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How to Use the Scriptome

Are you using the Scriptome on UNIX/Mac or Windows? Decide this based on where your data is sitting. So, for example, if you're sitting at a Windows machine, using telnet (or putty, or whatever) to access a UNIX machine that has your data on it, use the UNIX tools.

Software Requirements

You do not need to install or download these tools; you just cut and paste each tool into a terminal window.

A few of the tools use Bioperl. If you do bio, you may already have Bioperl installed, but if you get an error message like "Can't find in ..." then you may need to download it from


Note: if you're sitting at a Windows machine, but your data is on a UNIX computer that you log into (with ssh, telnet, etc.) then use the UNIX tools.

On Windows machines you probably need to install Perl. It's a free download from and a one-click install.

UNIX or Mac

If you're using UNIX or Mac, you already have Perl. For a few tools, you may need to download Bioperl from

Opening a Terminal Window

Scriptome tools are little UNIX/Mac or Windows commands. You run them by cutting and pasting from the website onto the "command line". To get a command line, you need to:


Open a terminal or xterm (or telnet or Putty from elsewhere).

Mac OS X

Open a terminal window. (In the Finder, go to File->Find, and search for "Terminal". The icon looks like a computer monitor.)


Open a Command prompt: Open your Start menu, go to Run, type cmd, and click OK.

Now use the "cd" command to change directories to where your data is sitting. For example, cd my/data/directory.

Using the Tools

Example tool (help_solve_all_my_problems)

Solve all of my data manipulation problems with just one tool that takes two important parameters

$param1 Important text
$param2 Important number
Input file(s) One important file
Input file(s) Other important file
Output file Results go here

perl -e ' $param1="something"; $param2=37; print "Input files were @ARGV\n"; warn "\nRan the example tool with these parameters: $param1, $param2\n\n"; ' infile1 infile2 > outfile

As you can see, the Scriptome tools are in colored boxes. (The boxes are green for Windows, Blue for Unix. On some versions of IE, the boxes aren't colored. But they still have a dashed line around them, and a larger margin than the rest of the text.)

The parameters that you might want to change - such as filenames, which column to read in tabular data, etc. - are written in bold, red text in the box. (Most scripts have one or two input files, an output file, and one or two other parameters. Others have fewer parameters.) The other stuff is gray, which means you can safely ignore it, unless you want to learn some Perl.

Use the form above the box to edit the parameters as needed. When you change the text in the form, the text of the tool in the colored box will be updated.

Cut and paste the text of the tool - i.e., everything in the colored box - onto the command line. Go ahead, try it! Then look at what the tool prints to the screen, and what it puts in the output file you specified. (This tool doesn't actually care whether the input files exist.)

The "Expand code" button inside the colored box is not required for using the tool. If you click it, the tool's Perl code is split onto many lines. You won't be able to cut and paste this tool onto the command line, but this format is much more readable. This is useful for people who want to see exactly what the tool is doing, or learn a bit of Perl. Click the "Shrink code" button to collapse the tool again.

The tools for Windows are a tiny bit different from the Unix/Mac tools. (See the FAQ.) Use the links in the top left of the page to switch from Unix/Mac to Windows and back. The page colors (and the upper left of the page) will let you know which section of the site you're in.

Tabular Data

All scripts that work on tabular data assume the data is tab-separated. Use a Change script to change, e.g., comma-separated data to tab-separated before using these scripts. Or save Excel files as tab-separated.

When working with tabular data, remember that the first column is called column 0, NOT 1. (Sorry.) The second column is column 1, the third is 2, etc. As a shortcut, the last column can also be referred to as column -1, second-to-last column is -2, etc.

More tips are available on the Tips Page.

Scriptome Protocols

A protocol is a series of steps to solve a biological problem, such as extracting DNA: A Scriptome protocol is a series of steps that are used to solve a data manipulation problem. Each step is carried out by running a Scriptome tool - often by running the tool on the output generated in an earlier step in the protocol.

Using Protocols

This site has "canned" protocols for Sequence Analysis or Microarray Data. The protocols are just lists of atoms in a row, and are used the same way an atom is. Namely, cut and paste everything in the colored box onto the Unix/Mac/Windows command line.

If you're less brave, cut and paste the single tools one at a time. This will allow you to edit each tool before executing it.

If you want to edit the filenames or other parameters in a protocol, you'll need to paste the protocol into a text editor or Word, edit, and then cut and paste from there onto the command line.

Building or Editing Protocols

You can add a tool into the middle of a protocol by (using a text editor, as described above and) pasting the tool in. Or you can build a protocol from scratch.


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