\HeaderA{makeAnnotations}{Function used to produce the annotation datasets provided
by the ann.Dmelanogaster.FlyBase.r51 package}{makeAnnotations}
\keyword{manip}{makeAnnotations}
\begin{Description}\relax
[TODO: Put a description]
\end{Description}
\begin{Usage}
\begin{verbatim}
  makeAnnotations(srcdir=".", destdir=".")
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{srcdir}] Path to the directory where the GFF files have been downloaded.

\item[\code{destdir}] Path to the directory where to save the generated annotation datasets.

\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\end{Details}
\begin{Value}
\end{Value}
\begin{Author}\relax
H. Pages
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{getAnnGenes}{getAnnGenes}},
\code{\LinkA{getAnnExonParents}{getAnnExonParents}},
\code{\LinkA{getAnnExons}{getAnnExons}},
\code{\LinkA{EXON2GENE}{EXON2GENE}},
\code{\LinkA{GENE\_ID2NAMES}{GENE.Rul.ID2NAMES}},
\code{\LinkA{GFFutils}{GFFutils}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  # Here is how the annotation datasets coming with the
  # ann.Dmelanogaster.FlyBase.r51 package were made:
  #
  #   1) From a Unix-shell, run the scripts provided in inst/scripts in
  #      a 'tmpdir':
  #        download-gff.sh && extract-gff.sh && clean-gff.sh && check-gff.sh
  #
  #   2) From R, call 'makeAnnotations(tmpdir)' where 'tmpdir' is the 
  #      directory containing the "clean" GFF files produced at 1).
\end{ExampleCode}
\end{Examples}

