
                                 vrnaplot 



Function

   Plot vrnafold output

Description

   This is a port of the Vienna RNA package program RNAplot.

Algorithm

   See the original documentation for the Vienna RNA package
   http://www.tbi.univie.ac.at/~ivo/RNA/

Usage

   Here is a sample session with vrnaplot


% vrnaplot 
Plot vrnafold output
Vienna RNAfold output file: ../vrnafold-keep/rna1.vrnafold
Vienna RNAfold output file [rna1.vrnaplot]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-structuresfile]    infile     Vienna RNAfold output file
  [-outfile]           outfile    [*.vrnaplot] Vienna RNAfold output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -layout             menu       [naview] Layout (Values: radial (Simple
                                  radial); naview (naview))
   -optype             menu       [ps] Type (Values: ps (postscript); gml
                                  (graph meta language); svg (scaleable vector
                                  graphics); xrna (XRNA save file))
   -pre                string     Pre-annotation (Any string is accepted)
   -post               string     Post-annotation (Any string is accepted)

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

   vrnaplot reads any normal sequence USAs.

  Input files for usage example

  File: ../vrnafold-keep/rna1.vrnafold

CACUACUCCAAGGACCGUAUCUUUCUCAGUGCGACAGUAA
.(((..((....)).(((((........)))))..))).. ( -3.50)

Output file format

   vrnaplot outputs a graph to the specified graphics device. outputs a
   report format file. The default format is ...

  Output files for usage example

  File: rna1.vrnaplot

%!PS-Adobe-3.0 EPSF-3.0
%%Creator: ePS_dot.c,v 1.6 2008/06/26 08:40:00 rice Exp $, ViennaRNA-1.7.2
%%CreationDate: Sun Jul 15 12:00:00 2007
%%Title: RNA Secondary Structure Plot
%%BoundingBox: 66 210 518 662
%%DocumentFonts: Helvetica
%%Pages: 1
%%EndComments

%Options:
% to switch off outline pairs of sequence comment or
% delete the appropriate line near the end of the file

%%BeginProlog
/RNAplot 100 dict def
RNAplot begin
/fsize  14 def
/outlinecolor {0.2 setgray} bind def
/paircolor    {0.2 setgray} bind def
/seqcolor     {0   setgray} bind def
/cshow  { dup stringwidth pop -2 div fsize -3 div rmoveto show} bind def
/min { 2 copy gt { exch } if pop } bind def
/max { 2 copy lt { exch } if pop } bind def
/drawoutline {
  gsave outlinecolor newpath
  coor 0 get aload pop 0.8 0 360 arc % draw 5' circle of 1st sequence
  currentdict /cutpoint known        % check if cutpoint is defined
  {coor 0 cutpoint getinterval
   {aload pop lineto} forall         % draw outline of 1st sequence
   coor cutpoint get aload pop
   2 copy moveto 0.8 0 360 arc       % draw 5' circle of 2nd sequence
   coor cutpoint coor length cutpoint sub getinterval
   {aload pop lineto} forall}        % draw outline of 2nd sequence
  {coor {aload pop lineto} forall}   % draw outline as a whole
  ifelse
  stroke grestore
} bind def
/drawpairs {
  paircolor
  0.7 setlinewidth
  [9 3.01] 9 setdash
  newpath
  pairs {aload pop
     coor exch 1 sub get aload pop moveto
     coor exch 1 sub get aload pop lineto
  } forall
  stroke
} bind def
% draw bases
/drawbases {


  [Part of this file has been deleted for brevity]

[76.515 91.594]
[88.932 77.646]
[107.552 76.227]
[116.182 63.958]
[124.812 51.689]
[133.442 39.420]
[142.071 27.151]
[136.924 12.513]
[141.395 -2.346]
[153.767 -11.712]
[169.282 -11.983]
[181.974 -3.056]
[186.962 11.637]
[182.330 26.446]
[169.857 35.678]
[154.340 35.781]
[145.711 48.050]
[137.081 60.319]
[128.451 72.587]
[119.821 84.856]
[124.925 99.035]
[120.932 113.567]
[109.299 123.146]
[110.447 138.102]
[111.596 153.058]
[121.300 166.278]
[114.456 181.181]
] def
/pairs [
[2 38]
[3 37]
[4 36]
[7 14]
[8 13]
[16 33]
[17 32]
[18 31]
[19 30]
[20 29]
] def

init

% switch off outline pairs or bases by removing these lines
drawoutline
drawpairs
drawbases
% show it
showpage
end
%%EOF

Data files

   For details of Vienna RNA file formats, see the original documentation
   http://www.tbi.univie.ac.at/~ivo/RNA/

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

    Program name                       Description
   einverted      Finds inverted repeats in nucleotide sequences
   vrnaalifold    RNA alignment folding
   vrnaalifoldpf  RNA alignment folding with partition
   vrnacofold     RNA cofolding
   vrnacofoldconc RNA cofolding with concentrations
   vrnacofoldpf   RNA cofolding with partitioning
   vrnadistance   RNA distances
   vrnaduplex     RNA duplex calculation
   vrnaeval       RNA eval
   vrnaevalpair   RNA eval with cofold
   vrnafold       Calculate secondary structures of RNAs
   vrnafoldpf     Secondary structures of RNAs with partition
   vrnaheat       RNA melting
   vrnainverse    RNA sequences matching a structure
   vrnalfold      Calculate locally stable secondary structures of RNAs
   vrnasubopt     Calculate RNA suboptimals

Author(s)

   Peter Rice (pmr © ebi.ac.uk)
   Informatics Division, European Bioinformatics Institute, Wellcome
   Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

History

   Converted (October 2005) by Alan Bleasby

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments
