SYNOPSISfa2dna [ option | file ... ]
DESCRIPTIONfa2dna 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.
- -V, --version
Print version number and exit.
- -o file, --output file
Write output to
should end in
and some downstream tools might stumble over a different
extension. Default is the genome name with the
- -m N, --maxn N
Sets the maximum number of
to be interpreted as IUPAC ambiguity codes to
any longer stretch is interpreted as separing contigs. Default is 2.
- -g name, --genome name
Sets the genome name to
This name is stored in the output file and will be used by
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
as description to the metadata. This is purely informational.
- -v, --verbose
Causes a progress indicator to be printed.
- The system wide configuration file for popt(3). fa2dna identifies itself as "fa2dna" to popt.
- Per user configuration file for popt(3).
AUTHORUdo Stenzel <[email protected]>