Abstraction of the ASTRAL database, which has sequences for all the
SCOP domains, as well as clusterings by percent id or evalue.
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__init__(self,
dir_path=None,
version=None,
scop=None,
ind_file=None,
astral_file=None,
db_handle=None)
Initialise the astral database. |
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domainsClusteredByEv(self,
id)
get domains clustered by evalue |
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domainsClusteredById(self,
id)
get domains clustered by percent id |
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getAstralDomainsFromFile(self,
filename=None,
file_handle=None)
Get the scop domains from a file containing a list of sids |
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getAstralDomainsFromSQL(self,
column)
Load a set of astral domains from a column in the astral table of a
MYSQL database (which can be created with writeToSQL(...) |
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getSeqBySid(self,
domain)
get the seq record of a given domain from its sid |
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getSeq(self,
domain)
Return seq associated with domain |
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hashedDomainsById(self,
id)
Get domains clustered by sequence identity in a dict |
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hashedDomainsByEv(self,
id)
Get domains clustered by evalue in a dict |
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isDomainInId(self,
dom,
id)
Returns true if the domain is in the astral clusters for percent ID |
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isDomainInEv(self,
dom,
id)
Returns true if the domain is in the ASTRAL clusters for evalues |
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writeToSQL(self,
db_handle)
Write the ASTRAL database to a MYSQL database |
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