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1 # This is a Python module.
2 """This module is DEPRECATED.
3
4 DBXref was used in building SeqRecords from Martel descriptions (see
5 Bio.builders.SeqRecord.sequence for more details).
6
7 Andrew Dalke is no longer maintaining Martel or Bio.Mindy, and these modules
8 and associate ones like Bio.DBXRef are now deprecated. They are no longer
9 used in any of the current Biopython parsers, and are likely to be removed
10 in a future release.
11 """
12
13 import warnings
14 warnings.warn("Martel and those parts of Biopython closely linked to it" \
15 +" (such as Bio.DBXRef which is not used elsewhere) are now" \
16 +" deprecated, and will be removed in a future release of"\
17 +" Biopython. If you want to continue to use this code,"\
18 +" please get in contact with the Biopython developers via"\
19 +" the mailing lists to avoid its permanent removal from"\
20 +" Biopython.", \
21 DeprecationWarning)
22
29
31 if self.reftype is None:
32 reftype = ""
33 else:
34 reftype = self.reftype + "="
35 s = "%s/%s%s" % (self.dbname, reftype, self.dbid)
36 if self.negate:
37 s = "not(%s)" % s
38 return s
39 __repr__ = __str__
40
47
48 dbname_conversions = {
49 "bioformat": BioformatDBName(),
50 "unknown": UnknownDBName(),
51 "sp": {"AARHUS/GHENT-2DPAGE": "x-aarhus-ghent-2dpage",
52 "CARBBANK": "x-carbbank",
53 "DICTYDB": "x-dictydb",
54 "ECO2DBASE": "x-eco2dbase",
55 "ECOGENE": "x-ecogene",
56 "EMBL": "embl", # EMBL (in GO)
57 "FLYBASE": "fb", # Flybase (in GO)
58 "GCRDB": "x-gcrdb",
59 "HIV": "x-hiv",
60 "HSC-2DPAGE": "x-hsc",
61 "HSSP": "x-hssp",
62 "MAIZE-2DPAGE": "x-maize",
63 "MAIZEDB": "x-maizedb",
64 "MENDEL": "x-mendel",
65 "MGD": "mgd", # (in GO)
66 "MIM": "x-mim",
67 "PDB": "x-pdb", # Protein Data Bank
68 "PFAM": "x-pfam",
69 "PIR": "pir", # GO
70 "PROSITE": "x-prosite",
71 "REBASE": "x-rebase",
72 "SGD": "sgd", # GO
73 "STYGENE": "x-stygene",
74 "SUBTILIST": "x-subtilist",
75 "SWISS-2DPAGE": "x-swiss",
76 "TIGR": "tigr", # GO
77 "TRANSFAC": "x-transfac",
78 "WORMPEP": "x-wormpep",
79 "YEPD": "x-yepd",
80 "ZFIN": "x-zfin",
81 },
82 "go": {"CGEN": "cgen", # Compugen, Inc.
83 "DDB": "ddb", # DictyBase (Dictyostelium discoideum)
84 "DDBJ": "ddbj", # DNA Database of Japan
85 "EC": "ec", # Enzyme Commission
86 "EMBL": "embl", # EMBL Nucleotide Sequence Data Library
87 "ENSEMBL": "ensembl", # ENSEMBL
88 "ENZYME": "enzyme", # ENZYME
89 "FB": "fb", # FlyBase
90 "GB": "gb", # GenBank
91 "GO": "go", # Gene Ontology
92 "GXD": "gxd", # Gene Expression Database (mouse)
93 "IPR": "ipr", # InterPro
94 "ISBN": "isbn", # International Standard Book Number
95 "IUBMB": "iubmb", # International Union of Biochemistry
96 # and Molecular Biology
97 "IUPAC": "iupac", # International Union of Pure and Applied
98 # Chemistry
99 "MEDLINE": "medline", # MEDLINE
100 "MGD": "mgd", # Mouse Genome Database
101 "MGI": "mgi", # Mouse Genome Informatics
102 "NC-IUBMB": "NC-IUBMB",
103 # Nomenclature Committee of the International
104 # Union of Biochemistry and Molecular Biology
105 "PIR": "pir", # PIR
106 "PMID": "pmid", # PubMed
107 "Pombase": "pombase", # Schizosaccharomyces pombe
108 "Pompep": "pompep", # Schizosaccharomyces pombe Protein
109 # Sequence Database
110 "RESID": "resid", # RESID (protein post-translational modifications)
111 "SGD": "sgd", # Saccharomyces Genome Database
112 "SP": "sp", # SWISS-PROT
113 "SWALL": "swall", # SWISS-PROT + TrEMBL + TrEMBLnew
114 "TAIR": "tair", # The Arabidopsis Information Resource
115 "taxonID": "taxonid", # Taxonomy ID
116 "TC": "tc", # Transport Commission
117 "TIGR": "tigr", # The Institute of Genome Research
118 "TR": "tr", # TrEMBL
119 "WB": "wb", # WormBase (Caenorhabditis elegans)
120 },
121 # http://www.ncbi.nlm.nih.gov/collab/db_xref.html
122 "genbank": {
123 "ATCC": "x-atcc", # American Type Culture Collection database
124 # /db_xref="ATCC:123456"
125 "ATCC(in host)": "x-atcc-host", # See above
126 "ATCC(dna)": "x-atcc-dna", # See above
127
128 "BDGP_EST": "x-bdgp-est", # Berkeley Drosophila Genome Project
129 # EST database
130 # /db_xref="BDGP_EST:123456"
131
132 "BDGP_INS": "x-bdgp-ins", # Berkeley Drosophila Genome Project
133 # database -- Insertion
134 # /db_xref="BDGP_INS:123456"
135
136
137 "dbEST": "x-dbest", # EST database maintained at the NCBI.
138 # /db_xref="dbEST:123456"
139
140 "dbSNP": "x-dbsnp", # Variation database maintained at the NCBI.
141 # /db_xref="dbSNP:4647"
142
143 "dbSTS": "x-dbsts", # STS database maintained at the NCBI.
144 # /db_xref="dbSTS:456789"
145
146 "ENSEMBL": "ensembl", # Database of automatically annotated genomic data
147 # /db_xref="ENSEMBL:HUMAN-Clone-AC005612"
148 # /db_xref="ENSEMBL:HUMAN-Gene-ENSG00000007102"
149
150 "ESTLIB": "x-estlib", # EBI's EST library identifier #'
151 # /db_xref="ESTLIB:1200"
152
153 "FANTOM_DB": "x-fantom-db", # Database of Functional Annotation of Mouse
154 # /db_xref="FANTOM_DB:0610005A07"
155
156 "FLYBASE": "fb", # Database of Genetic and molecular data of Drosophila.
157 # /db_xref="FLYBASE:FBgn0000024"
158
159 "GDB": "x-gdb", # Human Genome Database accession numbers.
160 # /db_xref="GDB:G00-128-600"
161
162 "GI": "x-gi", # GenInfo identifier, used as a unique sequence
163 # identifier for nucleotide and proteins.
164 # /db_xref="GI:1234567890"
165
166 "GO": "go", # Gene Ontology Database identifier
167 # /db_xref="GO:123"
168
169 "IMGT/LIGM": "x-imgt-ligm", # Immunogenetics database, immunoglobulins
170 # and T-cell receptors
171 # /db_xref="IMGT/LIGM:U03895"
172
173 "IMGT/HLA": "x-imgt-hla", # Immunogenetics database, human MHC
174 # /db_xref="IMGT/HLA:HLA00031"
175
176
177 "LocusID": "x-locus-id", # NCBI LocusLink ID.
178 # /db_xref="LocusID:51199"
179
180 "MaizeDB": "x-maizedb", # Maize Genome Database unique identifiers.
181 # /db_xref="MaizeDB:Probe/79847"
182
183 "MGD": "mgd", # Mouse Genome Database accession numbers.
184 # /db_xref="MGD:123456"
185
186 "MGI": "mgi", # Medicago Genome Initiative
187 # /db_xref="MGI:S:20819"
188
189 "MIM": "x-mim", # Mendelian Inheritance in Man numbers.
190 # /db_xref="MIM:123456"
191
192 "niaEST": "x-niaEST", # NIA Mouse cDNA Project
193 # /db_xref="niaEST:L0304H12-3"
194
195 "PIR": "pir", # Protein Information Resource accession numbers.
196 # /db_xref="PIR:S12345"
197
198 "PSEUDO": "x-pseudo-embl", # EMBL pseudo protein identifier
199 # /db_xref="PSEUDO:CAC44644.1"
200
201 "RATMAP": "x-ratmap", # Rat Genome Database
202 # /db_xref="RATMAP:5"
203
204 "RiceGenes": "x-ricegenes", # Rice database accession numbers.
205 # /db_xref="RiceGenes:AA231856"
206
207 "REMTREMBL": "x-remtrembl",
208 # Computer-annotated protein sequence database containing
209 # the translations of those codings sequences (CDS) present
210 # in the EMBL Nucleotide Sequence Database that won't be '
211 # included in SWISS-PROT. These include: immunoglobulins and
212 # T-cell receptors, synthetic sequences, patent application
213 # sequences, small fragments, CDS not coding for real
214 # proteins and truncated proteins.
215 # example: /db_xref="REMTREMBL:CAC01666"
216
217 "RZPD": "x-rzpd", # Resource Centre Primary Database Clone Identifiers
218 # /db_xref="RZPD:IMAGp998I142450Q6"
219
220 "SGD": "sgd", # Saccharomyces Genome Database accession numbers.
221 # /db_xref="SGD:L0000470"
222
223 "SoyBase": "x-soybase", # Glycine max Genome Database
224 # /db_xref="SoyBase:Satt005"
225
226 "SPTREMBL": "x-sptrembl", # is this the same as "swall" ?
227 # Computer-annotated protein sequence database
228 # supplementing SWISS-PROT and containing the
229 # translations of all coding sequences (CDS)
230 # present in the EMBL Nucleotide Sequence
231 # Database not yet integrated in SWISS-PROT.
232 # /db_xref="SPTREMBL:Q00177"
233
234 "SWISS-PROT": "sp", # Swiss-Prot protein database accession numbers.
235 # /db_xref="SWISS-PROT:P12345"
236
237 "taxon": "taxonid", # NCBI taxonomic identifier.
238 # /db_xref="taxon:4932"
239 },
240 }
241
243 try:
244 dbname = dbname_conversions[dbname_style][dbname]
245 except KeyError:
246 dbname = "x-unknown2-%s--%s" % (dbname_style, dbname)
247 return DBXRef(dbname, dbid, idtype, negate)
248
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