Generic protocol for ORF detection in DNA sequences.
- class gecco.orf.ORFFinder(object)¶
An abstract base class to provide a generic ORF finder.
- class gecco.orf.PyrodigalFinder(ORFFinder)¶
ORFFinderthat uses the Pyrodigal bindings to Prodigal.
Prodigal is a fast and reliable protein-coding gene prediction for prokaryotic genomes, with support for draft genomes and metagenomes.
Doug Hyatt, Gwo-Liang Chen, Philip F. LoCascio, Miriam L. Land, Frank W. Larimer and Loren J. Hauser. “Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification”, BMC Bioinformatics 11 (8 March 2010), p119
- __init__(metagenome: bool = True, mask: bool = False, cpus: int = 0) None ¶
Create a new
cpus (int) – The number of threads to use to run Pyrodigal in parallel. Pass
0to use the number of CPUs on the machine.
- find_genes(records: typing.Iterable[Bio.SeqRecord.SeqRecord], progress: typing.Optional[typing.Callable[[Bio.SeqRecord.SeqRecord, int], None]] = None, *, pool_factory: typing.Union[typing.Type[multiprocessing.pool.Pool], typing.Callable[[typing.Optional[int]], multiprocessing.pool.Pool]] = <class 'multiprocessing.pool.ThreadPool'>) Iterator[gecco.model.Gene] ¶
Find all genes contained in a sequence of DNA records.
records (iterable of
SeqRecord) – An iterable of DNA records in which to find genes.
progress (callable, optional) – A progress callback of signature
progress(record, total)that will be called everytime a record has been processed successfully, with
totalbeing the total number of records to process.
- Keyword Arguments
Gene– An iterator over all the genes found in the given records.