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
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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 |