.TH CONVERT_COORDS "1" "May 2016" "convert_coords 1.4" "User Commands"
.SH NAME
convert_coords \- converts coordinates of features in a GFF file according to a multiple alignment
.SH DESCRIPTION
Converts coordinates of features in a GFF file according to a multiple
alignment.  Will map from the coordinate system of any sequence to any
other sequence; can also map to or from the coordinate system of the
entire alignment.  In addition, supports translation of coordinates by
specified offset.
.SH OPTIONS
.TP
\fB\-m\fR <msa_fname>
(required) Name of file in which alignment is defined.
.TP
\fB\-f\fR <gff_fname>
(required) Name of file in which features are defined (GFF).
.TP
\fB\-s\fR <src_frame>
Index of frame of reference for feature coordinates, as
defined in the GFF file.  Use an integer 1\-N (if N seqs)
or 0 to indicate the coordinate system of the alignment
as a whole.  Default behavior is to match features with
alignment sequences by name (feature by feature).
\fB\-d\fR <dest_frame> Index of destination frame of reference.
Default is 0
(whole MSA).
\fB\-p\fR <coord_off>
Positive coordinate offset.  This value will be
added to all coordinates.  Useful when
the alignment (or sequence) for which the coordinates
are specified is a sub\-alignment of yours.
\fB\-n\fR <coord_off>
Negative coordinate offset.  This value will be
subtracted from all coordinates.  Useful when your
alignment is a sub\-alignment of the alignment (or
sequence) for which the coordinates are specified.
\fB\-i\fR FASTA|PHYLIP|MPM|SS
Alignment format.  Default is to guess format from file
contents