Scripts written just to make my life easier
- pileup2fasta.py
Run:
python pileup2fasta.py --input /sample.mpileup --reference /reference.fa --prefix sample
By default the program creates a consensus folder within the current working directory and places the output file (sample.fa) there.
Users can define a different output directory by using option --outdir, i.e.
python pileup2fasta.py --input /sample.mpileup --reference /reference.fa --outdir /outdir --prefix sample
- run_alignment.py
Run
python run_alignment.py --input /fasta1 /fasta2 --module /alignment.py
The script uses the alignment.py module, provided in the align2sequences folder. The alignment.py was adapted by version available at https://github.com/alevchuk/pairwise-alignment-in-python. This software implements the Smith-Waterman and Needleman-Wunsch algorithms to do local and global sequence analysis, respectively. The results for the global alignment were tested against results from http://www.ebi.ac.uk/Tools/psa/emboss_needle/.