Nodes¶

class pyrodigal.Nodes¶

A list of dynamic programming nodes used by Prodigal to score ORFs.

New in version 0.5.4.

__init__(*args, **kwargs)¶

clear()¶: Remove all nodes from the node list.

copy()¶: Create a copy of the Nodes object.

extract(sequence, *, closed=False, min_gene=90, min_edge_gene=60, translation_table=11)¶

Extract nodes from the given sequence based on the training info.

After calling this method, nodes won’t be sorted; make sure to call Nodes.sort before using this further.

Parameters:

sequence (Sequence) – The sequence to extract the nodes from.

Keyword Arguments:

closed (bool) – Set to True to prevent proteins from running off edges when finding genes in a sequence.
min_gene (int) – The minimum gene length. Defaults to the value used in Prodigal.
min_edge_gene (int) – The minimum edge gene length. Defaults to the value used in Prodigal.
translation_table (int) – The translation table to use. Check the Wikipedia page listing all genetic codes for the available values.

Returns:

int – The number of nodes added from the given sequence.

Note

This function is adapted from the add_nodes function in the node.c file of the Prodigal source code.

reset_scores()¶: Reset node scores.

score(sequence, training_info, *, closed=False, is_meta=False)¶: Score the start nodes currently stored.

Note

This function is reimplemented from the score_nodes function of node.c from the Prodigal source, and already contains the patch from hyattpd/Prodigal#88.

sort()¶: Sort all nodes in the vector by their index and strand.

classmethod with_capacity(capacity)¶: Create a new node array with the given capacity.

class pyrodigal.Node¶

A dynamic programming node used by Prodigal to score ORFs.

New in version 0.5.4.

cscore¶

The coding score for this node, based on 6-mer usage.

Type:: float

edge¶

True if the node runs off the edge.

Type:: bool

gc_bias¶

The frame of highest GC content within this node.

Type:: int

gc_cont¶

The GC content for the node.

Type:: float

index¶

The position of the node in the sequence.

Hint

This coordinate is zero-based: a node at index 0 will correspond to a start or stop codon at the very beginning of the sequence.

New in version 0.7.0.

Type:: int

rscore¶

The score for the RBS motif.

New in version 0.7.0.

Type:: float

score¶

The score of the total solution up to this node.

Type:: float

sscore¶

The score for the strength of the start codon.

New in version 0.7.0.

Type:: float

strand¶

-1 if the node is on the reverse strand, +1 otherwise.

New in version 0.7.0.

Type:: int

tscore¶

The score for the codon kind (ATG/GTG/TTG).

New in version 0.7.0.

Type:: float

type¶

The node type (ATG, GTG, TTG, or Stop).

Type:: str