# Copyright (c) 2006, John X. Gilman # This software is distributed under the new BSD Open Source License. # # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # # (1) Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # # (2) Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and or other materials provided with the distribution. # # (3) Neither the name of the University of California, Lawrence Berkeley # National Laboratory, U.S. Dept. of Energy nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. """Database access. In biological parlance, a 'database' is an organized collection of biological data. -- Dbxref - A database cross-reference, a resource identifier. -- DataSource - A source of biological data. -- databases - A list of standard databases. Usage: ref = Dbxref("Swiss-Prot:P12345") data = ref. """ import re import urllib from corebio.data import data_stream from corebio.utils import update, stdrepr __all__ = ['Dbxref','DataSource', 'default_registry', 'astral', 'scop' ] _dbxref = re.compile(r'\s*(?:/db_xref\s*=\s*\")?(\w+):(\w+)\"?\s*') class Dbxref(object) : """A database cross-reference, a kind of Universal Resource Name (URN) used to locate information in biological databases. -- database - the name of the database -- identifier - the internal identifier of the related information according to the naming conventions of the cross-referenced database. Examples: cross reference to GDB identifier: /db_xref="GDB:39999" cross reference to Swiss-Prot entry: /db_xref="Swiss-Prot:P12345" Refs: http://www.ncbi.nlm.nih.gov/collab/db_xref.html http://www.ebi.ac.uk/cgi-bin/emblfetch http://www.expasy.org/cgi-bin/lists?dbxref.txt """ __slots__ = ["database", "identifier"] def __init__(self, ref, identifier=None) : """ Dbxref('/db_xref="GDB:39999"') Dbxref("GDB:39999") Dbxref('GDB','39999') """ if identifier: self.database = ref self.identifier = identifier return m = _dbxref.match(ref) if m is None : raise ValueError, "Cannot parse database cross-reference." self.database = m.group(1) self.identifier = m.group(2) def __repr__(self) : return "Dbxref(%s, %s)" %(self.database, self.identifier) def __str__(self) : return "%s:%s" %(self.database, self.identifier) def datasource(self, registry = None) : if registry is None: registry = default_registry database = self.database.lower() if not (database in registry) : raise ValueError, "Unknown database: %s" % self.database return registry[database] def data_url(self) : return self.datasource().data_url(self.identifier) def data_stream(self) : return self.datasource().data_stream(self.identifier) def data_string(self) : return self.datasource().data_string(self.identifier) class DataSource(object) : """A collection of indexed biological data. Attributes: -- name - The name of the database. -- abbrev - Standard abrreviation -- alt_abbrev - A list of alternative abrreviations or names. -- url - Main URL of the database. -- resource_url - The URL of individual database resources, e.g. 'biocyc.org/getid?id=%s', where '%s' is replaced by the resource identifier. -- parser - A function that can convert raw data into an object. -- description - Description of the type of biological data in this database. E.g. ''Organism-specific gene databases' """ __slots__=['abbrev', 'alt_abbrev', 'name', 'url', 'resource_url', 'parser', 'description'] def __init__(self, **kwarg) : for s in self.__slots__ : setattr(self, s, None) update(self, **kwarg) def __repr__(self) : return stdrepr(self) def data_url(self, identifier) : url = self.resource_url if url is None : raise ValueError, "Cannot resolve resource." url = url % identifier # Fixme return url def data_stream(self, identifier) : url = self.data_url(identifier) return urllib.urlopen(url) def data_string(self, identifier) : return self.data_stream(identifier).read() def data_object(self, identifier) : parser = self.parser if parser == None : raise ValueError, "No parser for resource." stream = self.data_stream(identifier) return parser(stream) def _build_default_registry() : registry = dict() # Parse database specifications from standard 'dbxref' file. ds = _read_dbxref( data_stream('dbxref.txt') ) ds.append(DataSource( name= 'Swiss-Prot', abbrev = 'swissprot', alt_abbrev = ('uniprotkb', 'uniprot'), url = 'http://ca.expasy.org/sprot/', resource_url = 'http://www.expasy.ch/cgi-bin/get-sprot-raw.pl?%s', description='Protein knowledgebase', ) ) for d in ds : registry[d.abbrev.lower() ] = d if d.alt_abbrev : for alt in d.alt_abbrev : registry[alt.lower()] = ds return registry def _read_dbxref(stream) : """ Read the dbxref file and return a list of datasources.""" namemap = dict(Abbrev = 'abbrev', Name = 'name', Server = 'url', Db_URL = 'resource_url', Cat = 'description' ) ds_list = [] attr = None ds = None for line in stream : if len(line)<8 : continue typeof = line[0:6].strip() content = line[8:].strip() if typeof=='Abbrev' : # New record ds = DataSource() ds_list.append(ds) if content == 'None' : continue # No data if ds is None : continue # No record started if typeof == '' : # Continuation line if not attr is None : content = getattr(ds, attr) +' '+ content setattr(ds, attr, content) else : attr = None if typeof in namemap: attr = namemap[typeof] if attr == 'resource_url' or attr=='url' : content = ''.join(('http://',content)) setattr(ds, attr, content) return ds_list default_registry = _build_default_registry()