bionic (1) convert_coords.1.gz

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