wes-lewis/sw-bdsmm

Implementation of Smith-Waterman alignment algorithm for CBB 752

sw-bdsmm

Implementation of Smith-Waterman alignment algorithm for CBB 752.

Usage

python sw_align.py [-h] -i INPUT -s SCORE [-o OPENGAP] [-e EXTGAP]

Required arguments: -h, --help show this help message and exit -i INPUT, --input INPUT input file (text file of 2 sequences, one per line) -s SCORE, --score SCORE score file (tab- or space-delimited substitution matrix)

Optional arguments: -o OPENGAP, --opengap OPENGAP {Default: -2} open gap -e EXTGAP, --extgap EXTGAP {Default: -1} extension gap

Notes:

• It's assumed that your input sequences and substitution matrix files are properly formatted (no illegal characters, nonsensical values, etc.).
• You can pick your own gap-opening and gap-extension penalties, but they're expected to be negative values.

Example

python sw_align.py -i sample-input.txt -s blosum62.txt

If you run this example, the output should be equivalent to that found in sample-output.txt.