Reuturns a connector to a phylomeDB database.
host: hostname in which phylomeDB is hosted. user: username to the
database. passwd: password to connect database. port: port used to
connect database.
An object whose methods can be used to query the database.
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__init__(self,
host=' 84.88.66.245 ' ,
db=' phylomeDB ' ,
user=' public ' ,
passwd=' public ' ,
port=3306)
Connects to a phylomeDB database and returns an object to perform
custom queries on it. |
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_execute_block(self,
cmd)
Executes a multi-line SQL command and returns the nombre of affected
rows. |
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get_longest_isoform(self,
phyID)
returns the protID of the |
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get_id_by_external(self,
external)
Returns the phylomeID of the given external ID |
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get_id_translations(self,
seqid)
returns all the registered translations of a given seqid |
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search_id(self,
queryID)
Returns a list of phylome protein Ids associated to the given
external queryID. |
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get_proteomes(self)
Returns all current available proteomes |
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get_species(self)
Returns all current available species |
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get_phylomes(self)
Returns all current available phylomes |
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get_proteomes_in_phylome(self,
phylome_id)
Returns a list of proteomes associated to a given phylome_id |
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get_seqids_in_proteome(self,
proteome_id,
filter_isoforms=True)
Returns all sequences of a given proteome |
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get_seqs_in_proteome(self,
proteome_id,
filter_isoforms=True) |
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get_proteome_info(self,
proteome_id)
Returns all info about a registered proteome |
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get_seqid_info(self,
protid)
Returns orginal info about a given protid |
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get_phylome_info(self,
phylomeid)
Returns info on a given phylome |
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get_species_info(self,
taxid_or_code)
Returns all information on a given species_code |
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get_seed_ids(self,
phylome_id,
filter_isoforms=True) |
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get_available_trees(self,
seqid,
collateral=True) |
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get_available_trees_by_phylome(self,
seqid,
collateral=True) |
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get_available_trees_in_phylome(self,
seqid,
phylomeid) |
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get_tree(self,
protid,
method,
phylome_id)
Returns the method-tree associated to a given protid. |
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get_best_tree(self,
protid,
phylome_id)
Returns the winner ML tree |
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get_algs(self,
protid,
phylome_id)
Given a protID, it returns a tuple with the raw_alg, clean_alg and
the number of seqs included. |
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get_raw_alg(self,
protid,
phylome_id)
Given a protID, it returns a tuple with the raw_alg and the number of
seqs included. |
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get_clean_alg(self,
protid,
phylome_id)
Given a protID, it returns a tuple with the clean_alg and the number
of seqs included. |
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get_orthologs(self,
seqid,
sp2age=None)
Returns the orthology predictions of the given seqid in all
phylomes. |
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Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__repr__ ,
__setattr__ ,
__sizeof__ ,
__str__ ,
__subclasshook__
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