PhylomeDB3 Connector

class PhylomeDB3Connector(host='84.88.66.245', db='phylomedb_3', user='public', passwd='public', port=3306)

Returns a connector to a phylomeDB3 database.

db: database name in the host server. host: hostname in which phylomeDB is hosted. user: username to the database. port: port used to connect database. passwd: password to connect database.
An object whose methods can be used to query the database.
count_algs(phylome_id)

Returns how many alignments are for a given phylome

count_trees(phylome_id)

Retuns the frequency of each evolutionary method in the input phylome

get_algs(id, phylome_id, raw_alg=True, clean_alg=True)

Return the either the clean, the raw or both alignments for the input phylomeDB ID in the input phylome

get_all_isoforms(id)

Returns all the isoforms registered for the input phylomeDB ID

get_available_trees_by_phylome(id, collateral=True)

Returns information about which methods have been used to reconstruct every tree for a given phylomeDB ID grouped by phylome

get_best_tree(id, phylome_id)

return a tree for input id in the given phylome for the best fitting evolutionary model in terms of LK

get_clean_alg(id, phylome_id)

Return the raw alignment for the input phylomeDB ID in the given phylome

get_collateral_seeds(protid)

Return the trees where the protid is presented as part of the homolog sequences to the seed protein

get_external_ids(ids)

Returns all the external IDs registered in the ‘external_id’ table that are associated to the input phylomeDB IDs

get_genome_ids(taxid, version, filter_isoforms=True)

Returns the phylomeDB IDs for a given genome in the database filtering out, or not, the different isoforms for each ID

get_genome_info(genome)

Returns all available information about a registered genome/proteome

get_genomes()

Returns all current available genomes/proteomes

get_genomes_by_species(taxid)

Return all the proteomes/genomes registered for the input taxaid code

get_go_ids(ids)

Returns all available GO Terms associated to the input phylomeDB IDs

get_id_by_external(external)

Returns the protein id associated to a given external id

get_id_translations(id)

Returns all the registered translations of a given phylomeDB ID

get_info_homologous_seqs(protid, phylome_id, tree=None, tree_method=False, sequence=False)

Return all the available information for a given set of homologous sequences extracted from a tree from a given phylome.

get_longest_isoform(id)

Returns the longest isoform for a given phylomeDB ID

get_new_phylomedb_id(old_id)

Return the conversion between an old phylomeDB ID and a new one

get_old_phylomedb_ids(ids)

Returns all old phylomeDB IDs associated to each of the input phylomeDB IDs

get_phylome_algs(phylome_id)

Returns all alignments available for a given phylome

get_phylome_info(phylome_id)

Returns available information on a given phylome

get_phylome_seed_ids(phylome_id, filter_isoforms=True)

Returns the seed phylomeDB IDs for a given phylome being possible to filter out the longest isoforms

get_phylome_seed_ids_info(phylome_id, start=0, offset=None, filter_isoforms=False)
get_phylome_trees(phylome_id)

Returns all trees available for a given phylome

get_phylomes()

Returns all current available phylomes

get_phylomes_for_seed_ids(ids)

Given a list of phylomeDB IDs, return in which phylomes these IDs have been used as a seed

get_prot_gene_names(ids)

Returns all possible protein and gene names associated to the input phylomeDB IDs

get_proteomes_in_phylome(phylome_id)

Returns a list of proteomes associated to a given phylome_id

get_raw_alg(id, phylome_id)

Return the raw alignment for the input phylomeDB ID in the given phylome

get_seq_info_in_tree(id, phylome_id, method=None)

Return all the available information for each sequence from tree/s asociated to a tuple (protein, phylome) identifiers.

get_seq_info_msf(id, phylome_id)

Return all available information for the homologous sequences to the input phylomeDB ID in the input phylome using the best tree to compute the set of homologous sequences

get_seqid_info(id)

Returns available information about a given protid

get_seqs_in_genome(taxid, version, filter_isoforms=True)

Returns all sequences of a given proteome, filtering the

get_species()

Returns all current registered species in the database

get_species_in_phylome(phylome_id)

Returns a list of proteomes associated to a given phylome_id

get_species_info(taxid=None, code=None)

Returns all information on a given species/code

get_tree(id, phylome_id, method=None, best_tree=False)

Depending in the input parameters select either .- a tree with the best evolutionary model in terms of LK (best_tree) .- a tree reconstructed using a specific model (method) .- all available model/trees for the tuple (phylomeDB ID, phylome ID)

search_id(id)

Returns a list of the longest isoforms for each proteome where the ID is already registered. The ID can be a current phylomeDB ID version, former phylomeDB ID or an external ID.

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