The inputs folder contains a sample parsed reference template for chromosome 21 and a sample parsed reads dataset simulated with SimLord (150bp long, 100K reads; error rate 0.01) that can be used for testing the prototype. Note that the preprocessing run will generate several auxiliary files for the reference index.
Execute the following commands to create and activate virtual environment and install the required packages:
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt
Options for preprocessing, alignment, and postprocessing:
--chrnum: chromosome number
--nr: total number of reads
--rl: read length
--nrg: number of read groups
--nrb: number of read batches
--tcn: template chunk number
--rbn: read batch number
cd codes
Example commands for testing your installation:
python3 preprocessing.py --chrnum 21 --nr 100000 --rl 150 --nrg 2 --nrb 100
The above command creates "read_batch_x" and "template_chunk_y" folders in the results folder.
Expected terminal output (time in seconds):
Total preprocessing time: xx.x"
mpirun -np 2 python3 alignment.py --chrnum 21 --rl 150 --nrg 2 --nrb 100 --tcn 0 --rbn 0
The above command creates "template_chunk_x_read_batch_y" folders in the results folder.
Expected terminal output:
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0
python3 postprocessing.py --chrnum 21 --nr 100000 --rl 150 --nrg 2 --nrb 100 --tcn 0 --rbn 0
The above code generates final_alignments.json file within the "template_chunk_x_read_batch_y" folder.
Expected terminal output (time in seconds):
"Completed postprocessing in xx.x"
The preprocessing step transforms the reference template and reads to be sent to the clouds. The alignment step carries out the alignment between the two clouds (emulated using Message Passing Interface, MPI). The postprocessing step returns the final alignments to the results folder.
The job size for the above alignment task is a template size of 1M and 1000 reads. It takes about 2.5 minutes to run on an 8-core 8 GB RAM MacBook M1 machine.
This code is a prototype and is not intended for large-scale commercial applications.