Hi Peggy:
Though late, I can't resist this Perl variation:
# cat ./myalleles
#!/usr/bin/perl
use strict;
use warnings;
my ( @allele, %locus );
while (<>) {
chomp;
@allele = split /,/;
for my $n ( 1 .. @allele - 1 ) {
if ( !grep( /$allele[$n]/, @{ $locus{ $allele[0] } } ) ) {
push( @{ $locus{ $allele[0] } }, $allele[$n] );
}
}
}
for my $marker ( sort keys %locus ) {
@allele = ( @{ $locus{$marker} } );
print join ',', $marker, ( sort @allele );
print "\n";
}
1;
...using your input data:
# cat ./myalleles.data
RS1002244,1,1
RS1002244,1,3
RS1002244,3,3
RS1003719,2,2
RS1003719,2,4
RS1003719,4,4
RS757210,2,2
RS757210,2,3
RS757210,2,4
RS757210,3,3
RS757210,3,4
RS757210,4,4
...when run produces:
# ./myalleles ./myalleles.data
RS1002244,1,3
RS1003719,2,4
RS757210,2,3,4
The script reads lines of input. Commas delineate the fields of each line. The first field (zero in Perl) is used as a unique hash key to represent the locus. Alleles are then added into an array of data for each locus as long as the array for the locus under examination does _not_ already contain the allele. This eliminates duplicates immediately.
When all data has been read, the loci are sorted and listed with the alleles of each in sorted order.
Regards!
...JRF...
