In the directory of nussinov, it is a project of Nussinov's Algorithm.
If you want to access this project, go to the directory of nussinov
cd nussinov
You can install all the dependencies by
pip install -r requirements.txt
If you want to run nussinov's Algorithm you can go to the nussinov directory and simply run:
python main.py
with the following options:
optional arguments:
-h, --help show this help message and exit
--seq RNA sequence
--seq_file File for RNA Sequence
--output The output path of images of predicted secondary struction
--min_loop_length Min loop length
--score_metrics_file File of Score metrics
--circular_plot_file The output path of circular plot
For example, If you execute,
python main.py --seq CGAGUCGGAGUC --output demo/demo1.png --min_loop_length 0
Note: If you don't specify the scoring metrics, we will use {(A, C): 1, (C, G): 1} as a default.
You will get the following output:
std output:
DP Table
[[0. 1. 1. 1. 2. 2. 3. 3. 3. 3. 4. 5.]
[0. 0. 0. 0. 1. 2. 2. 2. 2. 2. 3. 4.]
[0. 0. 0. 0. 1. 1. 2. 2. 2. 2. 3. 4.]
[0. 0. 0. 0. 0. 1. 1. 1. 2. 2. 2. 3.]
[0. 0. 0. 0. 0. 0. 1. 1. 2. 2. 2. 3.]
[0. 0. 0. 0. 0. 0. 1. 1. 1. 1. 2. 3.]
[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 2.]
[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 2.]
[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 1.]
[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1.]
[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.]
[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.]]
Linear Representation:
(((.)))((.))
demo/demo1.png
The Score metrics use the following format:
[First Nucleotide] [Second Nucleotide] [Weight]
You can see an example in nussinov/score_metrics/score_1.txt. In this example, we let (A, C) with the weight 1, (C, G) with the weight 1, and (A, G) with the weight 100.
A U 1
C G 1
A G 100
And we can use score_metrics_file option to change the score_metrics.
For example, we can use:
python main.py --seq ACUG --output demo/demo2.png --min_loop_length 0 --score_metrics_file score_metrics/score_1.txt
And you will get the following output:
Std output:
DP Table:
[[ 0. 0. 1. 100.]
[ 0. 0. 0. 1.]
[ 0. 0. 0. 0.]
[ 0. 0. 0. 0.]]
Linear Representation:
(..)
demo/demo2.png
If you want to read a super long sequence, it might be more convenient to store the input in a file. In that case, you can use seq_file option.
For example, you can run store your input in seq/seq1.txt and then execute:
python main.py --seq_file seq/seq1.txt --min_loop_length 1 --output demo/demo3.pngAnd the output will be:
std output:
dp table:
[[0. 0. 0. 1. 1. 2. 2. 2. 3. 4. 4. 4. 5. 5. 6. 6.]
[0. 0. 0. 0. 1. 1. 1. 2. 3. 3. 3. 3. 4. 5. 6. 6.]
[0. 0. 0. 0. 0. 0. 1. 2. 3. 3. 3. 3. 4. 5. 5. 6.]
[0. 0. 0. 0. 0. 0. 1. 2. 2. 2. 2. 2. 3. 4. 5. 5.]
[0. 0. 0. 0. 0. 0. 1. 1. 2. 2. 2. 2. 3. 4. 4. 5.]
[0. 0. 0. 0. 0. 0. 0. 1. 1. 1. 1. 1. 2. 3. 4. 4.]
[0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 1. 1. 2. 2. 3. 3.]
[0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 1. 1. 2. 2. 3. 3.]
[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 2. 3. 3.]
[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 2. 2. 3.]
[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 1. 2. 2.]
[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 1. 1.]
[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.]
[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.]
[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.]
[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.]]
Linear Representation:
.((((.)))((.))).
demo/demo3.png
If you want to get the circular plot, you can use --circular_plot_file option.
For example, if you want to get the circular plot of the above sequence in seq/seq1.txt, you can use the following command
python main.py --seq_file seq/seq1.txt --min_loop_length 1 --output demo/demo3.png --circular_plot_file demo/circular.png
And you can get the output in demo/circular.png
If you want to run nussinov's Algorithm you can go to the nussinov directory and simply run:
python zuker.py
with the following options:
optional arguments:
-h, --help show this help message and exit
--seq RNA sequence
--seq_file File for RNA Sequence
--output The output path of images of predicted secondary struction
--circular_plot_file The output path of circular plot
python zuker.py --seq_file seq/seq1.txt --output demo/zuker1.png --circular_plot_file demo/zuker_circular.png
Convential Representation
Circular Representation
We have collected 3975 RNA sequence data with answer of secondary structure.
python compare.py --input [RNA sequence file]