## ----style, eval=TRUE, echo=FALSE, results='asis'------------------------
BiocStyle::latex()


## ----include=FALSE-------------------------------------------------------
library(knitr)
opts_chunk$set(tidy=FALSE)


## ----Homo.sapiens--------------------------------------------------------
library(Homo.sapiens)
columns(Homo.sapiens)


## ----Homo.sapiens2-------------------------------------------------------
keytypes(Homo.sapiens) 


## ----Homo.sapiens3-------------------------------------------------------
k <- head(keys(Homo.sapiens,keytype="ENTREZID"))
k


## ----Homo.sapiens4-------------------------------------------------------
result <- select(Homo.sapiens, keys=k, 
                 columns=c("TXNAME","TXSTART","TXSTRAND"), 
                 keytype="ENTREZID")
head(result)


## ----URI Example---------------------------------------------------------
   uri <- 'http://www.uniprot.org/uniprot/?query='
   ids <- c('P13368', 'Q6GZX4')
   idStr <- paste(ids, collapse="+or+")
   format <- '&format=tab'
   fullUri <- paste0(uri,idStr,format)
   read.delim(fullUri)


## ----web service code----------------------------------------------------
getUniprotGoodies  <- function(query, columns)
{
    ## query and columns start as a character vectors
    qstring <- paste(query, collapse="+or+")
    cstring <- paste(columns, collapse=",")
    uri <- 'http://www.uniprot.org/uniprot/?query='
    fullUri <- paste0(uri,qstring,'&format=tab&columns=',cstring)
    dat <- read.delim(fullUri, stringsAsFactors=FALSE)
    ## now remove things that were not in the specific original query...
    dat <- dat[dat[,1] %in% query,]
    dat
}


## ----xml_tree------------------------------------------------------------
library(XML)
uri <- "http://www.uniprot.org/uniprot/?query=P13368+or+Q6GZX4&format=xml"
xml <- xmlTreeParse(uri, useInternalNodes=TRUE)


## ----xml_namespace-------------------------------------------------------
defs <- xmlNamespaceDefinitions(xml, recurisve=TRUE)
defs


## ----xml_namespace_struct------------------------------------------------
ns <- structure(sapply(defs, function(x) x$uri), names=names(defs))


## ----xml_namespace2------------------------------------------------------
entry <- getNodeSet(xml, "//ns:entry", "ns")
xmlSize(entry)


## ----xml_xmlAttrs--------------------------------------------------------
nms <- xpathSApply(xml, "//ns:entry/ns:name", xmlValue, namespaces="ns")
attrs <- xpathApply(xml, "//ns:entry", xmlAttrs, namespaces="ns")
names(attrs) <- nms
attrs


## ----xml_xmlChildren-----------------------------------------------------
fun1 <- function(elt) unique(names(xmlChildren(elt)))
xpathApply(xml, "//ns:entry", fun1, namespaces="ns")


## ----xml_feature_type----------------------------------------------------
Q6GZX4 <- "//ns:entry[ns:accession='Q6GZX4']/ns:feature"
xmlSize(getNodeSet(xml, Q6GZX4, namespaces="ns"))

P13368 <- "//ns:entry[ns:accession='P13368']/ns:feature"
xmlSize(getNodeSet(xml, P13368, namespaces="ns"))


## ----xml_feature_type2---------------------------------------------------
path <- "//ns:feature"
unique(xpathSApply(xml, path, xmlGetAttr, "type", namespaces="ns"))


## ----xml_feature_type_P13368---------------------------------------------
path <- "//ns:entry[ns:accession='P13368']/ns:feature[@type='sequence conflict']"
data.frame(t(xpathSApply(xml, path, xmlAttrs, namespaces="ns")))


## ----xml_sequence--------------------------------------------------------
library(Biostrings)
path <- "//ns:entry/ns:sequence"
seqs <- xpathSApply(xml, path, xmlValue, namespaces="ns")
aa <- AAStringSet(unlist(lapply(seqs, function(elt) gsub("\n", "", elt)),
    use.names=FALSE))
names(aa) <- nms
aa


## ----WebServiceObject----------------------------------------------------
setClass("uniprot", representation(name="character"),
         prototype(name="uniprot"))


## ----makeInstanceWebServiceObj-------------------------------------------
    uniprot <- new("uniprot")


## ----onLoad2,eval=FALSE--------------------------------------------------
## .onLoad <- function(libname, pkgname)
## {
##     ns <- asNamespace(pkgname)
##     uniprot <- new("uniprot")
##     assign("uniprot", uniprot, envir=ns)
##     namespaceExport(ns, "uniprot")
## }


## ----keytypeUniprot------------------------------------------------------
setMethod("keytypes", "uniprot",function(x){return("UNIPROT")})
uniprot <- new("uniprot")
keytypes(uniprot)


## ----keytypeUniprot2-----------------------------------------------------
setMethod("columns", "uniprot", 
          function(x){return(c("ID", "SEQUENCE", "ORGANISM"))})
columns(uniprot)


## ----webServiceSelect----------------------------------------------------
.select <- function(x, keys, columns){
    colsTranslate <- c(id='ID', sequence='SEQUENCE', organism='ORGANISM')
    columns <- names(colsTranslate)[colsTranslate %in% columns]
    getUniprotGoodies(query=keys, columns=columns)
}
setMethod("select", "uniprot", 
    function(x, keys, columns, keytype)
{
    .select(keys=keys, columns=columns)
})


## ----webServiceSelect2, eval=FALSE---------------------------------------
## select(uniprot, keys=c("P13368","P20806"), columns=c("ID","ORGANISM"))


## ----classicConn,results='hide'------------------------------------------
drv <- SQLite()
library("org.Hs.eg.db")
con_hs <- dbConnect(drv, dbname=system.file("extdata", "org.Hs.eg.sqlite",
                        package = "org.Hs.eg.db"))
con_hs
dbDisconnect(con_hs)


## ----ourConn-------------------------------------------------------------
require(hom.Hs.inp.db)
str(hom.Hs.inp.db)


## ----ourConn2------------------------------------------------------------
hom.Hs.inp.db$conn
## or better we can use a helper function to wrap this:
AnnotationDbi:::dbconn(hom.Hs.inp.db)
## or we can just call the provided convenience function 
## from when this package loads:
hom.Hs.inp_dbconn()


## ----dbListTables--------------------------------------------------------
con <- AnnotationDbi:::dbconn(hom.Hs.inp.db)
head(dbListTables(con))
dbListFields(con, "Mus_musculus")


## ----dbGetQuery----------------------------------------------------------
dbGetQuery(con, "SELECT * FROM metadata")


## ----dbListTables2-------------------------------------------------------
head(dbListTables(con))


## ----dbListFields2-------------------------------------------------------
dbListFields(con, "Apis_mellifera")


## ----dbGetQuery2---------------------------------------------------------
head(dbGetQuery(con, "SELECT * FROM Apis_mellifera"))


## ----Anopheles,eval=FALSE------------------------------------------------
## head(dbGetQuery(con, "SELECT * FROM Anopheles_gambiae"))
## ## Then only retrieve human records
## ## Query: SELECT * FROM Anopheles_gambiae WHERE species='HOMSA'
## head(dbGetQuery(con, "SELECT * FROM Anopheles_gambiae WHERE species='HOMSA'"))
## dbDisconnect(con)


## ----getMetadata, echo=FALSE---------------------------------------------
library(hom.Hs.inp.db)
hom.Hs.inp_dbInfo()


## ----referenceClass,eval=FALSE-------------------------------------------
## .InparanoidDb <-
##     setRefClass("InparanoidDb", contains="AnnotationDb")


## ----onLoad,eval=FALSE---------------------------------------------------
## sPkgname <- sub(".db$","",pkgname)
## db <- loadDb(system.file("extdata", paste(sPkgname,
##                ".sqlite",sep=""), package=pkgname, lib.loc=libname),
##                packageName=pkgname)
## dbNewname <- AnnotationDbi:::dbObjectName(pkgname,"InparanoidDb")
## ns <- asNamespace(pkgname)
## assign(dbNewname, db, envir=ns)
## namespaceExport(ns, dbNewname)


## ----columns,eval=FALSE--------------------------------------------------
## .cols <- function(x)
## {
##     con <- AnnotationDbi:::dbconn(x)
##     list <- dbListTables(con)
##     ## drop unwanted tables
##     unwanted <- c("map_counts","map_metadata","metadata")
##     list <- list[!list %in% unwanted]
##     ## Then just to format things in the usual way
##     list <- toupper(list)
##     dbDisconnect(con)
##     list
## }
## 
## ## Then make this into a method
## setMethod("columns", "InparanoidDb", .cols(x))
## ## Then we can call it
## columns(hom.Hs.inp.db)


## ----keytypes,eval=FALSE-------------------------------------------------
## setMethod("keytypes", "InparanoidDb", .cols(x))
## ## Then we can call it
## keytypes(hom.Hs.inp.db)
## 
## ## refactor of .cols
## .getLCcolnames <- function(x)
## {
##     con <- AnnotationDbi:::dbconn(x)
##     list <- dbListTables(con)
##     ## drop unwanted tables
##     unwanted <- c("map_counts","map_metadata","metadata")
##     list <- list[!list %in% unwanted]
##     dbDisconnect(con)
##     list
## }
## .cols <- function(x)
## {
##     list <- .getLCcolnames(x)
##     ## Then just to format things in the usual way
##     toupper(list)
## }
## ## Test:
## columns(hom.Hs.inp.db)
## 
## ## new helper function:
## .getTableNames <- function(x)
## {
##     LC <- .getLCcolnames(x)
##     UC <- .cols(x)
##     names(UC) <- LC
##     UC
## }
## .getTableNames(hom.Hs.inp.db)


## ----keys,eval=FALSE-----------------------------------------------------
## .keys <- function(x, keytype)
## {
##     ## translate keytype back to table name
##     tabNames <- .getTableNames(x)
##     lckeytype <- names(tabNames[tabNames %in% keytype])
##     ## get a connection
##     con <- AnnotationDbi:::dbconn(x)
##     sql <- paste("SELECT inp_id FROM",lckeytype, "WHERE species!='HOMSA'")
##     res <- dbGetQuery(con, sql)
##     res <- as.vector(t(res))
##     dbDisconnect(con)
##     res
## }
## 
## setMethod("keys", "InparanoidDb", .keys(x, keytype))
## ## Then we can call it
## keys(hom.Hs.inp.db, "TRICHOPLAX_ADHAERENS")


## ----dbDisconnect--------------------------------------------------------
   dbDisconnect(con)


## ----makeNewDb-----------------------------------------------------------
drv <- dbDriver("SQLite")
dbname <- file.path(tempdir(), "myNewDb.sqlite")
con <- dbConnect(drv, dbname=dbname)


## ----exampleFrame--------------------------------------------------------
data = data.frame(id=c(1,2,9),
                  string=c("Blue",
                           "Red",
                           "Green"),
                  stringsAsFactors=FALSE)


## ----exercise2-----------------------------------------------------------
dbGetQuery(con, "CREATE Table genePheno (id INTEGER, string TEXT)")


## ----LabelledPreparedQueries---------------------------------------------
names(data) <- c("id","string")
sql <- "INSERT INTO genePheno VALUES ($id, $string)"
dbBegin(con)
dbGetPreparedQuery(con, sql, bind.data = data)
dbCommit(con)


## ----ATTACH--------------------------------------------------------------
db <- system.file("extdata", "TxDb.Hsapiens.UCSC.hg19.knownGene.sqlite", 
                  package="TxDb.Hsapiens.UCSC.hg19.knownGene")
dbGetQuery(con, sprintf("ATTACH '%s' AS db",db))


## ----ATTACHJoin----------------------------------------------------------
  sql <- "SELECT * FROM db.gene AS dbg, 
          genePheno AS gp WHERE dbg.gene_id=gp.id"
  res <- dbGetQuery(con, sql)
  res


## ----SessionInfo, echo=FALSE---------------------------------------------
sessionInfo()