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require 'formula'
class Blat < Formula
homepage 'http://genome.ucsc.edu/FAQ/FAQblat.html'
url 'http://users.soe.ucsc.edu/~kent/src/blatSrc35.zip'
sha1 'a2cae7407e512166bf7b1ed300db9be6649693bd'
def install
bin.mkpath
system "make", "MACHTYPE=darwin", "BINDIR=#{bin}"
end
def test
mktemp do
Pathname.new('db.fa').write <<-EOF.undent
>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
EOF
Pathname.new('query.fa').write <<-EOF.undent
>spam
CLYTHIGRNIYYGSY
EOF
system "#{bin}/blat", "-prot", "db.fa", "query.fa", "out.fa"
system "cat out.fa | grep spam"
end
end
end
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