SWAlgorithm

Smith-Waterman Algorithm for CB&B 752: Biomedical Data Science: Mining and Modeling

Python3 is required.

Installation

The script can be directly downloaded from Github using the following commands:

git clone https://github.com/dingyaozhang/SWAlgorithm.git
cd SWAlgorithm

You could directly use hw1.py in the folder.

If you want to install the package in the python:

pip install git+https://github.com/dingyaozhang/SW_Algorithm.git

Quick Start

If you directly download the script folder, you could use it directly

python hw1.py -i <input file> -s blosum62.txt 
# if you have your own substitution matrix file, you could change blosum62.txt.
# you could use > to output data to a file.

You could try the sample data:

python hw1.py -i tests/input.txt -s blosum62.txt > output.txt
python hw1.py -i tests/sample-input1.txt -s blosum62.txt > output1.txt 
diff -E -b output1.txt tests/sample-output1.txt #compare with standard results
python hw1.py -i tests/sample-input2.txt -s blosum62.txt > output2.txt
diff -E -b output2.txt tests/sample-output2.txt #compare with standard results

---

If you install the package in the python, then in the command line:

python -c "from SWAlgorithm.hw1 import runSW;runSW('<input file>','blosum62.txt',-2,-1)" > output.txt

You could try the sample data:

python -c "from SWAlgorithm.hw1 import runSW;runSW('tests/input.txt','blosum62.txt',-2,-1)" > output.txt
python -c "from SWAlgorithm.hw1 import runSW;runSW('tests/sample-input1.txt','blosum62.txt',-2,-1)" > output1.txt
diff -E -b output1.txt tests/sample-output1.txt #compare with standard results
python -c "from SWAlgorithm.hw1 import runSW;runSW('tests/sample-input2.txt','blosum62.txt',-2,-1)" > output2.txt
diff -E -b output2.txt tests/sample-output2.txt #compare with standard results

You could also use it in python like:

import sys
sys.stdout = open('file.txt', 'w')
from SWAlgorithm.hw1 import runSW
runSW('tests/input.txt','blosum62.txt',-2,-1)
sys.stdout.close()

Usage and Options

Usage: python hw1.py -i <input file> -s <score file>  [OPTION...]

input file (-i --input):
The name of input file.
score file (-s --score):
The name of score file.

Options (need to include values after the option switches):
--opengap:
The number of open gap penalty used. Default is -2.
--extgap:
The number of extension gap penalty used. Default is -1.

For installation by pip:

Usage: runSW('<input file>','<score file>',opengap,extgap)
python hw1.py -i  -s blosum62.txt  [OPTION...]

input file:
The name of input file.
score file:
The name of score file.
opengap:
The number of open gap penalty used. We suggest to use -2.
extgap:
The number of extension gap penalty used. We suggest to use -1.