Mercurial > repos > prog > lcmsmatching
view biodb-common.R @ 2:20d69a062da3 draft
planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8
| author | prog |
|---|---|
| date | Thu, 02 Mar 2017 08:55:00 -0500 |
| parents | 253d531a0193 |
| children |
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if ( ! exists('BIODB.XML')) { ############### # CACHE MODES # ############### BIODB.CACHE.READ.ONLY <- 'read-only' BIODB.CACHE.READ.WRITE <- 'read-write' BIODB.CACHE.WRITE.ONLY <- 'write-only' ####################### # ENTRY CONTENT TYPES # ####################### BIODB.HTML <- 'html' BIODB.TXT <- 'txt' BIODB.XML <- 'xml' BIODB.CSV <- 'csv' BIODB.DATAFRAME <- 'dataframe' BIODB.JSON <- 'json' ############# # DATABASES # ############# BIODB.CHEBI <- 'chebi' BIODB.KEGG <- 'kegg' BIODB.PUBCHEMCOMP <- 'pubchemcomp' # Compound database BIODB.PUBCHEMSUB <- 'pubchemsub' # Substance database BIODB.HMDB <- 'hmdb' BIODB.CHEMSPIDER <- 'chemspider' BIODB.ENZYME <- 'enzyme' BIODB.LIPIDMAPS <- 'lipidmaps' BIODB.MIRBASE <- 'mirbase' BIODB.NCBIGENE <- 'ncbigene' BIODB.NCBICCDS <- 'ncbiccds' BIODB.UNIPROT <- 'uniprot' BIODB.MASSBANK <- 'massbank' BIODB.MASSFILEDB <- 'massfiledb' BIODB.PEAKFOREST <- 'peakforest' BIODB.DATABASES <- c(BIODB.CHEBI, BIODB.KEGG, BIODB.PUBCHEMCOMP, BIODB.PUBCHEMSUB, BIODB.HMDB, BIODB.CHEMSPIDER, BIODB.ENZYME, BIODB.LIPIDMAPS, BIODB.MIRBASE, BIODB.NCBIGENE, BIODB.NCBICCDS, BIODB.UNIPROT, BIODB.MASSBANK, BIODB.MASSFILEDB, BIODB.PEAKFOREST) ########## # FIELDS # ########## BIODB.ACCESSION <- 'accession' BIODB.DESCRIPTION <- 'description' BIODB.PROTEIN.DESCRIPTION <- 'protdesc' BIODB.NAME <- 'name' BIODB.COMP.IUPAC.NAME.ALLOWED <- 'comp.iupac.name.allowed' BIODB.COMP.IUPAC.NAME.TRAD <- 'comp.iupac.name.trad' BIODB.COMP.IUPAC.NAME.SYST <- 'comp.iupac.name.syst' BIODB.COMP.IUPAC.NAME.PREF <- 'comp.iupac.name.pref' BIODB.COMP.IUPAC.NAME.CAS <- 'comp.iupac.name.cas' BIODB.FULLNAMES <- 'fullnames' BIODB.SYNONYMS <- 'synonyms' BIODB.SYMBOL <- 'symbol' BIODB.GENE.SYMBOLS <- 'genesymbols' BIODB.CHEBI.ID <- 'chebiid' BIODB.LIPIDMAPS.ID <- 'lipidmapsid' BIODB.KEGG.ID <- 'keggid' BIODB.HMDB.ID <- 'hmdbid' BIODB.ENZYME.ID <- 'enzymeid' BIODB.NCBI.CCDS.ID <- 'ncbiccdsid' BIODB.NCBI.GENE.ID <- 'ncbigeneid' BIODB.PUBCHEMCOMP.ID <- 'pubchemcompid' BIODB.PUBCHEMSUB.ID <- 'pubchemsubid' BIODB.CHEMSPIDER.ID <- 'chemspiderid' BIODB.UNIPROT.ID <- 'uniprotid' BIODB.CAS.ID <- 'casid' BIODB.PEAKFOREST.ID <- 'peakforestid' BIODB.SMILES <- 'smiles' BIODB.INCHI <- 'inchi' BIODB.INCHIKEY <- 'inchikey' BIODB.MSDEV <- 'msdev' BIODB.MSDEVTYPE <- 'msdevtype' BIODB.MSTYPE <- 'mstype' BIODB.MSMODE <- 'msmode' BIODB.MSPRECMZ <- 'msprecmz' # numeric BIODB.MSPRECANNOT <- 'msprecannot' BIODB.FORMULA <- 'formula' BIODB.SUPER.CLASS <- 'superclass' BIODB.MASS <- 'mass' BIODB.AVERAGE.MASS <- 'averagemass' BIODB.MONOISOTOPIC.MASS <- 'monoisotopicmass' BIODB.SEQUENCE <- 'sequence' BIODB.LOCATION <- 'location' BIODB.LENGTH <- 'length' BIODB.NB.PEAKS <- 'nbpeaks' BIODB.PEAKS <- 'peaks' BIODB.COMPOUNDS <- 'compounds' BIODB.NB.COMPOUNDS <- 'nbcompounds' BIODB.COMPOUND.ID <- 'compoundid' BIODB.COMPOUND.MASS <- 'compoundmass' BIODB.COMPOUND.COMP <- 'compoundcomp' BIODB.CHROM.COL <- 'chromcol' # Chromatographic column BIODB.CHROM.COL.RT <- 'chromcolrt' # Retention time measured on chromatographic column BIODB.ID <- 'id' BIODB.TITLE <- 'title' BIODB.PEAK.MZ <- 'mz' BIODB.PEAK.RT <- 'rt' BIODB.PEAK.MZEXP <- 'mzexp' BIODB.PEAK.MZTHEO <- 'mztheo' BIODB.PEAK.FORMULA <- 'formula' BIODB.PEAK.FORMULA.COUNT <- 'formula.count' BIODB.PEAK.COMP <- 'peakcomp' # Peak composition BIODB.PEAK.ATTR <- 'peakattr' # Peak attribution BIODB.PEAK.MASS <- 'mass' # BIODB.PEAK.ATTR <- 'attr' BIODB.PEAK.ERROR.PPM <- 'error.ppm' BIODB.PEAK.INTENSITY <- 'intensity' BIODB.PEAK.RELATIVE.INTENSITY <- 'relative.intensity' # Mode values BIODB.MSMODE.NEG <- 'neg' BIODB.MSMODE.POS <- 'pos' # Tolerance values BIODB.TOL <- 'mztol' BIODB.MZTOLUNIT.PPM <- 'ppm' BIODB.MZTOLUNIT.PLAIN <- 'plain' # same as mz: mass-to-charge ratio BIODB.MZTOLUNIT.VALS <- c(BIODB.MZTOLUNIT.PPM, BIODB.MZTOLUNIT.PLAIN) ######################## # MS-MS MEASURE VALUES # ######################## BIODB.MSMS.DIST.COS <- "cosine" BIODB.MSMS.DIST.WCOSINE <- "wcosine" BIODB.MSMS.DIST.PKERNEL <- "pkernel" BIODB.MSMS.DIST <- c(BIODB.MSMS.DIST.COS, BIODB.MSMS.DIST.WCOSINE, BIODB.MSMS.DIST.PKERNEL) ################# # CARDINALITIES # ################# BIODB.CARD.ONE <- '1' BIODB.CARD.MANY <- '*' ##################### #INTENSITy NOTATIONS# ##################### BIODB.GROUP.INTENSITY<-c(BIODB.PEAK.INTENSITY,BIODB.PEAK.RELATIVE.INTENSITY) ########################## # ENTRY FIELD ATTRIBUTES # ########################## # FIELD NAME CLASS CARDINALITY TYPE BIODB.FIELDS <- data.frame(matrix(c( BIODB.ACCESSION, 'character', BIODB.CARD.ONE, 'none', BIODB.DESCRIPTION, 'character', BIODB.CARD.ONE, 'none', BIODB.NAME, 'character', BIODB.CARD.ONE, 'name', BIODB.COMP.IUPAC.NAME.ALLOWED, 'character', BIODB.CARD.ONE, 'name', BIODB.COMP.IUPAC.NAME.TRAD, 'character', BIODB.CARD.ONE, 'name', BIODB.COMP.IUPAC.NAME.SYST, 'character', BIODB.CARD.ONE, 'name', BIODB.COMP.IUPAC.NAME.PREF, 'character', BIODB.CARD.ONE, 'name', BIODB.COMP.IUPAC.NAME.CAS, 'character', BIODB.CARD.ONE, 'name', BIODB.FULLNAMES, 'character', BIODB.CARD.MANY, 'name', BIODB.SYNONYMS, 'character', BIODB.CARD.MANY, 'name', BIODB.PROTEIN.DESCRIPTION, 'character', BIODB.CARD.ONE, 'none', BIODB.SYMBOL, 'character', BIODB.CARD.ONE, 'none', BIODB.GENE.SYMBOLS, 'character', BIODB.CARD.MANY, 'none', BIODB.NB.COMPOUNDS, 'integer', BIODB.CARD.ONE, 'none', BIODB.COMPOUNDS, 'object', BIODB.CARD.MANY, 'none', BIODB.CHEBI.ID, 'character', BIODB.CARD.ONE, 'none', BIODB.LIPIDMAPS.ID, 'character', BIODB.CARD.ONE, 'none', BIODB.KEGG.ID, 'character', BIODB.CARD.ONE, 'none', BIODB.HMDB.ID, 'character', BIODB.CARD.ONE, 'none', BIODB.ENZYME.ID, 'character', BIODB.CARD.ONE, 'none', BIODB.PUBCHEMCOMP.ID, 'character', BIODB.CARD.ONE, 'none', BIODB.PUBCHEMSUB.ID, 'character', BIODB.CARD.ONE, 'none', BIODB.PEAKFOREST.ID, 'character', BIODB.CARD.ONE, 'none', BIODB.UNIPROT.ID, 'character', BIODB.CARD.ONE, 'none', BIODB.NCBI.CCDS.ID, 'character', BIODB.CARD.ONE, 'none', BIODB.NCBI.GENE.ID, 'character', BIODB.CARD.ONE, 'none', BIODB.INCHI, 'character', BIODB.CARD.ONE, 'none', BIODB.INCHIKEY, 'character', BIODB.CARD.ONE, 'none', BIODB.MSDEV, 'character', BIODB.CARD.ONE, 'none', BIODB.MSDEVTYPE, 'character', BIODB.CARD.ONE, 'none', BIODB.MSTYPE, 'character', BIODB.CARD.ONE, 'none', BIODB.MSMODE, 'character', BIODB.CARD.ONE, 'none', BIODB.MSPRECMZ, 'double', BIODB.CARD.ONE, 'none', BIODB.PEAK.MZTHEO, 'double', BIODB.CARD.ONE, 'none', BIODB.MSPRECANNOT, 'character', BIODB.CARD.ONE, 'none', BIODB.FORMULA, 'character', BIODB.CARD.ONE, 'none', BIODB.SUPER.CLASS, 'character', BIODB.CARD.ONE, 'none', BIODB.MASS, 'double', BIODB.CARD.ONE, 'none', BIODB.AVERAGE.MASS, 'double', BIODB.CARD.ONE, 'none', BIODB.MONOISOTOPIC.MASS, 'double', BIODB.CARD.ONE, 'none', BIODB.SEQUENCE, 'character', BIODB.CARD.ONE, 'none', BIODB.LENGTH, 'integer', BIODB.CARD.ONE, 'none', BIODB.LOCATION, 'character', BIODB.CARD.ONE, 'none', BIODB.NB.PEAKS, 'integer', BIODB.CARD.ONE, 'none', BIODB.PEAKS, 'data.frame', BIODB.CARD.ONE, 'none', BIODB.SMILES, 'character', BIODB.CARD.ONE, 'none', BIODB.CHEMSPIDER.ID, 'character', BIODB.CARD.ONE, 'none', BIODB.CAS.ID, 'character', BIODB.CARD.ONE, 'none' ), byrow = TRUE, ncol = 4), stringsAsFactors = FALSE) colnames(BIODB.FIELDS) <- c('name', 'class', 'cardinality', 'type') ######################### # GET DATABASE ID FIELD # ######################### biodb.get.database.id.field <- function(database) { id.field <- NA_character_ if (database %in% BIODB.DATABASES) { id.field <- paste0(database, 'id') if ( ! id.field %in% BIODB.FIELDS[['name']]) stop(paste0('No ID field defined for database ', database, '.')) } return(id.field) } ##################### # COMPUTABLE FIELDS # ##################### BIODB.FIELD.COMPUTING <- list() BIODB.FIELD.COMPUTING[[BIODB.INCHI]] <- c(BIODB.CHEBI) BIODB.FIELD.COMPUTING[[BIODB.INCHIKEY]] <- c(BIODB.CHEBI) BIODB.FIELD.COMPUTING[[BIODB.SEQUENCE]] <- c(BIODB.NCBICCDS) #################### # PEAKS DATA FRAME # #################### # Example BIODB.PEAK.DF.EXAMPLE <- data.frame(mz = double(), int = double(), rel.int = integer(), formula = character(), formula.count <- integer(), mass = double(), error = double(), stringsAsFactors = FALSE) colnames(BIODB.PEAK.DF.EXAMPLE) <- c(BIODB.PEAK.MZ, BIODB.PEAK.INTENSITY, BIODB.PEAK.RELATIVE.INTENSITY, BIODB.PEAK.FORMULA, BIODB.PEAK.FORMULA.COUNT, BIODB.PEAK.MASS, BIODB.PEAK.ERROR.PPM) ################# # GET ENTRY URL # ################# # TODO Let the choice to use either jp or eu BIODB.MASSBANK.JP.WS.URL <- "http://www.massbank.jp/api/services/MassBankAPI/" BIODB.MASSBANK.EU.WS.URL <- "http://massbank.eu/api/services/MassBankAPI/" .do.get.entry.url <- function(class, accession, content.type = BIODB.HTML, base.url = NA_character_, token = NA_character_) { # Only certain databases can handle multiple accession ids if ( ! class %in% c(BIODB.MASSBANK, BIODB.CHEMSPIDER, BIODB.PUBCHEMCOMP, BIODB.PUBCHEMSUB, BIODB.PEAKFOREST) && length(accession) > 1) stop(paste0("Cannot build a URL for getting multiple entries for class ", class, ".")) # Get URL url <- switch(class, chebi = if (content.type == BIODB.HTML) paste0('https://www.ebi.ac.uk/chebi/searchId.do?chebiId=', accession) else NULL, chemspider = { token.param <- if (is.na(token)) '' else paste('&token', token, sep = '=') switch(content.type, html = paste0('http://www.chemspider.com/Chemical-Structure.', accession, '.html'), xml = paste0('http://www.chemspider.com/MassSpecAPI.asmx/GetExtendedCompoundInfoArray?', paste(paste0('CSIDs=', accession), collapse = '&'), token.param), NULL) }, enzyme = if (content.type == BIODB.TXT) paste0('http://enzyme.expasy.org/EC/', accession, '.txt') else NULL, hmdb = switch(content.type, xml = paste0('http://www.hmdb.ca/metabolites/', accession, '.xml'), html = paste0('http://www.hmdb.ca/metabolites/', accession), NULL), kegg = switch(content.type, txt = paste0('http://rest.kegg.jp/get/', accession), html = paste0('http://www.genome.jp/dbget-bin/www_bget?cpd:', accession), NULL), lipidmaps = if (content.type == BIODB.CSV) paste0('http://www.lipidmaps.org/data/LMSDRecord.php?Mode=File&LMID=', accession, '&OutputType=CSV&OutputQuote=No') else NULL, massbank = if (content.type == BIODB.TXT) paste0((if (is.na(base.url)) BIODB.MASSBANK.EU.WS.URL else base.url), 'getRecordInfo?ids=', paste(accession, collapse = ',')) else NULL, mirbase = if (content.type == BIODB.HTML) paste0('http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=', accession) else NULL, pubchemcomp = switch(content.type, xml = paste0('https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/', paste(accession, collapse = ','), '/XML'), html = paste0('http://pubchem.ncbi.nlm.nih.gov/compound/', accession), NULL), pubchemsub = switch(content.type, xml = paste0('https://pubchem.ncbi.nlm.nih.gov/rest/pug/substance/sid/', paste(accession, collapse = ','), '/XML'), html = paste0('http://pubchem.ncbi.nlm.nih.gov/substance/', accession), NULL), ncbigene = if (content.type == BIODB.XML) paste0('https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=', accession, '&rettype=xml&retmode=text') else NULL, ncbiccds = if (content.type == BIODB.HTML) paste0('https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=', accession), uniprot = if (content.type == BIODB.XML) paste0('http://www.uniprot.org/uniprot/', accession, '.xml'), peakforest = switch(content.type, html= paste0('https://peakforest.org/home?PFs=',accession), json= paste0('https://peakforest-alpha.inra.fr/rest/spectra/lcms/ids/',paste(accession,sep=','),'?token=',token), NULL ) ) return(url) } get.entry.url <- function(class, accession, content.type = BIODB.HTML, max.length = 0, base.url = NA_character_, token = NA_character_) { if (length(accession) == 0) return(NULL) full.url <- .do.get.entry.url(class, accession, content.type = content.type, base.url = base.url, token = token) if (max.length == 0 || nchar(full.url) <= max.length) return(if (max.length == 0) full.url else list(url = full.url, n = length(accession))) # Find max size URL a <- 1 b <- length(accession) while (a < b) { m <- as.integer((a + b) / 2) url <- .do.get.entry.url(class, accession[1:m], content.type = content.type, base.url = base.url, token = token) if (nchar(url) <= max.length && m != a) a <- m else b <- m } url <- .do.get.entry.url(class, accession[1:a], content.type = content.type, base.url = base.url, token = token) return(list( url = url, n = a)) } ################# # PRINT MESSAGE # ################# BIODB.DEBUG <- 1 BIODB.LEVEL.NAMES <- c('DEBUG') .print.msg <- function(msg, level = BIODB.DEBUG, class = NA_character_) { cat(paste0(BIODB.LEVEL.NAMES[[level]], if (is.na(class)) '' else paste0(", ", class), ": ", msg, "\n"), file = stderr()) } ##################### # BIODB GET ENV VAR # ##################### .biodb.get.env.var <- function(v) { # Get all env vars env <- Sys.getenv() # Make env var name env.var <- paste(c('BIODB', toupper(v)), collapse = '_') # Look if this env var exists if (env.var %in% names(env)) return(env[[env.var]]) return(NA_character_) } }