Question: ViennaPackage define output file name and location(RNAplfold)
0
gravatar for ete
5.3 years ago by
ete100
Germany
ete100 wrote:

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

sequence • 1.6k views
ADD COMMENTlink modified 5.2 years ago by Biostar ♦♦ 20 • written 5.3 years ago by ete100
1

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...

ADD REPLYlink modified 5.3 years ago • written 5.3 years ago by Martombo2.6k
2

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

ADD REPLYlink written 5.3 years ago by Martombo2.6k

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.

ADD REPLYlink written 5.3 years ago by ete100

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?

ADD REPLYlink written 4.1 years ago by Aishwarya Kulkarni80

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.

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by Martombo2.6k
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