Genojoin 1.0 Perl Utility

 

Steve DiFazio

Oak Ridge National Laboratory

difazios@ornl.gov

Introduction

 

The genojoin perl utility converts genomap genotype output files (see genomap_readme) to Joinmap format for a ‘CP’ population type.  Simply type

 

genojoin.pl <genotypefile> > <outputfile>

 

where

 

<genotypefile> is the genomap output file in genotype format, and

<outputfile> will be in joinmap format.

 

The program will check the genotypes of the parents and output the appropriate data for joinmap analysis.

 

Perl

 

This program is written in the PERL (Practical Extraction and Reporting Language) scripting language.  Each time the program is run, the PERL interpreter is automatically invoked, and this converts the script to machine language and executes it.  Because of this, the program will work equally well on any operating system as long as the proper PERL interpreter is installed.  Fortunately, this program is available for free!

 

Instructions for Installing The PERL Interpreter

 

UNIX/Linux

 

Unix and Linux systems should already have PERL installed.  You may have to change the first line of the program to match the location of your PERL executable.  Usually you can find this by typing

where perl

Then change the line

#! /usr/local/bin/perl

to match the location of your executable.  If by any chance PERL isn’t on your system, just follow the link under the windows section and you’ll find it easily enough.

 

Windows

 

Go to the following web site and follow the directions to download the program (~9 MB):

 

http://www.activestate.com/Products/Download/Get.plex?id=ActivePerl

 

If you’re using Window 2000 or XP, you should be able to install the ‘windows MSI’ version directly.  If you’re using an earlier version of Windows, you may need to download and install the ‘windows installer’ first.

 

After downloading, double-click the file and the installation should be self-explanatory!

 

PERL will install and run completely transparently (i.e., no user interface).