Mercurial > repos > prog > lcmsmatching
diff 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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--- a/biodb-common.R Tue Jul 12 12:02:37 2016 -0400 +++ b/biodb-common.R Sat Sep 03 17:02:01 2016 -0400 @@ -1,154 +1,189 @@ -if ( ! exists('RBIODB.COMPOUND')) { # Do not load again if already loaded +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. ############# - # CONSTANTS # + # DATABASES # ############# - - # Entry types - RBIODB.COMPOUND <- 'compound' - RBIODB.SPECTRUM <- 'spectrum' - - # Entry content types - RBIODB.HTML <- 'html' - RBIODB.TXT <- 'txt' - RBIODB.XML <- 'xml' - RBIODB.CSV <- 'csv' - RBIODB.ANY <- 'any' - # Class names - RBIODB.CHEBI <- 'chebi' - RBIODB.KEGG <- 'kegg' - RBIODB.PUBCHEM <- 'pubchem' - RBIODB.HMDB <- 'hmdb' - RBIODB.CHEMSPIDER <- 'chemspider' - RBIODB.ENZYME <- 'enzyme' - RBIODB.LIPIDMAPS <- 'lipidmaps' - RBIODB.MIRBASE <- 'mirbase' - RBIODB.NCBIGENE <- 'ncbigene' - RBIODB.NCBICCDS <- 'ncbiccds' - RBIODB.UNIPROT <- 'uniprot' - RBIODB.MASSBANK <- 'massbank' + 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 # + ########## - # Fields - RBIODB.COMPOUND <- 'compound' - RBIODB.ACCESSION <- 'accession' - RBIODB.DESCRIPTION <- 'description' - RBIODB.PROTEIN.DESCRIPTION <- 'protdesc' - RBIODB.NAME <- 'name' - RBIODB.FULLNAMES <- 'fullnames' - RBIODB.SYNONYMS <- 'synonyms' - RBIODB.SYMBOL <- 'symbol' - RBIODB.GENE.SYMBOLS <- 'genesymbols' - RBIODB.CHEBI.ID <- 'chebiid' - RBIODB.LIPIDMAPS.ID <- 'lipidmapsid' - RBIODB.KEGG.ID <- 'keggid' - RBIODB.HMDB.ID <- 'hmdbid' - RBIODB.ENZYME.ID <- 'enzymeid' - RBIODB.NCBI.CCDS.ID <- 'ncbiccdsid' - RBIODB.NCBI.GENE.ID <- 'ncbigeneid' - RBIODB.PUBCHEM.ID <- 'pubchemid' - RBIODB.UNIPROT.ID <- 'uniprotid' - RBIODB.INCHI <- 'inchi' - RBIODB.INCHIKEY <- 'inchikey' - RBIODB.MSDEV <- 'msdev' - RBIODB.MSDEVTYPE <- 'msdevtype' - RBIODB.MSTYPE <- 'mstype' - RBIODB.MSMODE <- 'msmode' - RBIODB.MSPRECMZ <- 'msprecmz' # numeric - RBIODB.MSPRECANNOT <- 'msprecannot' - RBIODB.FORMULA <- 'formula' - RBIODB.SUPER.CLASS <- 'superclass' - RBIODB.MASS <- 'mass' - RBIODB.AVERAGE.MASS <- 'averagemass' - RBIODB.MONOISOTOPIC.MASS <- 'monoisotopicmass' - RBIODB.SEQUENCE <- 'sequence' - RBIODB.LOCATION <- 'location' - RBIODB.LENGTH <- 'length' - RBIODB.NB.PEAKS <- 'nbpeaks' - RBIODB.NB.PEAKS <- 'nbpeaks' - RBIODB.PEAKS <- 'peaks' + 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 - RBIODB.MSMODE.NEG <- 'neg' - RBIODB.MSMODE.POS <- 'pos' + BIODB.MSMODE.NEG <- 'neg' + BIODB.MSMODE.POS <- 'pos' + + ################# + # CARDINALITIES # + ################# - # Cardinalities - RBIODB.CARD.ONE <- '1' - RBIODB.CARD.MANY <- '*' + BIODB.CARD.ONE <- '1' + BIODB.CARD.MANY <- '*' - # Field attributes - RBIODB.FIELDS <- data.frame(matrix(c( + ########################## + # ENTRY FIELD ATTRIBUTES # + ########################## + + BIODB.FIELDS <- data.frame(matrix(c( # FIELD NAME CLASS CARDINALITY - RBIODB.COMPOUND, 'BiodEntry', RBIODB.CARD.ONE, - RBIODB.ACCESSION, 'character', RBIODB.CARD.ONE, - RBIODB.DESCRIPTION, 'character', RBIODB.CARD.ONE, - RBIODB.NAME, 'character', RBIODB.CARD.ONE, - RBIODB.FULLNAMES, 'character', RBIODB.CARD.MANY, - RBIODB.SYNONYMS, 'character', RBIODB.CARD.MANY, - RBIODB.PROTEIN.DESCRIPTION, 'character', RBIODB.CARD.ONE, - RBIODB.SYMBOL, 'character', RBIODB.CARD.ONE, - RBIODB.GENE.SYMBOLS, 'character', RBIODB.CARD.MANY, - RBIODB.CHEBI.ID, 'character', RBIODB.CARD.ONE, - RBIODB.LIPIDMAPS.ID, 'character', RBIODB.CARD.ONE, - RBIODB.KEGG.ID, 'character', RBIODB.CARD.ONE, - RBIODB.HMDB.ID, 'character', RBIODB.CARD.ONE, - RBIODB.ENZYME.ID, 'character', RBIODB.CARD.ONE, - RBIODB.PUBCHEM.ID, 'character', RBIODB.CARD.ONE, - RBIODB.UNIPROT.ID, 'character', RBIODB.CARD.ONE, - RBIODB.NCBI.CCDS.ID, 'character', RBIODB.CARD.ONE, - RBIODB.NCBI.GENE.ID, 'character', RBIODB.CARD.ONE, - RBIODB.INCHI, 'character', RBIODB.CARD.ONE, - RBIODB.INCHIKEY, 'character', RBIODB.CARD.ONE, - RBIODB.MSDEV, 'character', RBIODB.CARD.ONE, - RBIODB.MSDEVTYPE, 'character', RBIODB.CARD.ONE, - RBIODB.MSTYPE, 'character', RBIODB.CARD.ONE, - RBIODB.MSMODE, 'character', RBIODB.CARD.ONE, - RBIODB.MSPRECMZ, 'double', RBIODB.CARD.ONE, - RBIODB.MSPRECANNOT, 'character', RBIODB.CARD.ONE, - RBIODB.FORMULA, 'character', RBIODB.CARD.ONE, - RBIODB.SUPER.CLASS, 'character', RBIODB.CARD.ONE, - RBIODB.MASS, 'double', RBIODB.CARD.ONE, - RBIODB.AVERAGE.MASS, 'double', RBIODB.CARD.ONE, - RBIODB.MONOISOTOPIC.MASS, 'double', RBIODB.CARD.ONE, - RBIODB.SEQUENCE, 'character', RBIODB.CARD.ONE, - RBIODB.LENGTH, 'integer', RBIODB.CARD.ONE, - RBIODB.LOCATION, 'character', RBIODB.CARD.ONE, - RBIODB.NB.PEAKS, 'integer', RBIODB.CARD.ONE, - RBIODB.PEAKS, 'data.frame', RBIODB.CARD.ONE + 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(RBIODB.FIELDS) <- c('name', 'class', 'cardinality') + colnames(BIODB.FIELDS) <- c('name', 'class', 'cardinality') - # How to compute a missing field ? - RBIODB.FIELD.COMPUTING <- list() - RBIODB.FIELD.COMPUTING[[RBIODB.INCHI]] <- c(RBIODB.CHEBI) - RBIODB.FIELD.COMPUTING[[RBIODB.INCHIKEY]] <- c(RBIODB.CHEBI) - RBIODB.FIELD.COMPUTING[[RBIODB.SEQUENCE]] <- c(RBIODB.NCBICCDS) + ##################### + # 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 - RBIODB.PEAK.MZ <- 'mz' - RBIODB.PEAK.FORMULA <- 'formula' - RBIODB.PEAK.FORMULA.COUNT <- 'formula.count' - RBIODB.PEAK.MASS <- 'mass' - RBIODB.PEAK.ERROR.PPM <- 'error.ppm' - RBIODB.PEAK.INTENSITY <- 'intensity' - RBIODB.PEAK.RELATIVE.INTENSITY <- 'relative.intensity' - RBIODB.PEAK.DF.EXAMPLE <- data.frame(mz = double(), int = double(), rel.int = integer(), formula = character(), formula.count <- integer(), mass = double(), error = double(), stringsAsFactors = FALSE) - colnames(RBIODB.PEAK.DF.EXAMPLE) <- c(RBIODB.PEAK.MZ, RBIODB.PEAK.INTENSITY, RBIODB.PEAK.RELATIVE.INTENSITY, RBIODB.PEAK.FORMULA, RBIODB.PEAK.FORMULA.COUNT, RBIODB.PEAK.MASS, RBIODB.PEAK.ERROR.PPM) + #################### + # 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 - RBIODB.MASSBANK.JP.WS.URL <- "http://www.massbank.jp/api/services/MassBankAPI/getRecordInfo" - RBIODB.MASSBANK.EU.WS.URL <- "http://massbank.eu/api/services/MassBankAPI/getRecordInfo" + 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" - get.entry.url <- function(class, accession, content.type = RBIODB.ANY) { + .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(RBIODB.ANY, RBIODB.HTML)) paste0('https://www.ebi.ac.uk/chebi/searchId.do?chebiId=', accession) else NULL, - chemspider = if (content.type %in% c(RBIODB.ANY, RBIODB.HTML)) paste0('http://www.chemspider.com/Chemical-Structure.', accession, '.html') else NULL, - enzyme = if (content.type %in% c(RBIODB.ANY, RBIODB.TXT)) paste0('http://enzyme.expasy.org/EC/', accession, '.txt') else NULL, + 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), @@ -159,9 +194,9 @@ 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(RBIODB.ANY, RBIODB.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(RBIODB.ANY, RBIODB.TXT)) paste0(RBIODB.MASSBANK.EU.WS.URL, '?ids=', paste(accession, collapse = ',')) else NULL, - mirbase = if (content.type %in% c(RBIODB.ANY, RBIODB.HTML)) paste0('http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=', accession) else 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) @@ -170,12 +205,49 @@ html = paste0('http://pubchem.ncbi.nlm.nih.gov/compound/', accession), NULL) }, - ncbigene = if (content.type %in% c(RBIODB.ANY, RBIODB.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(RBIODB.ANY, RBIODB.HTML)) paste0('https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&GO=MainBrowse&DATA=', accession), - uniprot = if (content.type %in% c(RBIODB.ANY, RBIODB.XML)) paste0('http://www.uniprot.org/uniprot/', accession, '.xml'), + 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()) + } + }