project2018

This repository is to predict 3 state 2nd structure of a protein.

usage:

command

cd ./2nd_stru/	#Bash

to use the predictor successfully, you must in /2nd_stru/ folder
If you want to run model built by sequence information.

 python3 ./script/input_seq.py ./input/input.txt #Bash

Attention:
- You can change your own test file path in <input sequence file>
If you want to run model built by pssm.

python3 ./script/input_pssm.py ./input/pssm/ #Bash

Attention:
- You can change your own pssm path in <input pssm folder>, path folder must end with '/'
- The pssm filename must starts with '>' and end with '.pssm'. For example: >1hnf-1-AS.pssm

mandatary file

./input/
./logs/model_pssm/
./logs/model_seq/
./script/
./output/

Output

Output is in /2nd_stru/output/
./output.txt
- Prediction by sequence model.
- Format: 3line.
  - First line: >ID
  - Second line: amino acid sequences
  - Third line: Topology sequences
./output_pssm.txt
- Prediction by pssm model.
- Format: 2line
  - First line: >ID
  - Second line: Topology sequences
- You can conbine your sequences and predicted topology on your own.

/2n_stru/ file introduction

/input/

/input.txt

contain a sequence to test

/script/

./input.py

the script to run

./StruPre.py

functions to extract data structures, sliding window, and onehotencode.

./traning_tesing_set.py

manually split dataset into 5-fold.

./cross_validation.py

manually do cross-validation and change parameter

/logs/

models and arrays produced during building the predictor.

./model/

contain the model I have built.

./CV_gourp_array

SVM input array. Use in cross-validation

/output/

contain the output file.

xyuany/project2018