renumbering individuals

Renumbering individuals in pedigree files

Author(s)

Stefan Gaget of Institute of Biologie of Lille, France (email: gaget@mail-good.pasteur-lille.fr )
motivation

The individual ID (second column in LINKAGE pedigree file) may jump around: 4, 8, 13,14... This script is to renumber these individuals sequentially starting from No.1: 1,2,3...

set up

You need a LINKAGE pedigree file which may look like this:


....
3       4       0       0       1       2344    .....
3       6       0       0       2       2345    .....
3       3       4       6       1       2346    .....
3       8       4       6       1       2347    .....
....

the Perl script (renum.pl)

output

The output is the new LINKAGE pedigree file with the renumbered individual IDs (sequentially starting from 1):


....
3       1       0       0       1       2344    .....
3       2       0       0       2       2345    .....
3       3       1       2       1       2346    .....
3       4       1       2       1       2347    .....
....

This is a companion page for W Li, F Haghighi, "Perl as a tool for linkage analysis", American Journal of Human Genetics, supplement to vol 65, page A260 (1999) (poster number 1452 at the Annual Meeting of American Society of Human Genetics 1999, San Francisco, CA)