I got the link for the Drosophila melanogaster ( ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.9_FB2008_06/fasta/ ) and have a doubt if "dmel-all-chromosome-r5.9.fasta.gz" is the file of whole genome.
For Drosophila yakuba, I think this link ( ftp://ftp.flybase.net/genomes/Drosophila_yakuba/dyak_r1.3_FB2011_08/fasta/ ) and the file dyak-all-chromosome-r1.3.fasta.gz is the whole genome file.
Please let me know if I am wrong.