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import re
from species import Species
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "Gavin.Huttley@anu.edu.au"
__status__ = "alpha"
_release = re.compile("\d+")
def get_version_from_name(name):
"""returns the release and build identifiers from an ensembl db_name"""
r = _release.search(name)
if r is None:
return None, None
# first number run is release, followed by build
# note, for the ensemblgenomes naming system, the second digit run is the
# standard Ensembl release and the first is for the specified genome
release = name[r.start(): r.end()]
b = [s for s in _name_delim.split(name[r.end():]) if s]
return release, b
_name_delim = re.compile("_")
def get_dbtype_from_name(name):
"""returns the data base type from the name"""
try:
name = _release.split(name)
name = [s for s in _name_delim.split(name[0]) if s]
except TypeError, msg:
print "Error:"
print name, type(name), msg
raise
dbtype = None
if name[0] == "ensembl":
dbtype = name[1]
else:
dbtype = "_".join(name[2:])
return dbtype
def get_db_prefix(name):
"""returns the db prefix, typically an organism or `ensembl'"""
name = _name_delim.split(name)
if name[0] == "ensembl":
prefix = "ensembl"
elif len(name) > 4:
prefix = "_".join(name[:2])
else:
raise RuntimeError("Unknown name structure: %s" % "_".join(name))
return prefix
class EnsemblDbName(object):
"""container for a db name, inferring different attributes from the name,
such as species, version, build"""
def __init__(self, db_name):
"""db_name: and Emsembl database name"""
if isinstance(db_name, EnsemblDbName):
db_name = db_name.Name
self.Name = db_name
self.Type = get_dbtype_from_name(db_name)
self.Prefix = get_db_prefix(db_name)
release, build = get_version_from_name(db_name)
self.Release = release
self.GeneralRelease = self.Release
if len(build) == 1:
if self.Type != 'compara':
self.Build = build[0]
else:
self.Build = None
self.GeneralRelease = build[0]
elif build:
self.Build = build[1]
self.GeneralRelease = build[0]
else:
self.Build = None
self.Species = None
self.Species = Species.getSpeciesName(self.Prefix)
def __repr__(self):
build = ['', "; Build='%s'" % self.Build][self.Build != None]
s = "db(Prefix='%s'; Type='%s'; Release='%s'%s)" % (self.Prefix, self.Type,
self.Release, build)
return s
def __str__(self):
return self.Name
def __cmp__(self, other):
if isinstance(other, type(self)):
other = other.Name
return cmp(self.Name, other)
def __hash__(self):
return hash(self.Name)
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