\HeaderA{readGeneInput}{Standardize reading of gene inputs}{readGeneInput}
\keyword{documentation}{readGeneInput}
\keyword{utilities}{readGeneInput}
\begin{Description}\relax
Internal function that will standardise the input of the many different form of sequences that can be used in Bioconductor.
\end{Description}
\begin{Usage}
\begin{verbatim}
    readGeneInput(gene, genename=NULL)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{gene}] 
\item[\code{genename}] 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function is not meant to be run directly by the user. It will take a number of genes either as a vector 
of characters, a path to a FASTA format file, as a vector of DNAstrings or as a readFASTA format. It will then output 
them in FASTA format for use with other functions. Optional variable genename forces a new name.

The primary objective of this function is to make the sequence input simpler for other functions.
\end{Details}
\begin{Value}
A list of all sequences and their names, in exactly the same format as obtained with the \LinkA{readFASTA}{readFASTA} function of the Biostrings package.
\end{Value}
\begin{Author}\relax
Lasse Folkersen
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{geneRegionScan}{geneRegionScan}},\code{\LinkA{plotOnGene}{plotOnGene}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

        somegene<-"ATACCTTGTAGGACCTGATGATAGATGCATAGTAATATCGTA"
        genename<-"My favourite gene"
        GeneRegionScan:::readGeneInput(somegene,genename=genename)

\end{ExampleCode}
\end{Examples}

