magnumopus module contains packages ispcr and nw, performing in silico PCR (isPCR), a simulation of the polymerase chain reaction (PCR) commonly used in wet-lab settings to amplify target DNA sequences, and the Needleman-Wunsch algorithm, respectively.

">" denotes a .py file intended to be run in the terminal.

ispcr.py performs 3 steps:

1. Perform a BLASTN search of a query file (primers) against the subject file (assembly) to identify primer annealing locations.
2. Identify pairs of primer annealing sites that would yield a valid amplicon (primers facing each other and within close proximity).
3. Extract amplified sequences within the assembly using seqtk.

q1.py takes as input the required files for ispcr.py functions.
--> Usage: ./q1.py

nw.py performs sequence alignment based on the Needleman-Wunsch algorithm:

1. Creates an alignment matrix.
2. Populates the matrix with gap values.
3. Calculates matrix scores based on sequence matches and mismatches.
4. Performs traceback to determine potential alignments.

q2.py takes as input 2 random DNA sequences.
--> Usage: ./q2.py

amplicon_align.py accepts command-line arguments.
--> Usage:
./amplicon_align.py -1 data/Pseudomonas_aeruginosa_PAO1.fna -2 data/Pseudomonas_protegens_CHA0.fna -p data/rpoD.fna -m 2000 --match 1 --mismatch=-1 --gap=-1

Steps performed by amplicon_align.py:

1. Performs isPCR to find amplicons in both assembly files (assuming 1 amplicon per assembly file).
2. Aligns the amplicons using the Needleman-Wunsch algorithm.
3. Reverse complements the second amplicon to explore possible better alternative alignments.
4. Determines the best alignment (indicated by a higher score) and prints the alignment along with its score.