Transpose For Tab-Delimited File?

Question: Transpose For Tab-Delimited File?

9.6 years ago by

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

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modified 9.6 years ago by Anton Nekrutenko ♦ 1.7k • written 9.6 years ago by Elaine Angelino • 20

9.6 years ago by

Cook, Malcolm • 30

Cook, Malcolm • 30 wrote:

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 ________________________________________ 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

ADD COMMENT • link written 9.6 years ago by Cook, Malcolm • 30

9.6 years ago by

Anton Nekrutenko ♦ 1.7k

Penn State

Anton Nekrutenko ♦ 1.7k wrote:

Dear Elaine: Suppose you have a list of SNP like this: SNP Individual A 1 B 1 C 1 A 2 D 2 E 3 If you use Group tool (Join, Subtract, Group -> Group) with parameters as shown in the attached figure you will get this: 1 ['A', 'B', 'C'] 2 ['A', 'D'] 3 E It does print these brackets for the moment, but this will be fixed once the Galaxy site in updated on Monday. Let me know if this helps. anton

ADD COMMENT • link written 9.6 years ago by Anton Nekrutenko ♦ 1.7k

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