Simple wrapper around Augustus to bring faster restitution times
Project description
Efficiently run Augustus in multi-core environments
parallel_augustus
cuts the input genome in chunks to feed to Augustus. The number of chunks and Augustus processes launched in parallel are configurable.
Installation
pip install --user parallel_augustus
Requirements
- Python >= 3.8
- Augustus
Execution
Before launching parallel_augustus
, please make sure that Augustus is available in your path. If you run augustus -h
and do not encounter an error, you are good to go.
parallel_augustus
first divides the genome (-g
argument) in the desired number of chunks (-c
argument, it can be any number > 1). After that it launches -p
processes of Augustus in parallel until there is no chunks left. You can pass parameters to Augustus via the --extra
flag. At least a --species=thing
is required by Augustus.
IMPORTANT: the --extra
argument should be the last one in the command line due to shortcomings in the argparse
python module.
With all that in mind, a typical parallel_augustus
command line will look like this:
parallel_augustus -g genome.fasta \
-o augustus_results \
-c 500 \
-p 20 \
--extra '--species=human'
This command creates the output directory augustus_results
, divides the genome into 500 chunks and launches 20 processes of Augustus in parallel. At the end, results are concatenated into augustus_results/augustus.gff
.
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