transposing marker data

Quite frequently one may find marker data ordered in this way:

alegarra@genotoul2 ~/save/progs $ cat ex_rachel

 1 a b

 1 b b

 1 c c

 2 b b

 2 c c

 2 d d

 3 a b

 3 b b

 3 c c

e.g. there are three animals (1 to 3) and three markers. Rachel and I would like them to be formatted one animal per line and markers one after each other, in this way:

alegarra@genotoul2 ~/save/progs $ cat out

         1 ab bb cc 

         2 bb cc dd 

         3 ab bb cc 

This is conceptually simple if animals are sorted:

1. Read a line
2. If the animal is the same as the old one, print the markers after the previous one
3. If the animal is different, start a new line, print the animal and the markers.
4. Add special cases for the first and last line

Here is an awk implementation

alegarra@genotoul2 ~/save/progs $ cat SNPcol2line.awk 

#! /bin/awk -f

# this program reads genotypes in one line per locus

# then puts them as

# individual allele1 allele2 allele1 allele 2

#

BEGIN{

idold=0

i=0

}

{

id=$1

# if new animal

if(id!=idold){

if(idold!=0){

# close previous line

printf("\n")

}

# write new id

printf("%10s%1s",id," ")

idold=id

}

printf("%1s%1s%1s",$2,$3," ")

}

END{

# last individual

printf("\n")

}

which works:

alegarra@genotoul2 ~/save/progs $ ./SNPcol2line.awk ex_rachel 

         1 ab bb cc 

         2 bb cc dd 

         3 ab bb cc