Iterative Searches

class pyhmmer.plan7.IterativeSearch

A helper class for running iterative queries like JackHMMER.

See Pipeline.iterate_seq and Pipeline.iterate_hmm for more information.

pipeline

The pipeline object to use to get hits on each iteration.

Type:

Pipeline

builder

The builder object for converting multiple sequence alignments obtained after each run to a HMM.

Type:

Builder

query

The query object to use for the first iteration.

Type:

DigitalSequence or HMM

converged

Whether the iterative search already converged or not.

Type:

bool

targets

The targets sequences to search for homologs.

Type:

DigitalSequenceBlock

ranking

A mapping storing the rank of hits from previous iterations.

Type:

KeyHash

iteration

The index of the last iteration done so far.

Type:

int

Yields:

IterationResult – A named tuple containing the hits, multiple sequence alignment and HMM for each iteration, as well as the iteration index and a flag marking whether the search converged.

References

• Johnson, Steven L., Eddy, Sean R. & Portugaly, Elon. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics 11, 431 (18 August 2010). doi:10.1186/1471-2105-11-431.

class pyhmmer.plan7.IterationResult

The results of a single iteration from an IterativeSearch.

hmm

The HMM used to search for hits during this iteration.

Type:

HMM

hits

The hits found during this iteration.

Type:

TopHits

msa

A multiple sequence alignment containing the hits from this iteration.

Type:

DigitalMSA

converged

A flag marking whether this iteration converged (no new hit found in the target sequences with respect to the pipeline inclusion thresholds).

Type:

bool

iteration

The number of iterations done so far. First iteration starts at 1.

Type:

int