ViennaPackage define output file name and location(RNAplfold)

Question

[ete]

Hi!

Does anybody knows whether it's possible to set the output file name and location of the ViennaPackage tool rnaplfold?

The default settings (sequence name and current directory) are not convenient. I am calling the tool via Python subprocess module.

Any help would be very apprenticed,

Thanks in advance!

Stefanie

[Martombo]

hey I am doing the exact same thing at the moment! I guess you are using the -o option to print a text file on the fly, right? unfortunately I think there is no way to define a file for the output or to send it to stdout, which is very cumbersome...

[Martombo]

if anybody is interested, you can find some code to parse RNAplfold with python here, have a look at the "plfold" function. it gets as input a nucleotide sequence and returns a list of plfold scores of the same length, which is the sum of all plfold scores for every base of the sequence

[ete]

Thanks! I am not using the -o paramater and RNAplfold creates automatically a file. Thanks for pointing me to this, I think I will try some of this tips:

http://stackoverflow.com/questions/4675728/redirect-stdout-to-a-file-in-python

Thanks for sharing your code but I am done with implementing my code and I don't need the sum of the scores.

[Aishwarya Kulkarni]

Hi @Martombo I am trying to make sense of the results from the -o option and the file looks something like this 1 32 0.0364564 2 30 0.0896707 2 37 0.0202369 2 41 0.135411 3 11 0.0100824 3 29 0.0610271 3 36 0.0134329 3 40 0.0894272 3 54 0.0288916 4 10 0.0104427 4 28 0.0460893 4 53 0.0281795 4 61 0.0662453 5 27 0.03682 5 37 0.0678596 5 52 0.0225399 5 60 0.0400364 6 14 0.0368866 What is to be interpreted from these results?

[Martombo]

the first two numbers are the positions of the nucleotides that bind each other and the third is the frequency / likelihood with which they do it. It must be explained in the docs, have a look there.