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1 """
2 BIANA: Biologic Interactions and Network Analysis
3 Copyright (C) 2009 Javier Garcia-Garcia, Emre Guney, Baldo Oliva
4
5 This program is free software: you can redistribute it and/or modify
6 it under the terms of the GNU General Public License as published by
7 the Free Software Foundation, either version 3 of the License, or
8 (at your option) any later version.
9
10 This program is distributed in the hope that it will be useful,
11 but WITHOUT ANY WARRANTY; without even the implied warranty of
12 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 GNU General Public License for more details.
14
15 You should have received a copy of the GNU General Public License
16 along with this program. If not, see <http://www.gnu.org/licenses/>.
17
18 """
19
20
21 import sets
22
23 # This file contains specific default user parameters used in biana
24
25 # DATABASE CONNECTION DEFAULT PARAMETERS
26 DBNAME = 'biana'
27 DBUSER = 'root'
28 DBPASS = 'root'
29 DBHOST = 'localhost'
30 DBPORT = None
31 DBSOCKET = '/home/jgarcia/local/mysql/var/mysql.sock'
32
33 EXTERNAL_ENTITY_TYPES = ["protein",
34 "DNA",
35 "RNA",
36 "mRNA",
37 "tRNA",
38 "rRNA",
39 "CDS",
40 "gene",
41 "sRNA",
42 "snRNA",
43 "snoRNA",
44 "structure",
45 "pattern",
46 "compound",
47 "drug",
48 "glycan",
49 "enzyme",
50 "relation",
51 "ontology",
52 "SCOPElement",
53 "taxonomyElement",
54 "PsiMiOboOntologyElement",
55 "GOElement"
56 ]
57
58
59
60
61
62 EXTERNAL_ENTITY_RELATION_TYPES = [ "interaction",
63 "no_interaction",
64 "reaction",
65 "functional_association",
66 "cluster",
67 "homology",
68 "pathway",
69 "alignment",
70 "complex",
71 "regulation",
72 "cooperation",
73 "forward_reaction",
74 "backward_reaction"
75 ]
76
77 # EXTERNAL ENTITY ATTRIBUTE TYPES
78 EXTERNAL_ENTITY_IDENTIFIER_ATTRIBUTES = [ ("CHEBI", "integer unsigned"),
79 ("COG", "varchar(10)"),
80 ("CYGD", "varchar(15)"), # normally 7 (YDR172w) but sometimes 9 (YLR312w-a) (in mips there are some errors... because of that, we increase it to 15
81 ("DIP", "varchar(6)"), # DIP:216N (~17000 entries)
82 ("EC", "varchar(30)"),
83 ("Encode", "varchar(14)"),
84 ("Ensembl", "varchar(40)"),
85 ("FlyBase", "varchar(13)"),
86 ("GDB", "integer(3) unsigned"),
87 ("GeneID", "integer(4) unsigned"),
88 ("GeneSymbol", "varchar(255)"),
89 ("GenomeReviews", "varchar(15)"),
90 ("GI", "integer(4) unsigned"),
91 ("GO", "integer(3) unsigned"),
92 ("HGNC", "integer(2) unsigned"),
93 ("HPRD", "integer(3) unsigned"),
94 ("Huge", "smallint unsigned"),
95 ("IMGT", "varchar(10)"),
96 ("IntAct", "integer(3) unsigned"),
97 ("IntEnz", "varchar(10)"),
98 ("InterPro", "varchar(12)"),
99 ("IPI", "varchar(20)"),
100 ("KeggCode", "char(6)"),
101 ("KeggGene", "varchar(155)"),
102 ("Method_id", "integer(2) unsigned"), #psi_mi obo mi code
103 ("MGI", "integer(3) unsigned"),
104 ("MIM", "integer(3) unsigned"),
105 ("MINT", "integer(3) unsigned"),
106 ("MIPS", "integer(2) unsigned"),
107 ("OrderedLocusName", "varchar(255)"),
108 ("ORFName", "varchar(255)"), # Actually at most 7: YAL213W: Yeast (Y) 1st (A) chromosome's left (L) at 213th (213) position on Watson (W) strand
109 ("PFAM", "varchar(255)"),
110 ("PIR", "varchar(8)"),
111 ("PRINTS", "varchar(15)"),
112 ("PRODOM", "varchar(15)"),
113 ("Prosite", "varchar(255)"),
114 ("psimi_name", "varchar(255)"),
115 ("PubChemCompound", "integer(3) unsigned"),
116 ("Ratmap", "integer(3) unsigned"),
117 ("Reactome", "integer unsigned"),
118 ("RGD", "integer unsigned"),
119 ("SCOP", "integer(3) unsigned"),
120 ("SGD", "varchar(15)"),
121 ("STRING", "varchar(25)"), # gives ordered locus names, so called ensembl codes and many more
122 ("Tair", "varchar(100)"),
123 ("TaxID", "integer(3) unsigned"),
124 ("Unigene", "varchar(10)"),
125 ("UniParc", "binary(10)"),
126 ("UniprotEntry", "varchar(15)"),
127 ("WormBaseGeneID", "integer(3) unsigned"),
128 ("WormBaseSequenceName", "varchar(255)"),
129 ("YPD", "varchar(15)")
130 ]
131
132
133 EXTERNAL_ENTITY_GENERAL_ATTRIBUTES = []
134
135
136 PROMISCUOUS_EXTERNAL_ENTITY_TYPES_DICT = [ ("SCOPElement", "PDB") ]
137
138
139 VALID_IDENTIFIER_REFERENCE_TYPES = ["unique", "previous", "alias", "cross-reference", "synonym","short-name", "exact_synonym", "related_synonym"]
140
141 CROSSABLE_ATTRIBUTES = sets.Set(["sequence","taxid","ipi","uniprotentry","uniprotaccession","genesymbol","geneid","refseq","ec"])
142
143
144 EXTERNAL_ENTITY_VERSIONABLE_IDENTIFIER_ATTRIBUTE_TYPES = [("AccessionNumber", "varchar(15)"),
145 ("RefSeq", "varchar(15)"),
146 ("TIGR", "varchar(255)"),
147 ("UniprotAccession", "varchar(9)"),
148 ]
149
150
151 EXTERNAL_ENTITY_DESCRIPTIVE_SEARCHABLE_ATTRIBUTE_TYPES = [("Disease", "text(2000)"),
152 ("Function", "text"),
153 ("Keyword", "varchar(50)"),
154 ("Description", "text"),
155 ("SubcellularLocation", "text(400)"),
156 ("Name", "varchar(255)")
157 ]
158
159 EXTERNAL_ENTITY_DESCRIPTIVE_ATTRIBUTE_TYPES = [("Pubmed", "integer(3) unsigned"),
160 ("Formula", "varchar(255)")
161 ]
162
163
164 EXTERNAL_ENTITY_NUMERIC_ATTRIBUTE_TYPES = [("Pvalue", "double"),
165 ("Score", "double") ]
166
167
168 EXTERNAL_ENTITY_SPECIAL_ATTRIBUTE_TYPES = { "PDB": {"fields": [ ("value","char(4)"),
169 ("chain","varchar(4)",True),
170 ("pdb_range","varchar(255)",True) ],
171 "indices": ("value","chain","pdb_range")},
172
173 "ProteinSequence": { "fields": [ ("value","binary(16)"),
174 ("sequenceType","ENUM(\"peptide\")",False) ],
175 "indices": ("value",) },
176
177 "NucleotideSequence": { "fields": [ ("value","binary(16)"),
178 ("sequenceType","ENUM(\"dna\",\"rna\")",False)],
179 "indices": ("value",)},
180
181 "SequenceMap": { "fields": [ ("value","binary(16)"),
182 ("seq_range","varchar(255)",False) ],
183 "indices": ()},
184
185 "Pattern": { "fields": [ ("value","varchar(255)"),
186 ("patternExpression","varchar(255)",False)],
187 "indices": ("value",)}, # Stores a regex
188
189 "STRINGScore": { "fields": [ ("value","int(2)"),
190 ("neighborhood","int(2)",True),
191 ("fusion","int(2)",True),
192 ("cooccurence","int(2)",True),
193 ("coexpression","int(2)",True),
194 ("experimental","int(2)",True),
195 ("db", "int(2)", True),
196 ("textmining","int(2)",True)],
197 "indices": () }
198 }
199
200
201 # EXTERNAL ENTITY RELATION PARTICIPANT ATTRIBUTE TYPES
202 EXTERNAL_ENTITY_RELATION_PARTICIPANT_ATTRIBUTE_TYPES = [ ("cardinality", "smallint unsigned"),
203 ("detection_method", "smallint unsigned"),
204 ("GO", "integer(3) unsigned"),
205 ("KeggCode", "varchar(6)"),
206 ("role", "ENUM(\"batch\",\"product\",\"substrate\",\"catalyst\",\"prey\",\"bait\",\"neutral\",\"acceptor\",\"donor\",\"self\",\"ancillary\",\"enzyme\",\"enzyme target\",\"inhibitor\",\"cofactor\",\"stimulator\",\"activates\",\"inhibits\",\"allosteric_inhibition\",\"competitive_inhibition\",\"irreversible_inhibition\",\"non_competitive_inhibition\",\"uncompetitive_inhibition\",\"allosteric_activation\",\"nonallosteric_activation\",\"transcription_factor\",\"regulated_DNA\",\"onward_effect\",\"reverse_effect\")")
207 ]
208
209
210
211
212
213 # EXTERNAL SOFTWARE EXECUTABLES
214 CLUSTALW_EXEC = '/usr/local/bin/clustalw'
215 FORMATDB_EXEC = '/soft/bio/sequence/blast-2.2.17/bin/formatdb'
216 BLASTALL_EXEC = '/soft/bio/sequence/blast-2.2.17/bin/blastall'
217 BL2SEQ_EXEC = '/soft/bio/sequence/blast-2.2.17/bin/bl2seq'
218 TCOFFEE_EXEC = '/Users/javigx2/phD/external_software/tcoffee/T-COFFEE_distribution_Version_7.04/bin/macosx/t_coffee'
219 #DSSP_EXEC = '/Users/javigx2/phD/external_software/dssp/dssp/dsspcmbi'
220 DSSP_EXEC = '/soft/bio/structure/dssp/dsspcmbi'
221 #CD_HIT_PATH = '/soft/bio/sequence/cd-hit/'
222 CD_HIT_PATH = '/home/jgarcia/programs/CD-HIT/cd-hit/'
223 # DEFAULT TEMPORAL DATA PATHS
224 TEMPORAL_PATH = None
225
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