Variables, Perl

The script uses Perl and ClustalW. If it fails to execute correctly, make sure these packages are installed on the machine, and are accessible from the command-line. In Unix, this may involve adding the directories that contain the ClustalW and Perl executables to the PATH environment variable. In Windows, it is advised to place the ClustalW executable in the current directory. Also, this scripts involves computationally costly alignments and may take several hours to complete. 

The Perl programs are installed to /usr/local/share/RNAz/perl. To make these programs available from other locations, the user can either add this directory to the PATH of executables environment variable or copy the Perl programs to an existing directory already in the PATH. Note 2 describes how to run Perl programs. 

Alternatively, the directory with the Perl programs can be added to the PATH variable by editing the. bashrc or. cshrc file in the home directory. 

On a Windows system the Perl programs should work if Perl has been installed as described in Subheading 2., Point 3. and the Path variable has been set as described in Subheading 3.1.2. 

To run the Perl programs, install the Perl interpreter from www.activestate.com. Choose the latest ActivePerl MSI installer package for Windows and simply follow the installation instructions. Be sure to selecte the Add Perl to the PATH environment variable and Create Perl file extension association options during installation. 

Notice that the mechanism for passing arguments is identical to an ordinary perl function - using the variable. The return value is simply a string. 

In this code snippet, the connection would already have been established and stored in the variable con. The con.prepareStatement method recognizes the use of the placeholder. The st. setlnt and st. setDouble methods are more specific than in the perl example, requiring the integer or double data type. 

The bind columns function requires as many perl variables as there are columns in the select statement. The names used here are indicative of the columns selected, making the code more understandable. The use of bind columns is also very efficient. 

Variables provide temporary storage for strings, numbers, and other values. In Perl, variables are arbitrary names preceded by a dollar sign. Examples of valid variable names are shown below. 

Perl variables are case sensitive. In the list above, x is one variable, and X is a different one entirely. 

Variable interpolation only extends to the contents of the variable itself. Perl will not try to evaluate arithmetic expressions or other programming statements that are embedded in double-quoted strings. For example, the statements... 

Finally, because adding a value to a variable and storing the smn back into the same variable is such a common operation, Perl provides the shortcnt operator -t = (read as plus equals ). This operator takes a numeric value on its right side, adds it to the contents of the variable on its left side, and stores the resnlt back into tbe same variable, all in one graceful step. Taking advantage of this feature gives statements of the form... 

Previous examples have worked with single-valued scalar variables only. However, Perl has the ability to work with multivalued variables as well. There are two basic multivalued variables, named arrays and hashes. An array is a list of data values indexed by number. A hash is a list of data values indexed by string. Both are very easy to use and incredibly handy. To imderstand arrays, consider how one might keep track of a large number of identifiers, such as clone names. With scalar variables, one approach could be to assign each clone name to a different variable ... 

This will—and should—look strange at first. The numeral in the square brackets, [ 2 ], is the index. Perl numbers its arrays starting with zero, so the first item is actually index 0, the second item is index 1, and the third item is index 2. Any expression can be placed within the square brackets, as long as that expression ultimately evaluates to an integer. As an example, if a scalar variable i contains a number, to address the next element in the series, it could be referred to as clones [ i-l-1 ]. More mystifying, however, is the at the beginning of the array name. What happened to clones ... 

Perl lists are closely related to arrays. Lists are a set of constants or variables enclosed in parentheses. An example of a list of strings would be ("one", "two", "buckle my shoe"), whereas an example of a list of variables would be ( a, b, c). A list that combines variables, constant strings, and constant numbers might be something like ( a, "the Roman empire", 3.141592 6, ipath). Lists can be thought of as being related to array variables in the same way that the constant 123.4 might be related to the scalar variable total. 

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