PROGRAM: convert_coords

USAGE: convert_coords -m <msa_fname> -f <feature_fname> [-s <src_frame>] [-d <dest_frame>] [-p] [-n] [-i PHYLIP|FASTA|MPM]

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.

OPTIONS:
    -m <msa_fname>  (required) Name of file in which alignment is defined.
    -f <gff_fname>  (required) Name of file in which features are defined (GFF). 
    -s <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).
    -d <dest_frame> Index of destination frame of reference.  Default is 0
                    (whole MSA).
    -p <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. 
    -n <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.
    -i FASTA|PHYLIP|MPM|SS
                    Alignment format.  Default is to guess format from file
                    contents