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| CONVERT_COORDS(1) |
User Commands |
CONVERT_COORDS(1) |
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
