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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.
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).
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