Downloading specific yeast genes in an automated manner?
These sequences do not have any standard i.d. The information in Saccharomyces Genome Database is also obsolete (2005) and does not have these identifiers.

These sequences can be found here (in the same site).

Each species has a short name:


ORGANISM        Short Name
S.cerevesiae    Scer
S. bayanus      Sbay
S. paradoxus    Spar
A. gossypii     Agos

.... and so on. 

First letter of genus name in uppercase + first 3 letters of species name in lowercase.

The fasta file (for all ORFs) is:
 www.broadinstitute.org/regev/orthogroups/nt/&lt;Shortname&gt;.fasta

From there you can use grep to retrieve the sequence.

So, if you have saved shortnames and gene names two separate files you can do something like this: 

for shortname in `cat shortname.txt`; do wget -O tmp.fa "http://www.broadinstitute.org/regev/orthogroups/nt/"$shortname.fasta; grep -A 1 -f ids.txt tmp.fa &gt;&gt; $shortname"_Select.fa"; done