Domain Annotation

Compatibility wrapper for HMMER binaries and output.

gecco.hmmer.embedded_hmms() → Iterator[gecco.hmmer.HMM]

Iterate over the embedded HMMs that are shipped with GECCO.

class gecco.hmmer.HMM(object)

A Hidden Markov Model library to use with HMMER.

id: str

Alias for field number 0

version: str

Alias for field number 1

url: str

Alias for field number 2

path: str

Alias for field number 3

size: Optional[int]

Alias for field number 4

relabel_with: Optional[str]

Alias for field number 5

md5: Optional[str]

Alias for field number 6

relabel(domain: str) → str

Rename a domain obtained by this HMM to the right accession.

This method can be used with HMM libraries that have separate HMMs for the same domain, such as Pfam.

class gecco.hmmer.DomainAnnotator(object)

An abstract class for annotating genes with protein domains.

__init__(hmm: gecco.hmmer.HMM, cpus: Optional[int] = None, whitelist: Optional[Container[str]] = None) → None

Prepare a new HMMER annotation handler with the given hmms.

Parameters

• hmm (str) – The path to the file containing the HMMs.

• cpus (int, optional) – The number of CPUs to allocate for the hmmsearch command. Give None to use the default.

• whitelist (container of str) – If given, a container containing the accessions of the individual HMMs to annotate with. If None is given, annotate with the entire file.

abstract run(genes: Iterable[gecco.model.Gene]) → List[gecco.model.Gene]

Run annotation on proteins of genes and update their domains.

Parameters

genes (iterable of Gene) – An iterable that yield genes to annotate with self.hmm.

class gecco.hmmer.PyHMMER(DomainAnnotator)

A domain annotator that uses pyhmmer.

run(genes: Iterable[gecco.model.Gene], progress: Optional[Callable[[pyhmmer.plan7.HMM, int], None]] = None, bit_cutoffs: Optional[str] = None) → List[gecco.model.Gene]

Run annotation on proteins of genes and update their domains.

Parameters

genes (iterable of Gene) – An iterable that yield genes to annotate with self.hmm.