Mercurial > repos > prog > lcmsmatching
view biodb-common.R @ 1:253d531a0193 draft
planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 36c9d8099c20a1ae848f1337c16564335dd8fb2b
| author | prog |
|---|---|
| date | Sat, 03 Sep 2016 17:02:01 -0400 |
| parents | e66bb061af06 |
| children | 20d69a062da3 |
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if ( ! exists('BIODB.COMPOUND')) { # Do not load again if already loaded ############### # ENTRY TYPES # ############### BIODB.COMPOUND <- 'compound' BIODB.SPECTRUM <- 'spectrum' ####################### # ENTRY CONTENT TYPES # ####################### BIODB.HTML <- 'html' BIODB.TXT <- 'txt' BIODB.XML <- 'xml' BIODB.CSV <- 'csv' BIODB.DATAFRAME <- 'dataframe' BIODB.ANY <- 'any' # Value used when we do not care about the type. ############# # DATABASES # ############# BIODB.CHEBI <- 'chebi' BIODB.KEGG <- 'kegg' BIODB.PUBCHEM <- 'pubchem' 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' ########## # FIELDS # ########## BIODB.ACCESSION <- 'accession' BIODB.DESCRIPTION <- 'description' BIODB.PROTEIN.DESCRIPTION <- 'protdesc' BIODB.NAME <- 'name' 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.PUBCHEM.ID <- 'pubchemid' BIODB.UNIPROT.ID <- 'uniprotid' 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.COMPOUND.ID <- 'compoundid' BIODB.PEAK.MZ <- 'peakmz' BIODB.PEAK.COMP <- 'peakcomp' # Peak composition BIODB.PEAK.ATTR <- 'peakattr' # Peak attribution BIODB.CHROM.COL <- 'chromcol' # Chromatographic column BIODB.CHROM.COL.RT <- 'chromcolrt' # Retention time measured on chromatographic column BIODB.ID <- 'id' BIODB.TITLE <- 'title' # Mode values BIODB.MSMODE.NEG <- 'neg' BIODB.MSMODE.POS <- 'pos' ################# # CARDINALITIES # ################# BIODB.CARD.ONE <- '1' BIODB.CARD.MANY <- '*' ########################## # ENTRY FIELD ATTRIBUTES # ########################## BIODB.FIELDS <- data.frame(matrix(c( # FIELD NAME CLASS CARDINALITY BIODB.COMPOUND, 'BiodEntry', BIODB.CARD.ONE, BIODB.ACCESSION, 'character', BIODB.CARD.ONE, BIODB.DESCRIPTION, 'character', BIODB.CARD.ONE, BIODB.NAME, 'character', BIODB.CARD.ONE, BIODB.FULLNAMES, 'character', BIODB.CARD.MANY, BIODB.SYNONYMS, 'character', BIODB.CARD.MANY, BIODB.PROTEIN.DESCRIPTION, 'character', BIODB.CARD.ONE, BIODB.SYMBOL, 'character', BIODB.CARD.ONE, BIODB.GENE.SYMBOLS, 'character', BIODB.CARD.MANY, BIODB.CHEBI.ID, 'character', BIODB.CARD.ONE, BIODB.LIPIDMAPS.ID, 'character', BIODB.CARD.ONE, BIODB.KEGG.ID, 'character', BIODB.CARD.ONE, BIODB.HMDB.ID, 'character', BIODB.CARD.ONE, BIODB.ENZYME.ID, 'character', BIODB.CARD.ONE, BIODB.PUBCHEM.ID, 'character', BIODB.CARD.ONE, BIODB.UNIPROT.ID, 'character', BIODB.CARD.ONE, BIODB.NCBI.CCDS.ID, 'character', BIODB.CARD.ONE, BIODB.NCBI.GENE.ID, 'character', BIODB.CARD.ONE, BIODB.INCHI, 'character', BIODB.CARD.ONE, BIODB.INCHIKEY, 'character', BIODB.CARD.ONE, BIODB.MSDEV, 'character', BIODB.CARD.ONE, BIODB.MSDEVTYPE, 'character', BIODB.CARD.ONE, BIODB.MSTYPE, 'character', BIODB.CARD.ONE, BIODB.MSMODE, 'character', BIODB.CARD.ONE, BIODB.MSPRECMZ, 'double', BIODB.CARD.ONE, BIODB.MSPRECANNOT, 'character', BIODB.CARD.ONE, BIODB.FORMULA, 'character', BIODB.CARD.ONE, BIODB.SUPER.CLASS, 'character', BIODB.CARD.ONE, BIODB.MASS, 'double', BIODB.CARD.ONE, BIODB.AVERAGE.MASS, 'double', BIODB.CARD.ONE, BIODB.MONOISOTOPIC.MASS, 'double', BIODB.CARD.ONE, BIODB.SEQUENCE, 'character', BIODB.CARD.ONE, BIODB.LENGTH, 'integer', BIODB.CARD.ONE, BIODB.LOCATION, 'character', BIODB.CARD.ONE, BIODB.NB.PEAKS, 'integer', BIODB.CARD.ONE, BIODB.PEAKS, 'data.frame', BIODB.CARD.ONE ), byrow = TRUE, ncol = 3), stringsAsFactors = FALSE) colnames(BIODB.FIELDS) <- c('name', 'class', 'cardinality') ##################### # 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 # #################### # Columns BIODB.PEAK.MZ <- 'mz' BIODB.PEAK.FORMULA <- 'formula' BIODB.PEAK.FORMULA.COUNT <- 'formula.count' BIODB.PEAK.MASS <- 'mass' BIODB.PEAK.ERROR.PPM <- 'error.ppm' BIODB.PEAK.INTENSITY <- 'intensity' BIODB.PEAK.RELATIVE.INTENSITY <- 'relative.intensity' # 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/getRecordInfo" BIODB.MASSBANK.EU.WS.URL <- "http://massbank.eu/api/services/MassBankAPI/getRecordInfo" .do.get.entry.url <- function(class, accession, content.type = BIODB.ANY) { # TODO Only Massbank can handle multiple accession ids if (class != 'massbank' && length(accession) > 1) stop(paste0("Cannot build a URL for getting multiple entries for class ", class, ".")) url <- switch(class, chebi = if (content.type %in% c(BIODB.ANY, BIODB.HTML)) paste0('https://www.ebi.ac.uk/chebi/searchId.do?chebiId=', accession) else NULL, chemspider = if (content.type %in% c(BIODB.ANY, BIODB.HTML)) paste0('http://www.chemspider.com/Chemical-Structure.', accession, '.html') else NULL, enzyme = if (content.type %in% c(BIODB.ANY, 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), any = 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), any = paste0('http://www.genome.jp/dbget-bin/www_bget?cpd:', accession), NULL), lipidmaps = if (content.type %in% c(BIODB.ANY, BIODB.CSV)) paste0('http://www.lipidmaps.org/data/LMSDRecord.php?Mode=File&LMID=', accession, '&OutputType=CSV&OutputQuote=No') else NULL, massbank = if (content.type %in% c(BIODB.ANY, BIODB.TXT)) paste0(BIODB.MASSBANK.EU.WS.URL, '?ids=', paste(accession, collapse = ',')) else NULL, mirbase = if (content.type %in% c(BIODB.ANY, BIODB.HTML)) paste0('http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=', accession) else NULL, pubchem = { accession <- gsub(' ', '', accession, perl = TRUE) accession <- gsub('^CID', '', accession, perl = TRUE) switch(content.type, xml = paste0('http://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/', accession, '/XML/?response_type=save&response_basename=CID_', accession), html = paste0('http://pubchem.ncbi.nlm.nih.gov/compound/', accession), NULL) }, ncbigene = if (content.type %in% c(BIODB.ANY, BIODB.XML)) paste0('http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=', accession, '&rettype=xml&retmode=text') else NULL, ncbiccds = if (content.type %in% c(BIODB.ANY, BIODB.HTML)) paste0('https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=', accession), uniprot = if (content.type %in% c(BIODB.ANY, BIODB.XML)) paste0('http://www.uniprot.org/uniprot/', accession, '.xml'), NULL ) return(url) } get.entry.url <- function(class, accession, content.type = BIODB.ANY, max.length = 0) { if (length(accession) == 0) return(NULL) full.url <- .do.get.entry.url(class, accession, content.type = content.type) 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) 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) 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()) } }