NAME

       fa2dna - format fasta database for use with ANFO

SYNOPSIS

       fa2dna [ option | file ... ]

DESCRIPTION

       fa2dna reads one or more files in fasta format and reformats them into a database suitable
       for anfo(1).  The input file(s) can contain more than one sequence, and each sequence  can
       be  broken  up  into  multiple  contigs by a stretch of Ns.  All IUPAC ambiguity codes are
       fully supported.

OPTIONS

       -V, --version
              Print version number and exit.

       -o file, --output file
              Write output to file.file should end in .dna,  because  anfo  and  some  downstream
              tools  might  stumble  over a different extension.  Default is the genome name with
              the .dna extension.

       -m N, --maxn N
              Sets the maximum number of Ns to be interpreted as IUPAC ambiguity codes to N;  any
              longer stretch is interpreted as separing contigs.  Default is 2.

       -g name, --genome name
              Sets  the  genome name to name.  This name is stored in the output file and will be
              used by anfo to identify the matched genome in its output.  The genome should be  a
              prefix  of  the  output  file  name to allow downstream tools to find it.  The name
              should be short, but unique, something like "hg18" or "pt2" for human or chimpanzee
              genomes would work fine.

       -d text, --description text
              Adds text as description to the metadata.  This is purely informational.

       -v, --verbose
              Causes a progress indicator to be printed.

FILES

       /etc/popt
              The  system  wide  configuration  file  for  popt(3).   fa2dna identifies itself as
              "fa2dna" to popt.

       ~/.popt
              Per user configuration file for popt(3).

BUGS

       None known.

AUTHOR

       Udo Stenzel <udo_stenzel@eva.mpg.de>

SEE ALSO

       anfo(1), fa2dna(1) popt(3), fasta(5)