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fa2dna - format fasta database for use with ANFO

FA2DNA(1) User Manuals FA2DNA(1)

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)
 
OCTOBER 2009 Applications