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- OrganismBase
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- RSATOrganism
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- Microbe
class Microbe(RSATOrganism) |
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The standard organism in cmonkey is Microbe. It builds on the
data dependencies established in RSATOrganism and adds a Microbes Online
dependency to retrieve possible operon information
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- Method resolution order:
- Microbe
- RSATOrganism
- OrganismBase
Methods defined here:
- __init__(self, code, kegg_organism, rsat_info, go_taxonomy_id, microbes_online_db, network_factories, search_distances, scan_distances, use_operons=True, ratios=None, synonyms=None, fasta_file=None)
- create an Organism instance
- operon_map(self)
- Returns the operon map for this particular organism.
Microbes Online works on VNG names, but RSAT is working on
feature ids, so this function also maps VNG names to feature ids
- sequences_for_genes_scan(self, genes, seqtype='upstream')
- The default sequence retrieval for microbes is to
fetch their operon sequences
- sequences_for_genes_search(self, genes, seqtype='upstream')
- The default sequence retrieval for microbes is to
fetch their operon sequences
Methods inherited from RSATOrganism:
- __str__(self)
- cog_organism(self)
- returns the COG organism name
- features_for_genes(self, genes)
- returns a map of features for the specified list of genes aliases
used for operon information
- read_features(self, feature_ids)
- Returns a list containing the features for the specified feature
ids
- read_sequences(self, features, distance, extractor)
- for each feature, extract and set its sequence
- species(self)
- Retrieves the species of this object
- taxonomy_id(self)
- Returns the taxonomy id
- thesaurus(self)
- reads the thesaurus from a feature_names file. The thesaurus
is also cached, because it is used many times
Methods inherited from OrganismBase:
- feature_ids_for(self, gene_aliases)
- Helper method to retrieve a list of feature_ids for the
specified alias list
- networks(self)
- returns this organism's networks
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class RSATOrganism(OrganismBase) |
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An organism class that does most things automatically by relying on information
stored retrieved from RSAT.
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Methods defined here:
- __init__(self, code, kegg_organism, rsat_info, go_taxonomy_id, network_factories, search_distances, scan_distances, ratios=None, synonyms=None, fasta_file=None)
- create an Organism instance
- __str__(self)
- cog_organism(self)
- returns the COG organism name
- features_for_genes(self, genes)
- returns a map of features for the specified list of genes aliases
used for operon information
- read_features(self, feature_ids)
- Returns a list containing the features for the specified feature
ids
- read_sequences(self, features, distance, extractor)
- for each feature, extract and set its sequence
- species(self)
- Retrieves the species of this object
- taxonomy_id(self)
- Returns the taxonomy id
- thesaurus(self)
- reads the thesaurus from a feature_names file. The thesaurus
is also cached, because it is used many times
Methods inherited from OrganismBase:
- feature_ids_for(self, gene_aliases)
- Helper method to retrieve a list of feature_ids for the
specified alias list
- networks(self)
- returns this organism's networks
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