Bacterial Wrapper

[joshfactorial]

We will create a wrapper that will be designed to run neat on a small genome from a bacteria, with multiple generations of mutations. We will need to find some example data. I'm envisioning the following steps:

1. gather some example bacteria data (NCBI, check around). We will need any data we can find, but especially fasta references files. If we can find fastq and bam data, even better.
2. Write a script that takes a bacterial reference fasta file. For each chromosome in the file, add a new chromosome where the original chromosome is split halfway through the sequence, then stitch them back together so that the old ends are now the middle: => ABBCBBC -> ABBC BBC -> BBC ABBC -> BBCABBC
   • Be careful with memory usage.
   • Ideally, we would want this to use standard Python modules (check the environment file to see what is already available). The main thing is to avoid biopython. We can discuss any other modules to use.
   • Try calling neat with subprocess (check Keshav's code for an example of calling NEAT this way).
3. Further improvements, as time allows:
   • Add a feature to allow a user to run multiple loops, which will output only on the last loop
   • If the process is running slow, we might try splitting the file and running multiple instances of neat (concurrently or sequentially)
   • Add a script to stitch the output files back together (Keshav may have done this part, and we just need to use that code).
   • Cross reference the synthetic variants with a gene map of the bacteria to see if there were any mutations in coding regions.

Keshav's scripts:

• wrapper to parallelize neat: https://github.com/ncsa/NEAT/blob/144-break-uprecombine-larger-genomes/neat/read_simulator/utils/parallelize.py
• Functions to split the inputs: https://github.com/ncsa/NEAT/blob/144-break-uprecombine-larger-genomes/neat/read_simulator/utils/split_inputs.py
• Recombine the outputs: https://github.com/ncsa/NEAT/blob/144-break-uprecombine-larger-genomes/neat/read_simulator/utils/stitch_outputs.py

[joshfactorial]

Next steps: incorporating bacterial wrapper into NEAT.

Look at the example of gen_mut_model. NEAT always starts with the main CLI, then calls subfunctions. The subfunctions take their own arguments and call a runner script. Start with just getting a help message when you try the command

neat bacterial-wrapper -h

(that doesn't have to be the final name of the tool). Create an area in the repo where the bacterial wrapper code will live and name the files similar to what is in gen-mut-model (you may not need more than just a runner script). The end goal with this part is to be able to call the bacterial wrapper directly with NEAT:

neat bacterial-wrapper -c bacteria-config.yml -o bac-wrap

for example, which will activate the bacterial wrapper code and produce an output in a folder called bac-wrap.