|
draw is used to draw secondary structures as Postscript images.
These Postscript images can be drawn in a variety of ways,
including annotated or circularized. Every individual structure
is sized to fit on a single Postscript page.
USAGE: draw <ct file> <ps file> [options]
| <ct file> |
The name of a CT file
or Dot-Bracket
file containing data for the structure to be drawn. |
| <output file> |
The name of an image file to which output will be
written. Usually, this is a Postscript image file,
although the user can specify that it be an SVG image file
instead. To specify SVG images, the \"--svg\" flag must be
specified in conjunction with a structure number flag (see
the flags below). |
| -c, -C, --circle |
Specify that the structure should be drawn with its
backbone around a circle. Note that pseudoknotted
structures will be drawn circularized by default even if
this option is not specified.
Default is to show a collapsed structure. |
| -f, -F, --flat |
Specify that the structure should be drawn with its
backbone stretched in a straight line. Note that
pseudoknotted structures can be drawn linearized if this
option is specified.
Default is to show a collapsed structure. |
| -h, -H, --help |
Display the usage details message. |
| -l, -L, --levorotatory |
Specify that the drawn structure is rendered
counterclockwise.
Default is to render drawn structures clockwise. |
| --svg |
Specify that the output file should be an SVG image
file, rather than a Postscript image file.
Note that only one SVG image can be written into a
particular file, so the structure number flag (below) must
also be specified when writing an SVG document. |
| -u, -U, --uncircled |
Specify that no circles should surround nucleotides
when drawing.
Default is to surround nucleotides with circles. |
| -n, -N, --number |
Specify a particular structure to be output,
one-indexed.
Default is -1, which signifies all structures output to
one file. |
| -p, -P, --probability |
Specify the name of the file from which base pairing
probability data will be read for annotation. This file
must be a partition function save file generated by the partition interface.
Default is no probability annotation file used. |
| -s, -S, --SHAPE |
Specify the name of the SHAPE
annotation file from which SHAPE data will be read
for annotation.
Default is no SHAPE annotation file used. |
| -t, -T, --text |
Specify the name of the text file from which base
pairing probability data will be read for annotation (generated, for example, by partition-cuda).
This file should describe pairing data for the predicted
structure, not the accepted structure.
Default is no probability annotation file used. |
- Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction
and analysis."
BMC Bioinformatics, 11:129. (2010).
|
