Elaine, et al,

Here is a small perl script that might help you. It uses the perl module Array::Transpose.

#!/usr/bin/env perl

# PURPOSE: output the tab-delimited transpose of whitespace-delimited # matrix. Take input from STDIN unless -t provided, in which case use # the test __DATA__ (below). # AUTHOR: malcolm_cook@stowers.org

use strict; use warnings; use Getopt::Std; use Array::Transpose; our $opt_t; getopts('t'); *ARGV=*DATA if $opt_t; my @L; while (<>) { push(@L,[split]); } local($,,$)=("\t","\n"); print @$_ foreach transpose(@L); exit 0; __DATA__ a b c d 1 2 3 4

________________________________________ From: galaxy-user-bounces@bx.psu.edu [galaxy-user-bounces@bx.psu.edu] On Behalf Of Elaine Angelino [elaine.angelino@gmail.com] Sent: Thursday, April 16, 2009 5:56 PM To: galaxy-user@bx.psu.edu Subject: [galaxy-user] transpose for tab-delimited file?

hi there!

i'm very new to galaxy and it looks very cool.

short version of my question: is there a way to take the transpose of a tabular file?

longer:

i have a tab-delimited file of SNP data, where each row corresponds to a SNP and each column corresponds to an individual (or other attribute with per-SNP information, ex. chromosome or gene information).

for example, i would like to make a tab-delimited file where each row corresponds to an individual and each column corresponds to a SNP. then i would like to convert to hapmap format, etc.

thanks for any help!

elaine