Extracting information from data

This practice will continue work on the two data files created in Working with text (data) file. The aim is to present how to extract interesting information out of the data, using some simple but powerful command-line tools of Linux.

You should have the following two files in the present working directory:

$ cat score_math.dat
Thomas 81
Percy 65
Emily 75
James 55

$ cat score_lang.dat
Thomas 53
Percy 85
Emily 70
James 65

Data sorting

If we wonder who has the highest score in the language course, a way to get the answer is applying the sort command on the text file. For example,

$ sort -k 2 -n -r score_lang.dat
Percy 85
Emily 70
James 65
Thomas 53

Here we use option -k to sort data on the second column, -n to treat the data as numerical value (instead of text characters by default), and make the sorting decendent with option -r. Voila, Percy has the highest score in the language class.

Data processing

Using the awk, a pattern scanning and processing language, one can already perform some statistical calculation on the data without the need of advanced tools such as R. The example below shows a way to calculate the arithmetic mean of the score in the language class.

$ awk 'BEGIN {cnt=0; sum=0;} {cnt += 1; sum += $2;} END {print "mean:", sum/cnt}' score_lang.dat
mean: 68.25

The example above shows the basic structure of the awk language. It consists of three parts. For the explanation here, we call them the pre-processor, processor and post-processor. They are explained below:

  • Pre-processor starts with a keyword BEGIN followed by a piece of codes enclosed by the curly braces (i.e. BEGIN{ ... }). It defines what to do before awk starts processing the data file. In the example above, we initiate two variables called cnt and sum for storing the number of students and the sum of the scores, respectively.
  • The context of the processor is merely enclosed by the curly braces (i.e. { ... }), and it follows right after the pre-processor. The processor defines what to do for each line in the data file. It uses the index variables to refer to the data in a specific column in a line. The variable $0 refers to the whole line; and variables $n to the data in the n-th column. In the example, we simply add 1 to the conunter cnt, and increase the sum by the score taken from the 2nd column.
  • Post-processor is initiated with a keyword END with context enclosed again by another curly braces (i.e. END{ ... }). Here in the example, we simply calculate the arithmetic mean and print it.

Data filtering

One can also use awk to create filters on the data. The example below selects only those with score lower than 70.

$ awk '{ if ( $2 < 70 ) print $0}' score_math.dat
Percy 65
James 55

Data processing pipeline

Every running command is treated as a process in the Linux system. Every process is attached with three data streams for receiving data from an input device (e.g. a keyboard), and for printing outputs and errors to an output device (e.g. a screen). These data streams are technically called STDIN, STDOUT and STDERR standing for the standard input, standard output and standard error, respectively.

An import feature of these data streams is that the output stream (e.g. STDOUT) of a process can be connected to the input stream (STDIN) of another process to form a data processing pipeline. The very symbol for constructing the pipeline is |, the pipe.

In the following example, we assume that we want to make a nice-looking table out of the two score files. The table will list the name of the student, the score for each class, and the total score of the student.

Firstly we have to put the data from the two text files together, using the paste command:

$ paste score_lang.dat score_math.dat
Thomas 53    Thomas 81
Percy 85     Percy 65
Emily 70     Emily 75
James 65     James 55

But the output looks ugly! Furthermore, it’s just half way to what we want to have. It is where the process pipeline plays a role. We now revise our command to as the follows:

$ paste score_lang.dat score_math.dat | awk 'BEGIN{print "name\tlang\tmath\ttotal"; print "---"} {print $1"\t"$2"\t"$4"\t"$2+$4}'
name    lang    math    total
---
Thomas  53      81      134
Percy   85      65      150
Emily   70      75      145
James   65      55      120

Note

In the Linux shell, the string "\t" represents the Tab key. It is a way to align data in a column.

Here the pipeline is constructed in such that we firstly put together the data in the two files using the paste command, and connect the output stream of it to the input stream of the awk command to create the nice-looking table.

Saving output to file

When you have processed the data and produced a nice-looking table, it would be a good idea to save the output to the file rather than print to the screen. Here we will discuss another important feature of the STDOUT and STDERR data streams: the output redirection.

The following command will produce the nice-looking table again, but instead of printing table to the terminal, it will be saved to a file called score_table.txt by redirecting the output.

$ paste score_lang.dat score_math.dat | awk 'BEGIN{print "name\tlang\tmath\ttotal"; print "---"} {print $1"\t"$2"\t"$4"\t"$2+$4}' > score_table.txt

Tip

Output redirection with > symbol will override the content of an existing file. One could use the >> symbol to append new data to the existing file.

Note that the above command only redirects the STDOUT stream to a file, data to the STDERR stream will still be printed to the terminal.

There are two approaches to save the STDERR stream to file:

  1. Merge STDERR to STDOUT
$ paste score_lang.dat score_math.dat | awk 'BEGIN{print "name\tlang\tmath\ttotal"; print "---"} {print $1"\t"$2"\t"$4"\t"$2+$4}' > score_table.txt 2>&1
  1. Save STDERR to separate file
$ paste score_lang.dat score_math.dat | awk 'BEGIN{print "name\tlang\tmath\ttotal"; print "---"} {print $1"\t"$2"\t"$4"\t"$2+$4}' 1>score_table.txt 2>score_table.err