Window Python Script

-Uses biopython version 1.81

• This script is designed to analyze an alignment file in FASTA format, calculating the number of differences (SNPs) within a specified sliding window across the alignment.

• This script will work if the alignment contains amino acids (AA) or nucleotide sequences, but both sequences have to be in the same format.

• The script will report the number of differences between the sequences within the 'Window'

• The "Window" is the number of basepairs that will be examined for differences. You specify the size of the window with -w, or --window.

• The "Step" variable is the number of basepairs the window will "Step" up the sequence. You specifcy the step of the window with -s, or --step.

• You are required to specify the fasta file with the -a, --alignment argument.

• If you set window and step for 10 the output will show the differences for every 10 base pairs.

Test files are included with the repository. Here is an example command to run the script:
python Window.py -a TEST.fasta -w 10 -s 10

Help command python Window.py -h