FEV_KEGG.KEGG.DataTypes module

class FEV_KEGG.KEGG.DataTypes.EcEnzyme(content)

Bases: object

An enzyme found in KEGG pathways, defined by its EC number.

Variables:

• self.uniqueID (str) – Unique string identifying the EC number, e.g. ‘4.1.2.48’.
• self.description (str) – Human-readable description of the EC number, e.g. ‘low-specificity L-threonine aldolase;LtaE’.
• self.name (str) – Short human-readable name of the EC number, e.g. ‘LtaE’. The shortest of all words in self.description.

class FEV_KEGG.KEGG.DataTypes.Gene(content)

Bases: object

Gene as defined by a gene description file in KEGG GENE database.

All attributes might be None, depending on whether they actually occur in the gene description! Occurence varies between organisms and sources.

Parameters:

content (str) – A multi-line gene description.

Variables:

• self.number (str) – The name of the gene, e.g. ‘Acav_0021’.
• self.symbol (str) – Colloquial name of the gene product, e.g. ‘ThrC’.
• self.name (str) – Long name of the gene, e.g. ‘(GenBank) Homoserine dehydrogenase’.
• self.isProtein (bool) –
• self.ecNumbers (List[str]) –
• self.isEnzyme (bool) – If isProtein and has EC numbers.
• self.keggOrthologyNames (List[str]) – Names for each KEGG Orthology ID associated with this gene, e.g. ‘homoserine dehydrogenase’.
• self.keggOrthologyIDs (List[str]) – Each KEGG Orthology ID assocaited with this gene, e.g. ‘K00003’.
• self.keggOrthologies (List[Tuple[str, str, List[str]]]) – List of each associated KEGG Orthology entry, represented as a tuple of (ID, name, EC numbers), e.g. (‘K00003’, ‘homoserine dehydrogenase’, [‘1.1.1.3’]).
• self.organismAbbreviation (str) –
• self.organismName (str) –
• self.organismTnumber (str) – KEGG Onthology ID of the organism this gene belongs to, e.g. ‘T01445’.
• self.pathways (List[Tuple[str, str]]) – List of organism-specific pathways this gene occurs in, represented as a tuple of (ID, name), e.g. (‘aaa00260’, ‘Glycine, serine and threonine metabolism’).
• self.positionFrom (int) – Nucleotide sequence position this gene starts at.
• self.positionTo (int) – Nucleotide sequence positon this gene ends at.
• self.positionIsComplement (bool) – Whether the positions are on the complement strand.
• self.aaseqLength (int) –
• self.aaseq (str) –
• self.ntseqLength (int) –
• self.ntseq (str) –

getGeneID() → GeneID

class FEV_KEGG.KEGG.DataTypes.Substance(content)

Bases: object

A compound/glycan found in KEGG pathways.

Depending on whether this is a compound or a glycan, there are more attributes than listed below.

Variables:

• self.uniqueID (str) – Unique string identifying a substance, e.g. ‘C00084’.
• self.description (str) – Human-readable description of a substance, e.g. ‘Acetaldehyde;Ethanal’.
• self.name (str) – Short human-readable description of a substance, e.g. ‘Acetaldehyde’. The shortest of all words in self.description.