the neuron_data-2.txt file, calculates the number of primary neurons, their total length, and the shortest and the longest lengths.

Write the results to a file using string formatting.

You can repeat the exercise for secondary neurons.

See the solution to challenge #7