.\" ANFO short read aligner
.\" (C) 2009 Udo Stenzel
.\"
.\" This program is free software; you can redistribute it and/or modify
.\" it under the terms of the GNU General Public License as published by
.\" the Free Software Foundation; either version 3 of the License, or (at
.\" your option) any later version.  See the COPYING file for details.

.\" Process this file with
.\" groff -man -Tascii patman.1
.\"
.TH FA2DNA 1 "OCTOBER 2009" Applications "User Manuals"
.SH NAME
fa2dna \- format fasta database for use with ANFO
.SH SYNOPSIS
.B fa2dna [
.I option
.B |
.I file
.B ... ]
.SH DESCRIPTION
.B fa2dna
reads one or more files in fasta format and reformats them into a
database suitable for 
.BR 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.

.SH OPTIONS
.IP "-V, --version"
Print version number and exit.

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

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

.IP "-g name, --genome name"
Sets the genome name to
.IR name .
This name is stored in the output file and will be used by
.B 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.

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

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


.SH FILES
.I /etc/popt
.RS
The system wide configuration file for
.BR popt (3).
.B fa2dna
identifies itself as "fa2dna" to popt.
.RE

.I ~/.popt
.RS
Per user configuration file for
.BR popt (3).
.RE

.SH BUGS
None known.

.SH AUTHOR
Udo Stenzel <udo_stenzel@eva.mpg.de>

.SH "SEE ALSO"
.BR anfo "(1), " fa2dna "(1) " popt "(3), " fasta (5)