2.5 Commands for data processing

Linux provides plenty of tools to study, filter and modify data files. These tools are often useful when data files need to be modified from one format to another or when specific data needs to be extracted from large data sets. However, plain linux tools have their limitations. If you are going to do more complex data management, scripting languages like Python and Perl may be more efficient tools to use. In the case of numerical data many application programs, for example MatLab and R, provide tools for both complex analysis tasks and automating the analysis.

2.5.1 Grep selects rows that match a given string

The grep command is used to select rows from a file. This command is very useful for picking data from large files, however using grep requires that you are well aware of the contents of the file you are working with. The basic syntax of grep is:

grep pattern target_file
This command goes through the target file and prints out rows that contain the given search pattern.
For example, say we have a file called authors.txt that contains following rows:
Eeva Pekkanen. Oulu 50
Markus Aho. Turku 50
Pekka Niemi. Tampere 26
Leena Virtanen. Kuopio 32
In that case, the command :
grep Pekka authors.txt
Would print two rows:
Eeva Pekkanen. Oulu 50
Pekka Niemi. Tampere 26

as also Pekkanen matches the search string Pekka. If we want to use full names as search strings, including the space character between the names, we need to embrace the search string within quotation marks.

grep "Pekka Niemi" authors.txt
prints out just:
Pekka Niemi. Tampere 26
An inverse selection is done using option -v . For example, the command:
grep -v Pekka authors.txt
prints out :
Markus Aho. Turku 50
Leena Virtanen. Kuopio 32
By default grep is case sensitive and thus the command:
grep pekka authors.txt
would not result any hits. With the option -i , grep ignores the difference between upper and lower case letters.
grep -i pekka authors.txt
prints again:
Eeva Pekkanen. Oulu 50
Pekka Niemi. Tampere 2

Grep interprets the given search string as a regular expression, where some characters have a special meaning and they are interpreted as part of the regular expression string. The same regular expression syntax is used with awk and sed commands too. For example:

  • the dot (.) is used to define any single character.
  • ^ means the beginning of a line
  • $ means the end of a line
  • [ ] matches any of the characters inside the brackets. For example [abc] would match a,b or c.
  • [^ ] matches any character, except the characters inside the brackets. For example [^abc] would select all rows that contain also other characters than just a,b and c.
  • * matchs zero or more of the preceding character or expression
  • \{n,m\} matches n to m occurrences of the preceding character or expression

For example:

grep "i." authors.txt
prints the following two rows as the search criterion is in this case: i and any other character.
Pekka Niemi. Tampere 26
Leena Virtanen. Kuopio 32
In these kind of situations you can use the backslash character (\) to define that the following character should not be interpreted as part of a regular expression. Thus the command:
grep "i\." authors.txt
now returns just one row:
Pekka Niemi. Tampere 26

Grep is often used to filter the output of other commands. For example, to so see what files in the current directory are from the year 2010 we can use command ls -l and pipe it to grep. With grep we can select from the output only those rows that include the string 2010. However, some file names may contain the string "2010", even though they are not dating from 2010. To make the filtering more effective, we can use quotation marks to include the space before and after the year number to the search string. ls -l | grep " 2010 ". In addition to the normal grep command, there exist several other grep-like tools. For example zgrep or bzgrep can be used to search rows from files compressed with gzip or bzip2. On Taito, there is also a tool called agrep that can be used to select rows that can have certain amount of mismatches to the search string.  

 

2.5.2 Using sed to select rows by row number

The stream editor sed can be used to select and modify rows from a text file. Many of the grep operations, described above can be done with sed too. The sed command is discussed a bit more in detail in the chapter 2.5.8 Replacing characters and strings. Here we only show how sed can be used to select a certain row from a file. For example the third row of the file authors.txt could be selected with command sed -n "3"p authors.txt In this case the result is: Pekka Niemi. Tampere 26 This row picking method is handy in loops. For example the following loop would print out three rows from the example file:

for i in 4 3 2
do
set row=(`sed -n "$i"p authors.txt `)
echo "Row $i looks like: $row"
done

 

2.5.3 Simple column selection with cut

The cut command provides a simple tool to select character regions (-c ) or columns (-f) from a linux text file. When selecting by character numbers the syntax of the command is:

cut -cstart-end
For example command:
cut -c2-5 authors.txt

prints text from the second to the fifth character from each row of the authors.txt file. Assuming this is the same file that was used in the grep examples above, the output looks like:

eva
arku
ekka
eena

With option -f columns can be printed. By default tabulator is used and the column delimiter, other delimiters can be defined with the option -d . For example, to select the first and third column (-f1,3) from the file authors.txt, we need to define space as the delimiter (-d " "):

kkayttaj@c305:~> cut -d " " -f1,3 authors.txt
Eeva Oulu
Markus Turku
Pekka Tampere
Leena Kuopio

 

2.5.4 Using awk to work with columns

Awk is a scripting language that can be used to process text files in linux environments. Awk is a rather old programming language, and nowadays more modern scripting tools are normally used for creating data management scripts. However, due to very simple syntax awk is still frequently used to perform simple filtering and editing tasks. In this guide we don't provide a general overview to awk programming. Instead we show some examples how awk can be used to work with files or as a part of linux command pipeline. In the simple command line usage, the basic syntax of awk is: awk -F "field delimiter" 'statement {command1}{command2}...' infile.dat Awk can be used to process the input data as columns. By default awk uses both space and tab characters as column delimiters (note that unlike the cut command, awk interprets all successive spaces as one single column separator). The columns can be accessed in awk with variables named $1 (the first column), $2 (second column), $3 (third column) etc. $0 can be used to refer to "all the columns". For example, the following command prints the first and third column of the file authors.txt.

kkayttaj@c305:~> awk '{print $1 $3}' authors.txt
EevaOulu
MarkusTurku
PekkaTampere
LeenaKuopio

In the example above, the fields are not separated in the output. To do that you add the space or tabulator character (\t) to the print statement. You can also add other text to the output. Then next example adds text and changes the order of columns.

kkayttaj@c305:~> awk '{print "Location: "$3"\t Name: "$1" "$2}' authors.txt
Location: Oulu   Name: Eeva Pekkanen.
Location: Turku  Name: Markus Aho.
Location: Tampere   Name: Pekka Niemi.
Location: Kuopio    Name: Leena Virtanen.

A more sophisticated way to do the modification above is to use the printf command instead of print. The syntax of the awk printf command is similar to that of the linux command printf discussed in chapter 2.7.5.

awk '{printf "Location:%s\tName: %s %s \n", $3, $1, $2}' authors.txt

One of the nice features of awk is that you can use conditional statements in the command. You can compare both strings and numbers. For example, the following command prints data only when the third column is "Tampere"

kkayttaj@c305:~> awk '{if ( $3 == "Tampere")  print "Location: "$3"\tName: "$1" "$2}' authors.txt
Location: Tampere       Name: Pekka Niemi.
Alternatively, the condition could be defined in the statement part before the awk commands:
awk ' $3 == "Tampere" {print "Location: "$3"\t Name: "$1" "$2}' authors.txt

If the columns contain numerical values, awk can also do numerical operations. For example, let's use awk to calculate how much disk space jpg image files take in the current folder. We can first list the jpg files with command: ls -l *.jpg

kkayttaj@c305:~> ls -l *.jpg
-rw-------+ 1 kkayttaj csc   85112 Dec 19  2002 Image_2.jpg
-rw-r--r--+ 1 kkayttaj csc  105542 Nov  6  2006 Screen.jpg
-rw-r--r--+ 1 kkayttaj csc  167598 May 15  2008 casa1.jpg
-rw-------+ 1 kkayttaj csc  550031 Mar 25  2008 hexa.jpg
-rw-------+ 1 kkayttaj csc  869534 Dec 23  2005 img.jpg
-rw-------+ 1 kkayttaj csc   19159 Jul 23  2003 kuva.jpg
-rw-r-xr-x+ 1 kkayttaj csc  433268 Dec 23  2005 plot3.jpg
-rw-------+ 1 kkayttaj csc 1591444 Jan 26 12:27 copy.jpg
To sum up the values of the file sizes in the fifth column, we pipe the output to awk:
kkayttaj@c305:~>ls -l *.jpg | awk '{total+=$5} END {print "JPG files in total: "total}'
JPG files in total: 3821688

Note that in the awk command above the total is a variable name used by awk. The END defines that the following command is executed only when all input lines are processed. In the second awk computing example, we calculate and display a cumulative sum and average of ages from the file authors.txt.

awk '{ tot_age = tot_age + $4 }{ aver=tot_age/NR}{ print $0 " cumulative age sum:" tot_age " average:" aver}' authors.txt
Here we use the automatic NR row count variable to calculate average of the age. This command prints out:
Eeva Pekkanen. Oulu 50 cumulative age sum:50 average:50
Markus Aho. Turku 50 cumulative age sum:100 average:50
Pekka Niemi. Tampere 26 cumulative age sum:126 average:42
Leena Virtanen. Kuopio 32 cumulative age sum:158 average:39.5

 

2.5.5 Using sort to order rows

The sort command can be used to order rows of a text file or other input data into alphabetical or numerical order. The syntax of the sort command is simple: sort -options files_to_sort By default the sort command orders the rows of the file alphabetically using case sensitive sorting. With option -f, case insensitive sorting is performed. If the data contains columns, separated by the space or tabulator character you can ask the sort command to use a certain column (or columns) for ordering the data. The columns to be used can be selected with the option -k column number. For example, to sort the data in the file authors.txt (the example file used previously in this chapter), according to the family names that are located in the second column, you use command:

sort -k 2 authors.txt
That prints out:
Markus Aho. Turku 50
Pekka Niemi. Tampere 26
Eeva Pekkanen. Oulu 50
Leena Virtanen. Kuopio 32

You can also define other column separators with option -t separator. Note that by default, sort orders also numbers alphabetically. Option -n makes sort to use a numerical ordering instead. The option -r reverses the order. Numerical sorting according to the fourth column can now be done with the command

sort -k4 -n authors.txt
Result:
Pekka Niemi. Tampere 26
Leena Virtanen. Kuopio 32
Eeva Pekkanen. Oulu 50
Markus Aho. Turku 50

You can also define that several columns will be used for sorting. For example, the following command uses the numerical order of the fourth column as the primary sorting criteria ( -k4n ). In cases where several rows have the same value in the fourth column, the alphabetic order is used as the secondary sorting criteria (-k2)

sort -k4n -k2 authors.txt
In this case, the result is:
Pekka Niemi. Tampere 26
Leena Virtanen. Kuopio 32
Markus Aho. Turku 50
Eeva Pekkanen. Oulu 50

The sorted data can be saved to a new file either by using option -o or redirecting the standard output to a file with >. For example, both commands below create the same file containing the sorted version of the file authors.txt.

sort -k4n -k2 -o authors_sorted.txt authors.txt
sort -k4n -k2 authors.txt > authors_sorted.txt

 

2.5.6 Removing duplicate rows with uniq

The command uniq is often used in combination with the sort command to remove redundancy from a data set. The uniq command checks if two successive rows in the input file or standard input are identical. By default, uniq removes the successive duplicate rows. Note that uniq does not check if an identical row exists elsewhere in the input. Because of that, the data is normally sorted before applying the uniq command. As an example, say we have a file called names that contains following rows:

Pekka
Pekka
Leena
Markus
Eeva
Leena
Running command:
uniq names
will give following output:
Pekka
Leena
Markus
Eeva
Leena

In the output, row "Leena" still occurs twice as the two identical names were not in the successive rows. The situation can be fixed by sorting the rows before uniq is applied, for example:

sort names | uniq
prints the following output
Eeva
Leena
Markus
Pekka

It is often useful to know, how many identical rows were found. This information can be added to the output of uniq with the option -c. For example:

sort names | uniq -c
Gives the following output:
      1 Eeva
      2 Leena
      1 Markus
      2 Pekka

Note that also space and tabulator characters are used when uniq compares the rows. Thus a row containing "Leena" is not identical to a row containing "Leena ". By default uniq is case sensitive, but using option -i makes uniq to ignore the cases and consider "leena" and "Leena" to be identical. However, note that if you use case insensitive uniq, you may need to do also the sorting in case insensitive mode using command sort -f.

2.5.7 Replacing characters with tr

The tr command ("translate") is used to replace individual characters. Tr reads the standard input and writes the translated data to the standard output. The syntax of tr command is

tr search_character replacement_character
For example, dots (.) in the file authors.txt could be replaced with commas (,) with command:
 tr "." "," < authors.txt
this prints out:
Eeva Pekkanen, Oulu 50
Markus Aho, Turku 50
Pekka Niemi, Tampere 26
Leena Virtanen, Kuopio 32

Note that the command above does not modify the original input file in any way. In the examples here, the results of tr command are printed to the screen. When tr is used to modify large files, the output should of course be redirected to a new file instead of the screen. For example:

tr "." "," < authors.txt > authors_mod.txt
If you would like to remove the dots, you could use the option -d with just one character set, telling what characters are to be removed:
tr -d "."  < authors.txt

Note that the tr translates individual characters, not words. Thus command tr "Oulu" "Turku" would not change the word "Oulu" to "Turku". Instead it would do the following character conversions to all the text O->T, l->r, u->k. The tr command can do translations with special characters like tabulator (\t) and newline (\n) and with predefined character sets like all lower case letters ([:lower:]) and all upper case letters ([:upper:] ). For example:

tr "." "\n" < authors.txt
would replace the dots with line breaks in the file authors.txt :
Eeva Pekkanen
 Oulu 50
Markus Aho
 Turku 50
Pekka Niemi
 Tampere 26
Leena Virtanen
 Kuopio 32
Modifying the file so that all the text is written with upper case letters can be done with:
 tr "[:lower:]" "[:upper:]" < authors.txt
Resulting:
EEVA PEKKANEN, OULU 50
MARKUS AHO, TURKU 50
PEKKA NIEMI, TAMPERE 26
LEENA VIRTANEN, KUOPIO 32
Check the manual page of tr (man tr) to see the list of all special characters and character sets that tr can use.

 

2.5.8 Replacing words and strings with sed

Replacing text strings can be done with sed. Sed is a stream editor that can be used for many different text processing operations. Sed reads string data, either from a file or piped from another command, and does the edition operations defined by the user and then prints the edited string to the standard output. Sed is a very powerful tool for automatic text editing, though a bit hard to learn. In this guide we do not provide a general introduction to sed, as even a modest overview would take several pages. Instead we show few practical examples how sed can be used. Sed is commonly used with the syntax:

sed -e sed_script input-file

The sed script is typically short formulation that defines what kind of editing should be done. For example to do a replacement operation we could use the sed operation s/"search string"/"replacement string"/g. In this formulation s means search and replace operation. The g in the end of the formulation means that the replacement operation is global i.e. all matching strings will be replaced. You could replace, for example, just the first or second occurrence of the search string on a row by using number 1 or 2 instead of g. For example the operation where Oulu is replaced by Turku in the file authors.txt can be done with the command:

sed -e s/"Oulu"/"Turku"/g authors.txt
Result:
Eeva Pekkanen. Turku 50
Markus Aho. Turku 50
Pekka Niemi. Tampere 26
Leena Virtanen. Kuopio 32

Just like the grep command, sed interprets the given search string as a regular expression. This means that some characters are interpreted as special regular expression defining characters. For example the dot (.) is used to define any single character. Thus the sed command s/"."/","/g would change not just dots but all characters to commas (,). In these kind of situations you can use the backslash character (\) to tell the sed command that the following character should not be interpreted as part of a regular expression. On the other hand using the regular expressions can make sed very effective. Below are some regular expression examples applied to the authors.txt file with sed.

Example 1. Using the $ character to define the end of a line (note the single quotation marks (' ) that prevent the $ character to be interpreted as bash variable indicator) :

sed -e s/'0$'/"1 changed"/g authors.txt
Prints out:
Eeva Pekkanen. Oulu 51 changed
Markus Aho. Turku 51 changed
Pekka Niemi. Tampere 26
Leena Virtanen. Kuopio 32

 

Example 2. Using dot (.) to define any single character:

sed -e s/"e.a"/"EXA"/g authors.txt
Prints out:
EEXA Pekkanen. Oulu 50
Markus Aho. Turku 50
Pekka Niemi. Tampere 26
LeEXA Virtanen. Kuopio 32

 

Example 3. Using "^" to define beginning of a line.

sed -e s/"^P"/"START:P"/g authors.txt
Prints out:
Eeva Pekkanen. Oulu 50
Markus Aho. Turku 50
START:Pekka Niemi. Tampere 26
Leena Virtanen. Kuopio 32

 

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