NAME

       convert_coords - converts coordinates of features in a GFF file according to a multiple alignment

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

convert_coords 1.4                                  May 2016                                   CONVERT_COORDS(1)