The following will loop through all lines of the input file (assuming you opened the file prior to calling the sub), populate the array, then return the array. I think your code was exiting the sub after reading only one line. 
sub get_oligo_seqs{
    my ($fh) = shift;
    my @seqs;
    while(<$fh>){
        my @fields = split /\t/;
        my $oligos = $fields[1];
        push(@seqs,($oligos));
    }
    return @seqs;
}

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In reply to Re^3: printing sub return values to a file by toolic
in thread printing sub return values to a file by lomSpace

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