tabulate_variants.py

import bjorn_support as bs
import mutations as bm


# FASTA must include reference NC_045512.2 (e.g. use cat to add the reference)
fasta_filepath = '/valhalla/2021-02-08_release/msa/2021-02-08_release.fa'
# specify name for output alignment
msa_filepath = 'msa.fa'
# run alignment (uses MAFFT but can be changed from bjorn_support.py)
bs.align_fasta(fasta_filepath, msa_filepath);
# load alignment
msa_data = bs.load_fasta(msa_filepath, is_aligned=True)
# identify variants for each sample
# must identify insertions before anything else, otherwise information is lost
try: 
  insertions, _ = bm.identify_insertions_per_sample(msa_data)
except:
  insertions = None
substitutions, _ = bm.identify_replacements_per_sample(msa_data)
deletions, _ = bm.identify_deletions_per_sample(msa_data)

script for tabulating mutations for each sample inside the input fasta file. mutations are computed relative to the reference sequence named 'NC_045512.2' and present inside the input fasta.

as a rough estimate of runtime, this takes a total of 43.7 seconds on 245 SARS-CoV-2 samples collected between December 2020 and February 2021 using 8 cores on a linux machine.

link to supporting code (bjorn): https://github.com/andersen-lab/bjorn

Writing myself a comment to remind myself: in the code snippet above, insertions, substitutions, and deletions are just DataFrames, which can then be exported to a spreadsheet using the DataFrame.to_csv() function

Hi Niema, please do let me know if there are any issues or lack of clarity

Thank you, will do! I appreciate it!

import bjorn_support as bs
ModuleNotFoundError: No module named 'bjorn_support'