C2110 UNIX and Programming
12th lesson awk- second part
Petr Kulhánek
kulhanek@chemi.muni.cz
National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno
UNIX and Programming 12th lesson
Content
> AWK
Data file analysis Regular expressions Arrays
.0 UNIX and Programming
12th lesson
Process of the Script Execution
BEGIN {
}
{
}
/PATTERN/ { }
END { }
BEGIN block (1) is executed (if it is part of the script) before the file analysis.
• Record is read from the file. By default, the record is one line of the analyzed file or stream. The record is split into fields. By default, the fields are individual words of the record.
• Block (2) is executed for the given record.
• If the record matches the pattern, the block (3) is executed
• ... potential execution of other blocks ...
Block END (4) is executed (if it is included in the script) after analysis of the whole file.
Each block is enclosed in curly braces {}. The mentioned program blocks are optional. By default, line is set as record.
.0 UNIX and Programming
12th lesson
Regular Expressions
/PATTERN/ {
If PATTERN is found in the record, the block is executed.
}
Pattern is a regular expression.
Regular expression is a language that describes the structure of the text string. It is used to search text strings and to replace parts of strings.
Examples of simple regular expressions:
TEXT      - is fulfilled if given record contains pattern TEXT (anywhere) ATEXT    - is fulfilled if given record starts with pattern TEXT TEXT$    - is fulfilled if given record ends with pattern TEXT
10 UNIX and Programming
12th lesson
Exercise
1. From the file rst.out, extract evolution of temperature in time. Plot temperature in time using gnuplot.
NSTEP = 1000      TIME(PS)   = 1.000    TEMP(K)   =      305.69 PRESS = 0.0
Etot      = 907.8481    EKtot      = 160.3711    EPtot = 747.4770
BOND      = 40.6154    ANGLE      = 273.9238    DIHED = 164.5827
1-4 NB = 14.6900    1-4  EEL = 973.2602    VDWAALS = -67.6091
EELEC    = -488.9232    EGB = -163.0629    RESTRAINT = 0.3793
EAMBER  (non-restraint)    = 747.0977
2. From the file rst.out, extract evolution of total energy (Etot), kinetic energy (EKtot) and potential energy (EPtot) in time. Plot individual energies in time using gnuplot. Verify that the sum of potential and kinetic energy equals to the total energy.
10 UNIX and Programming
12th lesson
-5-
Arrays
AWK uses associative arrays. Each element of the array can be accessed by using the key. The key may have any value or type. Key may be taken from variable.
Assigning values:
My array[key]   = value;
Obtaining values:
value = my array[key];
Examples:
i = 5;
my array[i]   = 15; print my array[i]; print my array[5];
a = "word";
my array[a]     = "value";
print my array["word"],  my array[i];
UNIX and Programming 12th lesson
Arrays,
Browsing the list of keys:
for( variable in array ) {
print array[variable];
}
Executes a loop for each key that was used save a value to the array. The key value is assigned to the variable.
Deleting a record by key:
delete array[key];
.0 UNIX and Programming
12th lesson
Exercise
1. From the file rst.out, extract evolution of temperature in time. The resulting file will not contain the last two values, which are the mean value and its fluctuations. Plot temperature in time using gnuplot.
2. From the file rst.out, extract evolution of temperature in time and calculate its average value. Compare the calculated value with the average value printed in the file rst.out. Why do the values differ?
UNIX and Programming 12th lesson