PianaGlobals
index
../../../../piana/code/PianaDB/PianaGlobals.py

 File       : PianaGlobals.py
 Author     : R. Aragues & D. Jaeggi
 Creation   : 2003
 Contents   : class that controls piana vocabularies, default values and database names for tables and columns
 Called from: all across piana modules
 
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File that sets piana vocabularies, default values and database names for tables and columns

 
Modules
       
PianaGlobals
sys
utilities

 
Data
        DBAliclusterID_col = 'DBAliclusterID'
DBAliclusteringMethod_col = 'DBAliclusteringMethod'
a_col = 'a'
accessionNumber_col = 'accessionNumber'
accessionNumber_table = 'accessionNumber'
array_score_col = 'array_score'
array_score_transferred_col = 'array_score_transferred'
bit_score_col = 'bit_score'
blastResults_table = 'blastResults'
c_col = 'c'
cathID_col = 'cathID'
cf_col = 'cf'
chain_col = 'chain'
cogDescription_col = 'cogDescription'
cogFunction_col = 'cogFunction'
cogID_col = 'cogID'
cogSource_col = 'sourceDBID'
cog_table = 'cog'
combined_score_col = 'combined_score'
conflictID_col = 'conflictID'
data_class_col = 'data_class'
databaseDate_col = 'date'
databaseDescription_col = 'databaseDescription'
databaseFile_col = 'parsed_file'
databaseInteger_col = 'databaseInteger'
databaseName_col = 'databaseName'
databaseType_col = 'databaseType'
databaseVersion_col = 'databaseVersion'
database_score_col = 'database_score'
database_score_transferred_col = 'database_score_transferred'
description_col = 'description'
dot_edge_lenght = '1'
dot_node_font_size = '10'
dot_node_height = '0.15'
dot_node_shape = 'box'
dot_node_style = 'filled'
dot_node_width = '0.15'
dot_orientation = 'portrait'
dot_overlap = 'scale'
dot_pack = 'true'
dot_standard_node_fill_color = 'lightblue'
ecDescription_col = 'ecDescription'
ecID_col = 'ecID'
ecSource_col = 'sourceDBID'
ec_table = 'ec'
end_A_col = 'end_A'
end_B_col = 'end_B'
ensembl_col = 'ensembl'
ensembl_table = 'ensembl'
equiv_fscore_col = 'equiv_fscore'
equiv_hscore_col = 'equiv_hscore'
equiv_nscore_col = 'equiv_nscore'
equiv_nscore_transferred_col = 'equiv_nscore_transferred'
equiv_pscore_col = 'equiv_pscore'
expansion_types = {'cog': ['cog', 'expansionsamecog'], 'ec': ['ec', 'expansionsameec'], 'interpro': ['interpro', 'expansionsameinterpro'], 'scop': ['scop', 'expansionsamescop']}
experimental_score_col = 'experimental_score'
experimental_score_transferred_col = 'experimental_score_transferred'
externalDatabaseType_table = 'externalDatabaseType'
externalDatabase_table = 'externalDatabase'
externalIdColumn_col = 'externalIdColumn'
externalIdDescription_col = 'externalIdDescription'
externalIdType_col = 'externalIdType'
fa_col = 'fa'
filter_col = 'filter'
gaps_col = 'gaps'
geneID_col = 'geneID'
geneID_table = 'geneID'
geneName_col = 'geneName'
geneName_table = 'geneName'
giID_col = 'giID'
gi_table = 'gi'
goID_col = 'goID'
goSource_col = 'sourceDBID'
go_acc_col = 'acc'
go_distance2root = 'distance2root'
go_name_col = 'name'
go_parent_col = 'go_parent'
go_son_col = 'go_son'
go_table = 'go'
go_term2term_distance_col = 'distance'
go_term2term_distance_table = 'go_term2term_distance'
go_term2term_distance_term1_col = 'go_term1'
go_term2term_distance_term2_col = 'go_term2'
go_term_type_col = 'term_type'
h_col = 'h'
huge_depth = 1000
huge_distance = 1000
huge_value = 100
identities_col = 'identities'
infra_expressed_protein = 'under_expressed'
intdbID_col = 'intdbID'
interProDescription_col = 'interProDescription'
interProID_col = 'interProID'
interProSource_col = 'sourceDBID'
interPro_table = 'interPro'
interactionConfidence_col = 'interactionConfidence'
interactionCounter_col = 'interactionCounter'
interactionFeatures_table = 'interactionFeatures'
interactionMethod_table = 'interactionMethod'
interactionPiana_col = 'interactionPiana'
interactionProteinSource_table = 'interactionProteinSource'
interactionScores_table = 'interactionScores'
interaction_line_styles = {'extended': 'dashed', 'normal': 'solid', 'propagated': 'dotted'}
interaction_source_databases_colors = {'': 'black', 'bind': 'grey', 'biogrid': 'pink', 'dip': 'red', 'hprd': 'blue', 'intact': 'brown', 'intersection': 'cyan', 'mint': 'lightblue', 'mips': 'darkgreen', 'ori': 'green', ...}
interaction_table = 'interaction'
isPrimary_col = 'isPrimary'
isSourceA_col = 'isSourceA'
isSourceB_col = 'isSourceB '
line_separators = {'html': '<br>', 'txt': '\n'}
methodID_col = 'methodID'
method_names = {'3dstruct': ['3dstruct', 'three dimensional structure', '3d structure', 'xcryst', 'x-ray crystallograph', 'x-ray crystallography', 'x-ray: x-ray crystallography', 'x-ray crystallography', 'xscat', 'x-ray scattering', 'pdb_int', 'coming from pdb', 'x-ray diffraction', 'co-crystal structure'], 'adenylate': ['adenylate', 'adenylate cyclase'], 'adhesion': ['adhesion', 'interaction adhesion', 'interaction adhesion assay'], 'affinchrom': ['affinchrom', 'affinity chromatogra', 'affinity chromatography technology', 'affinity chromatography', 'affinity chromatography technologies', 'affinity technology', 'affinity chrom', 'affinity techniques', 'affinity technologies', 'chromatography', 'chromatography technologies', 'reverse phase chrom', 'affinity capture-luminescence', 'affinity capture-rna', 'affinity capture-western', 'pulldown', 'pull down', 'gst pull down', 'his pull down', 'tandaffin', ...], 'alanine': ['alanine', 'alanine scanning'], 'antibodyarray': ['antibodyarray', 'antibody array'], 'arraytec': ['arraytec', 'peptide array', 'protein array', 'Epistatic MiniArray Profile', 'array technologies', 'microarray'], 'atomic': ['atomic', 'atomic force microsc', 'atomic force microscopy'], 'betagalactcompl': ['betagalactcompl', 'galactosidase', 'beta galactosidase', 'beta galactosidase complementation'], 'betalactcompl': ['betalactcompl', 'beta lactamase complementation'], ...}
mimID_col = 'mimID'
mimSource_col = 'sourceDBID'
mim_keywords_col = 'mimKeywords'
mim_table = 'mim'
mim_title_col = 'mimTitle'
negative_location_value = {'dot': '', 'html': 'no', 'sif': '', 'txt': 'different'}
negative_root_value = {'dot': '', 'html': 'no', 'sif': '', 'txt': 'not-root'}
negative_species_value = {'dot': '', 'html': 'no', 'sif': '', 'txt': 'different'}
node_border_colors = {'expanded': 'blue', 'normal': 'black', 'over_and_under_expressed': 'orange', 'over_expressed': 'red', 'under_expressed': 'green'}
node_fill_colors = {'keyword': 'red', 'normal': 'lightblue', 'root': 'yellow', 'root_keyword': 'orange'}
organelle_col = 'organelle'
organism_col = 'organism'
over_and_infra_expressed_protein = 'over_and_under_expressed'
over_expressed_protein = 'over_expressed'
patchResidues_col = 'patchResidues'
pdbID_col = 'pdbID'
pdb_chain_col = 'pdb_chain'
pdb_table = 'pdb'
pfamDescription_col = 'pfamDescription'
pfamID_col = 'pfamID'
pfamSource_col = 'sourceDBID'
pfam_table = 'pfam'
positive_location_value = {'dot': '', 'html': 'yes', 'sif': '', 'txt': 'same'}
positive_root_value = {'dot': '', 'html': 'yes', 'sif': '', 'txt': 'is-root'}
positive_species_value = {'dot': '', 'html': 'yes', 'sif': '', 'txt': 'same'}
program_col = 'program'
prositeID_col = 'prositeID'
prositeSource_col = 'sourceDBID'
proteinCathSource_col = 'sourceDBID'
proteinCath_table = 'proteinCath'
proteinCogSource_col = 'sourceDBID'
proteinCog_table = 'proteinCog'
proteinConflicts_table = 'proteinConflicts'
proteinCorrespondence_table = 'proteinCorrespondence'
proteinDBAliCluster_table = 'proteinDBAliCluster'
proteinDescriptionSource_col = 'sourceDBID'
proteinDescription_col = 'proteinDescription'
proteinDescription_table = 'proteinDescription'
proteinDiseaseSource_col = 'sourceDBID'
proteinDisease_col = 'proteinDisease'
proteinDisease_table = 'proteinDisease'
proteinECSource_col = 'sourceDBID'
proteinEC_table = 'proteinEC'
proteinExternalId_col = 'proteinExternalId'
proteinExternalId_table = 'proteinExternalId'
proteinFunctionSource_col = 'sourceDBID'
proteinFunction_col = 'proteinFunction'
proteinFunction_table = 'proteinFunction'
proteinGoSource_col = 'sourceDBID'
proteinGo_table = 'proteinGo'
proteinKeywordSource_col = 'sourceDBID'
proteinKeyword_col = 'proteinKeyword'
proteinKeyword_table = 'proteinKeyword'
proteinMIMSource_col = 'sourceDBID'
proteinMIM_col = 'mimID'
proteinMIM_table = 'proteinMIM'
proteinPianaA_col = 'proteinPianaA'
proteinPianaB_col = 'proteinPianaB '
proteinPianaCounter_col = 'proteinPianaCounter'
proteinPianaCounter_table = 'proteinPianaCounter'
proteinPiana_col = 'proteinPiana'
proteinProsite_table = 'proteinProsite'
proteinReactomeSource_col = 'sourceDBID'
proteinReactome_table = 'proteinReactome'
proteinScopSource_col = 'sourceDBID'
proteinScop_table = 'proteinScop'
proteinSimilarity_table = 'proteinSimilarity'
proteinSourceDB_table = 'proteinSourceDB'
proteinSubcellularLocationSource_col = 'sourceDBID'
proteinSubcellularLocation_col = 'proteinSubcellularLocation'
proteinSubcellularLocation_table = 'proteinSubcellularLocation'
proteinTable_col = 'proteinTable'
proteinTypeId_col = 'proteinTypeId'
protein_table = 'protein'
pubmedID_col = 'pubmedID'
range_col = 'range'
reactomeDescription_col = 'pathwayDescription'
reactomeID_col = 'reactomeID'
reactomeSource_col = 'sourceDBID'
reactome_table = 'reactome'
refseq_col = 'refseq'
refseq_table = 'refseq'
res_end_col = 'res_end'
res_start_col = 'res_start'
score_col = 'score'
segmentID_col = 'segmentID'
sequenceIDCounter_col = 'sequenceIDCounter'
sequenceID_A_col = 'sequenceID_A'
sequenceID_B_col = 'sequenceID_B'
sequenceID_col = 'sequenceID'
sequenceIP_col = 'sequenceIP'
sequenceLength_col = 'sequenceLength'
sequenceMD5_col = 'sequenceMD5'
sequenceMW_col = 'sequenceMW'
sequence_col = 'sequence'
sequence_table = 'sequence'
sf_col = 'sf'
similarity_col = 'similarity'
sourceDBID_col = 'sourceDBID'
speciesDescription_col = 'speciesDescription'
speciesKingdom_col = 'speciesKingdom'
speciesName_col = 'speciesName'
speciesSource_col = 'sourceDBID'
species_table = 'species'
start_A_col = 'start_A'
start_B_col = 'start_B'
t_col = 't'
tab_separators = {'html': ' ', 'txt': '\t'}
taxID_col = 'taxID'
temp_externalID_col = 'temp_externalID'
temporalData_table = 'temporalData'
textmining_score_col = 'textmining_score'
textmining_score_transferred_col = 'textmining_score_transferred'
unigene_col = 'unigene'
unigene_table = 'unigene'
uniprotAcc_col = 'uniprotAcc'
uniprotAcc_table = 'uniprotAcc'
uniprotEntry_col = 'uniprotEntry'
uniprotEntry_table = 'uniprotEntry'
validProteinIds_table = 'valid_protein_ids'
verbose = 0