Question: Drawing secondary structure using RNAplot from command line
gravatar for biousex
2.4 years ago by
biousex0 wrote:

Hi all, i need to draw secondary structure using RNAplot from command line whit Php. I get dot-bracket notation using RNAcofold, with Php command exec (seq.txt contain my RNA sequence):

exec(RNAcofold < seq.txt", $output1, $return_var1);

Then i write another file (named notation.txt), structured as follow:

LINE1: -> RNA sequence

LINE2: -> Dot-bracket notation

Well, if i call "RNAplot -o svg < notation.txt" using Dos prompt, i get the svg file.

But if i call RNAplot whit Php:

exec(RNAplot < notation.txt", $output2, $return_var2);

i don't get the file. What's wrong? If i print $return_var2, i get 0, so in theory the command works fine.

Thanks in advance.

rnaplot • 926 views
ADD COMMENTlink modified 2.4 years ago by genomax60k • written 2.4 years ago by biousex0

Ok, the problem seems to be the path: Php save the svg file using the root of the project. I need a way to redirect output in "svgfiles" folder. If i use this sintax:

exec(RNAplot < notation.txt > svgfiles\image.svg", $output2, $return_var2);

i get a empty svg file. Any advice?

Thanks in advance.

ADD REPLYlink written 2.4 years ago by biousex0

From the documentation:

If the sequence was preceded by a line of the form


the output file will be named "" otherwise "" is used. Existing files of the same name will be overwritten.

IIRC the filename is hardcoded so you can either issue a system command to move/rename the file afterwards, or edit the code to either print to stdout or file.

ADD REPLYlink written 2.4 years ago by fanli.gcb650
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