ORF Finder

class chamois.orf.ORFFinder

An abstract base class to provide a generic ORF finder.

abstractmethod find_genes(clusters, progress=None)

Find all genes from a DNA sequence.

class chamois.orf.PyrodigalFinder(ORFFinder)

An ORFFinder that 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. Since BGCs are short sequences, only “meta” mode can be used for detecting genes in the input.

References

• Martin Larralde. “Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes”, Journal of Open Source Software, 7(72), 4296,.

• 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__(mask=False, cpus=None)

Create a new PyrodigalFinder instance.

Parameters:

• mask (bool) – Whether or not to mask genes running across regions containing unknown nucleotides, defaults to False.

• cpus (int) – The number of threads to use to run Pyrodigal in parallel. Pass 0 to use the number of CPUs on the machine.

find_genes(clusters, progress=None, *, pool_factory=<class 'multiprocessing.pool.ThreadPool'>)

Find all genes contained in a sequence of DNA records.

Parameters:

• clusters (iterable of ClusterSequence) – An iterable of raw cluster sequences in which to find genes

• progress (callable, optional) – A progress callback of signature progress(cluster, total) that will be called everytime a record has been processed successfully, with record being the ClusterSequence instance, and total being the total number of records to process.

Keyword Arguments:

pool_factory (type) – The callable for creating pools, defaults to the multiprocessing.pool.ThreadPool class, but multiprocessing.pool.Pool is also supported.

Yields:

Protein – An iterator over all the genes found in the given records.

class chamois.orf.CDSFinder(ORFFinder)

An ORFFinder that simply extracts CDS annotations from records.

__init__(feature='CDS', translation_table=11, locus_tag='locus_tag')

find_genes(clusters, progress=None)

Find all genes contained in a sequence of DNA records.