bash
####################
# 12 Flies downloaded from UCSC hgdownload on 14 December 2011 using:
for g in droAna3 dreEre2 droGri2 droMoj3 dp4 droVir3 droWil1; do
    wget http://hgdownload.cse.ucsc.edu/goldenPath/droAna3/bigZips/$g.fa.gz && \
    gunzip $g.fa.gz && \
    perl -ple "s/>/>$g./" -i $g.fa
done

for g in dm3 droSim1; do
    wget http://hgdownload.cse.ucsc.edu/goldenPath/$g/bigZips/chromFa.tar.gz
    tar -xvzf chromFa.tar.gz && \
        cat chr*.fa > $g.fa && \
        perl -ple "s/>/>$g./" -i $g.fa && \
        rm chromFa.tar.gz chr*.fa
done

for g in droPer1 droSec1; do
    wget http://hgdownload.cse.ucsc.edu/goldenPath/$g/bigZips/scaffoldFa.gz && \
    gunzip scaffoldFa.gz && mv scaffoldFa $g.fa && \
    perl -ple "s/>/>$g./" -i $g.fa
done

wget http://hgdownload.cse.ucsc.edu/goldenPath/droYak2/bigZips/chromFa.tar.gz && \
     tar -xvzf chromFa.tar.gz && \
     cat 2*/* 3*/* 4/* M/* U*/* X*/* Yh/* > droYak2.fa && \
     perl -ple "s/>/>droYak2./" -i droYak2.fa && \
     rm -rf 2*/ 3*/ 4/ M/ U*/ X*/ Yh/ chromFa.tar.gz

####################
# 8 Flies downloaded from NCBI on 25 January 2012 using:
curl -O "ftp://anonymous@ftp.ncbi.nih.gov/genbank/wgs/wgs.{AFFD,AFFE,AFFF,AFFG,AFFH,AFFI,AFPQ,AFPP}.1.fsa_nt.gz"
curl -O "ftp://anonymous@ftp.ncbi.nih.gov/genbank/wgs/wgs.{AFPP}.2.fsa_nt.gz"
for f in *.fsa_nt.gz; do gunzip $f; done
# Where the mapping to species names is:
mv wgs.AFFD.1.fsa_nt droBia.fa
mv wgs.AFFE.1.fsa_nt droBip.fa
mv wgs.AFFF.1.fsa_nt droEle.fa
mv wgs.AFFG.1.fsa_nt droFic.fa
mv wgs.AFFH.1.fsa_nt droKik.fa
mv wgs.AFFI.1.fsa_nt droTak.fa
mv wgs.AFPP.1.fsa_nt droRho.1.fa
mv wgs.AFPP.2.fsa_nt droRho.2.fa
mv wgs.AFPQ.1.fsa_nt droEug.fa
cat droRho.1.fa droRho.2.fa > droRho.fa && rm droRho.1.fa droRho.2.fa
for g in droBia droBip droEle droFic droKik droTak droRho droEug; do
    perl -ple "s/^>gi\|\d+\|\S+?\|.*?(\S+),.*/>$g.\$1/" -i $g.fa
done

####################
# Repeat masking performed by using RepeatMasker and the drosophila melanogaster repeat library along with TRF to find simple repeats (this is the UCSC standard pipeline).