Python interface to Prodigal, an ORF finder for genomes, progenomes and metagenomes.
Project description
🔥 Pyrodigal
Python interface to Prodigal, an ORF finder for genomes, progenomes and metagenomes.
🗺️ Overview
📋 Features
The library now features everything needed to run Prodigal in metagenomic mode. It does not yet support single mode, which requires more configuration from the user but offers more flexibility.
Roadmap:
- Metagenomic mode
- Thread safety
- Single mode
- External training file support (
-tflag) - Region masking (
-mflag)
📋 Memory
Contrary to the Prodigal command line, Pyrodigal attempts to be more conservative about memory usage. This means that most of the allocations will be lazy, and that some functions will reallocate their results to exact-sized arrays when it's possible. This leads to Pyrodigal using about 30% less memory, but with some more overhead
🧶 Thread-safety
pyrodigal.Pyrodigal instances are not thread-safe: concurrent find_genes
calls will overwrite the internal memory used for dynamic programming and
could lead to unexpected crashes. A solution to process sequences in parallel
is to use a consumer/worker pattern, and have on Pyrodigal instance in each
worker. Using a pool spawning Pyrodigal instances on the fly is also fine,
but prevents recycling internal buffers:
with multiprocessing.pool.ThreadPool() as pool:
pool.map(lambda s: Pyrodigal(meta=True).find_genes(s), sequences)
💡 Example
Using Biopython, load a sequence from a GenBank file, use Prodigal to find all genes it contains, and print the proteins in FASTA format:
record = Bio.SeqIO.read("sequence.fa", "genbank")
p = pyrodigal.Pyrodigal(meta=True)
for i, gene in enumerate(p.find_genes(str(record.seq))):
print(f"> {record.id}_{i+1}")
print(textwrap.fill(record.translate()))
📜 License
This library, like the original Prodigal software, is provided under the GNU General Public License v3.0.
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