Genes¶

class pyrodigal.Genes¶

A list of raw genes found by Prodigal in a single sequence.

New in version 0.5.4.

sequence¶

The compressed input sequence for which the gene predictions were made.

Type: pyrodigal.Sequence

training_info¶

A reference to the training info these predictions were obtained with.

Type: pyrodigal.TrainingInfo

nodes¶

A collection of raw nodes found in the input sequence.

Type: pyrodigal.Nodes

write_genes(file, prefix='gene_', width=70)¶

Write nucleotide sequences of genes to file in FASTA format.

Parameters

file (io.TextIOBase) – A file open in text mode where to write the nucleotide sequences.
prefix (str) – The prefix to use to make identifiers for each predicted gene.
width (int) – The width to use to wrap sequence lines. Prodigal uses 70 for nucleotide sequences.

Returns

int – The number of bytes written to the file.

write_gff(file, prefix='gene_', width=60)¶

Write the genes to file in General Feature Format.

Parameters

file (io.TextIOBase) – A file open in text mode where to write the features.
prefix (str) – The prefix to use to make identifiers for each predicted gene.

Returns

int – The number of bytes written to the file.

write_scores(file, header=True)¶

Write the start scores to file in tabular format.

Parameters

file (io.TextIOBase) – A file open in text mode where to write the features.
header (bool) – True to write a header line, False otherwise.

Returns

int – The number of bytes written to the file.

New in version 0.7.0.

write_translations(file, prefix='gene_', width=60, translation_table=None)¶

Write protein sequences of genes to file in FASTA format.

Parameters

file (io.TextIOBase) – A file open in text mode where to write the protein sequences.
prefix (str) – The prefix to use to make identifiers for each predicted gene.
width (int) – The width to use to wrap sequence lines. Prodigal uses 60 for protein sequences.
translation_table (int, optional) – A different translation to use to translation the genes. If None given, use the one from the training info.

Returns

int – The number of bytes written to the file.

class pyrodigal.Gene¶

A single raw gene found by Prodigal within a DNA sequence.

New in version 0.5.4.

__init__(*args, **kwargs)¶

confidence()¶

Estimate the confidence of the prediction.

Returns: float – A confidence percentage (between 0 and 100).

sequence()¶: Build the nucleotide sequence of this predicted gene.

New in version 0.5.4.

translate(translation_table=None, unknown_residue='X')¶

Translate the predicted gene into a protein sequence.

Parameters

translation_table (int, optional) – An alternative translation table to use to translate the gene. Use None (the default) to translate using the translation table this gene was found with.
unknown_residue (str) – A single character to use for residues translated from codons with unknown nucleotides.

Returns

str – The proteins sequence as a string using the right translation table and the standard single letter alphabet for proteins.

Raises

ValueError – when translation_table is not a valid genetic code number.

begin¶

The coordinate at which the gene begins.

Type: int

cscore¶

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

New in version 0.5.1.

Type: float

end¶

The coordinate at which the gene ends.

Type: int

gc_cont¶

The GC content of the gene (between 0 and 1).

Type: float

partial_begin¶

whether the gene overlaps with the start of the sequence.

Type: bool

partial_end¶

whether the gene overlaps with the end of the sequence.

Type: bool

rbs_motif¶

The motif of the Ribosome Binding Site.

Possible non-None values are GGA/GAG/AGG, 3Base/5BMM, 4Base/6BMM, AGxAG, GGxGG, AGGAG(G)/GGAGG, AGGA, AGGA/GGAG/GAGG, GGAG/GAGG, AGGAG/GGAGG, AGGAG, GGAGG or AGGAGG.

Type: str, optional

rbs_spacer¶

The number of bases between the RBS and the CDS.

Possible non-None values are 3-4bp, 5-10bp, 11-12bp or 13-15bp.

Type: str, optional

rscore¶

The score for the RBS motif.

New in version 0.5.1.

Type: float

score¶

The gene score, sum of the coding and start codon scores.

New in version 0.7.3.

Type: float

sscore¶

The score for the strength of the start codon.

New in version 0.5.1.

Type: float

start_node¶

The start node at the beginning of this gene.

Type: Node

start_type¶

The start codon of this gene.

Can be one of ATG, GTG or TTG, or Edge if the OrfFinder has been initialized in open ends mode and the gene starts right at the beginning of the input sequence.

Type: str

stop_node¶

The stop node at the end of this gene.

Type: Node

strand¶

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

Type: int

translation_table¶

The translation table used to find the gene.

Type: int

tscore¶

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

New in version 0.5.1.

Type: float

uscore¶

The score for the upstream regions.

New in version 0.5.1.

Type: float