Pipelines

class pyinfernal.cm.Pipeline

An Infernal accelerated sequence/covariance model comparison pipeline.

The Infernal pipeline handles the comparison of digital sequences to CMs. Since Infernal 1.1, the pipeline is accelerated using the HMMER platform acceleration to compute initial SSV/MSV/Viterbi filters before actually attempting full alignments.

alphabet

The alphabet for which the pipeline is configured.

Type:

Alphabet

randomness

The random number generator being used by the pipeline.

Type:

Randomness

search_cm(query, sequences)

__init__(*args, **kwargs)

clear()

Reset the pipeline to its default state.

E

The per-target E-value threshold for reporting a hit.

Type:

float

F1

The MSV filter threshold.

Type:

float

F2

The Viterbi filter threshold.

Type:

float

F3

The uncorrected Forward filter threshold.

Type:

float

F4

The glocal Forward filter threshold.

Type:

float

F5

The glocal envelope definition filter threshold.

Type:

float

F6

The CYK filter threshold.

Type:

float

T

The per-target score threshold for reporting a hit.

If set to a non-None value, this threshold takes precedence over the per-target E-value threshold (Pipeline.E).

Type:

float or None

Z

The number of effective targets searched.

It is used to compute the independent e-value for each hit. If None, the parameter number will be set automatically after all the comparisons have been done. Otherwise, it can be set to an arbitrary number.

Type:

int or None

incE

The per-target E-value threshold for including a hit.

Type:

float

incT

The per-target score threshold for including a hit.

If set to a non-None value, this threshold takes precedence over the per-target E-value inclusion threshold (Pipeline.incE).

Type:

float or None

seed

The seed given at pipeline initialization.

Setting this attribute to a different value will cause the random number generator to be reseeded immediately.

Type:

int