msgenome

MSFeature

A class that defines attributes of a genome feature:

msfeat = MSFeature(feature_id, sequence, description=None)

  • feature_id, sequence, & description str: The ID, sequence, and description of the genome feature.

add_ontology_term()

Returns the collection of genes for all roles of all complexes from the template reaction:

msfeat.add_ontology_term(ontology_term, value)

  • ontology_term str: The ontological term that will be added to the dictionary of ontological terms.

  • value str: The sequence that corresponds to the ontological term.

MSGenome

A class that edits and parses a genome:

msgen = MSGenome()

from_fasta()

staticMethod Defines genome features from a FASTA file:

genome = msgen.from_fasta(filename, split='|', h_func=None)

  • filename str: The name of the FASTA file that will be parsed and populated in the genome features.

  • split str: The delimiter that separates the sequence ID from the sequence description.

  • h_func function: A custom function that parses the file line of a FASTA file into its sequence ID and descriptoin.

Returns genome modelseedpy.core.msgenome.MSGenome: The genome whose features have been parsed from a fasta file.

from_protein_sequences_hash()

staticMethod Defines genome features from a dictionary of protein sequences:

genome_class = msgen.from_protein_sequences_hash(sequences)

  • sequences dict: Protein sequences (values) for various sequence IDs (keys) that will be added to the genome features.

Returns genome modelseedpy.core.msgenome.MSGenome: The genome whose features have been parsed from a fasta file.

alias_hash()

Returns the gene for each alias in each gene of the features:

alias_hash = msgen.alias_hash()

Returns alias_hash dict: The collection of all alias-gene (key:value) pairs for each gene in the genome features.

search_for_gene()

Returns the sought gene based upon a query term of features or aliases:

gene = msgen.search_for_gene(query)

  • query str: The search term of a feature ID or gene alias.

Returns gene modelseedpy.core.msgenome.MSGenome: The gene that matches the search term, where None signifies that no match was discerned.