Nothing
R/createAnnObjs.R
In PAnnBuilder: Protein annotation data package builder
Defines functions
dbGetTable
createMAPCOUNTS
createSeeds
createAnnObjs
createAnnObjs.SP
createAnnObjs.REFSEQ
createAnnObjs.IPI
createAnnObjs.BACELLO
createAnnObjs.DBSUBLOC
createAnnObjs.GOA
createAnnObjs.SYSBODYFLUID
createAnnObjs.HOMOLOGENE
createAnnObjs.INPARANOID
createAnnObjs.SYSPTM
Documented in
createAnnObjs
createSeeds
## dbschema is from "AnnotationDbi" package.
setMethod("dbschema", "DBIConnection",
function(x, file="", show.indices=FALSE)
{
schema <- dbmeta(x, "DBSCHEMA")
version <- dbmeta(x, "DBSCHEMAVERSION")
file <- system.file("DBschemas",
paste("schemas_", version, sep=""),
paste(schema, ".sql", sep=""),
package="PAnnBuilder")
lines <- readLines(file)
if (!show.indices) {
## Remove the CREATE INDEX lines
createIndexStart <- "CREATE INDEX"
createIndexEnd <- ";"
ii <- which(substr(lines, 1, nchar(createIndexStart)) == createIndexStart
& substr(lines, nchar(lines)-nchar(createIndexEnd)+1, nchar(lines)) == createIndexEnd)
ii <- setdiff(ii, grep(createIndexEnd, substr(lines, 1, nchar(lines)-nchar(createIndexEnd)), fixed=TRUE))
if( length(ii)>0 ){
## Remove comments preceding the CREATE INDEX blocks
beforeLastBlock <- function(ii, i)
{
while ((i >= 1) && !(i %in% ii))
i <- i - 1
while ((i >= 1) && (i %in% ii))
i <- i - 1
i
}
i <- max(ii)
while (i >= 1) {
i <- beforeLastBlock(ii, i)
while (i >= 1) {
if (substr(lines[i], 1, 2) != "--")
break
ii <- c(i, ii)
i <- i - 1
}
}
lines <- lines[-ii]
}
}
## Remove empty trailing lines
ii <- integer(0)
i <- length(lines)
while ((i >= 1) && (lines[i] == "")) {
ii <- c(i, ii)
i <- i - 1
}
lines <- lines[-ii]
cat(lines, sep="\n")
}
)
setMethod("dbschema", "environment",
function(x, file="", show.indices=FALSE)
dbschema(dbconn(x), file=file, show.indices=show.indices))
setMethod("dbschema", "AnnDbObj",
function(x, file="", show.indices=FALSE)
dbschema(x@datacache, file=file, show.indices=show.indices))
## dbGetTable is from "AnnotationDbi" package, and modified by Hong Li.
dbGetTable <- function (conn, tablename, extra.SQL = NULL)
{
SQL <- paste("SELECT * FROM ", tablename, sep = "")
if (!is.null(extra.SQL))
SQL <- paste(SQL, extra.SQL)
dbGetQuery(conn, SQL)
}
## createMAPCOUNTS is from "AnnotationDbi" package, and modified by Hong Li.
createMAPCOUNTS <- function (dbconn, prefix){
data <- dbGetTable(dbconn, "map_counts", "WHERE map_name != 'TOTAL' ORDER BY map_name")
MAPCOUNTS <- data[[2]]
names(MAPCOUNTS) <- paste(prefix, data[["map_name"]], sep = "")
MAPCOUNTS
}
createSeeds <- function(type){
type = toupper(type)
switch(type,
SP = return(list(
list(
objName="SPAC",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="sp_ac"
)
)
),
list(
objName="LEN",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="len"
)
)
),
list(
objName="MW",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="mw"
)
)
),
list(
objName="DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="de",
Lcolname="sp_id",
Rcolname="de"
)
)
),
list(
objName="SYMBOL",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="symbol"
)
)
),
list(
objName="UNIGENE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="unigene_id"
)
)
),
list(
objName="KEGG",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="kegg",
Lcolname="sp_id",
Rcolname="kegg_id"
)
)
),
list(
objName="FUNCTION",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="functions"
)
)
),
list(
objName="SUBCELL",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="subcelluar"
)
)
),
list(
objName="TISSUE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="tissue"
)
)
),
list(
objName="DISEASE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="disease"
)
)
),
list(
objName="SPACs",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="spac",
Lcolname="sp_id",
Rcolname="sp_acs"
)
)
),
list(
objName="PMID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="pubmed",
Lcolname="sp_id",
Rcolname="pubmed_id"
)
)
),
list(
objName="REFSEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="refseq",
Lcolname="sp_id",
Rcolname="ref_id"
)
)
),
list(
objName="GENEID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="geneid",
Lcolname="sp_id",
Rcolname="gene_id"
)
)
),
list(
objName="PDB",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="pdb",
Lcolname="sp_id",
Rcolname="pdb_id"
)
)
),
list(
objName="GN",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="alias",
Lcolname="sp_id",
Rcolname="alias_symbol"
)
)
),
list(
objName="INT",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="int",
Lcolname="sp_id",
Rcolname="sp_ac_b"
)
)
),
list(
objName="PATH",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="path",
Lcolname="sp_id",
Rcolname="path_id"
)
)
),
list(
objName="INTERPRO",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="interpro",
Lcolname="sp_id",
Rcolname="interpro_id"
)
)
),
list(
objName="PFAM",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="pfam",
Lcolname="sp_id",
Rcolname="pfam_id"
)
)
),
list(
objName="PROSITE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="prosite",
Lcolname="sp_id",
Rcolname="prosite_id"
)
)
),
list(
objName="GO",
Class="GoAnnDbBimap",
L2Rchain=list(
list(
tablename="go", # no rightmost table for a Go3AnnDbBimap
Lcolname="sp_id",
tagname=c(Evidence="{evidence}"),
Rcolname="go_id",
Rattribnames=c(Ontology="{ontology}")
)
)
),
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="seq",
Lcolname="sp_id",
Rcolname="seq"
)
)
)
)),
IPI = return(list(
list(
objName="IPIAC",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="ipi_ac"
)
)
),
list(
objName="IPIACs",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="ipiac",
Lcolname="ipi_id",
Rcolname="ipi_acs"
)
)
),
list(
objName="LEN",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="len"
)
)
),
list(
objName="MW",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="mw"
)
)
),
list(
objName="DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="de"
)
)
),
list(
objName="SYMBOL",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="symbol"
)
)
),
list(
objName="SPAC",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="sp_ac"
)
)
),
list(
objName="SPID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="sp_id"
)
)
),
list(
objName="REFSEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="ref_id"
)
)
),
list(
objName="GI",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="gi"
)
)
),
list(
objName="GENEID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="gene_id"
)
)
),
list(
objName="UNIGENE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="unigene_id"
)
)
),
list(
objName="KEGG",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="kegg_id"
)
)
),
list(
objName="PATH",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="path",
Lcolname="ipi_id",
Rcolname="path_id"
)
)
),
list(
objName="INTERPRO",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="interpro",
Lcolname="ipi_id",
Rcolname="interpro_id"
)
)
),
list(
objName="PFAM",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="pfam",
Lcolname="ipi_id",
Rcolname="pfam_id"
)
)
),
list(
objName="PROSITE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="prosite",
Lcolname="ipi_id",
Rcolname="prosite_id"
)
)
),
list(
objName="GO",
Class="GoAnnDbBimap",
L2Rchain=list(
list(
tablename="go", # no rightmost table for a Go3AnnDbBimap
Lcolname="ipi_id",
tagname=c(Evidence="{evidence}"),
Rcolname="go_id",
Rattribnames=c(Ontology="{ontology}")
)
)
),
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="seq",
Lcolname="ipi_id",
Rcolname="seq"
)
)
)
)),
REFSEQ = return(list(
list(
objName="REFSEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="gi",
Rcolname="ref_id"
)
)
),
list(
objName="GENEID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="gi",
Rcolname="gene_id"
)
)
),
list(
objName="SYMBOL",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="gi",
Rcolname="symbol"
)
)
),
list(
objName="DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="gi",
Rcolname="de"
)
)
),
list(
objName="KEGG",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="gi",
Rcolname="kegg_id"
)
)
),
list(
objName="PATH",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="path",
Lcolname="gi",
Rcolname="path_id"
)
)
),
list(
objName="GO",
Class="GoAnnDbBimap",
L2Rchain=list(
list(
tablename="go", # no rightmost table for a Go3AnnDbBimap
Lcolname="gi",
tagname=c(Evidence="{evidence}"),
Rcolname="go_id",
Rattribnames=c(Ontology="{ontology}")
)
)
),
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="seq",
Lcolname="gi",
Rcolname="seq"
)
)
)
)),
SYSBODYFLUID = return(list(
list(
objName="BF",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="sysbodyfluid",
Lcolname="ipi_id",
Rcolname="pubmed_id",
Rattribnames=c(BF="{body_fluid}")
)
)
),
list(
objName="BF2IPI",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="sysbodyfluid",
Lcolname="body_fluid",
Rcolname="pubmed_id",
Rattribnames=c(IPIID="{ipi_id}")
)
)
),
list(
objName="PMID2TITLE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="paper",
Lcolname="pubmed_id",
Rcolname="title"
)
)
),
list(
objName="PMID2PLATFORM",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="paper",
Lcolname="pubmed_id",
Rcolname="platform"
)
)
),
list(
objName="PMID2BF",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="paper",
Lcolname="pubmed_id",
Rcolname="body_fluid"
)
)
),
list(
objName="PMID2ENGINE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="paper",
Lcolname="pubmed_id",
Rcolname="search_engine"
)
)
),
list(
objName="PMID2SAMPLE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="paper",
Lcolname="pubmed_id",
Rcolname="sample"
)
)
)
)),
SYSPTM = return(list(
list(
objName="PTMTYPE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="sysptm",
Lcolname="ptm_site",
Rcolname="ptm_type"
)
)
),
list(
objName="ORGANISM",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sysptm_id",
Rcolname="organism"
)
)
),
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sysptm_id",
Rcolname="seq"
)
)
),
list(
objName="GENEID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sysptm_id",
Rcolname="gene_id"
)
)
),
list(
objName="DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="de",
Lcolname="sysptm_id",
Rcolname="de"
)
)
),
list(
objName="GN",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="alias",
Lcolname="sysptm_id",
Rcolname="alias_symbol"
)
)
),
list(
objName="IDs",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="xref",
Lcolname="sysptm_id",
Rcolname="database",
Rattribnames=c(IDs="{protein_id}")
)
)
)
)),
SCOP = return(list(
list(
objName="TYPE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="des",
Lcolname="scop_id",
Rcolname="type"
)
)
),
list(
objName="CLASSIFICATION",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="des",
Lcolname="scop_id",
Rcolname="class"
)
)
),
list(
objName="NAME",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="des",
Lcolname="scop_id",
Rcolname="name"
)
)
),
list(
objName="DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="des",
Lcolname="scop_id",
Rcolname="de"
)
)
),
list(
objName="PARENT",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="parent",
Lcolname="scop_id",
Rcolname="parent_id"
)
)
),
list(
objName="CHILDREN",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="children",
Lcolname="scop_id",
Rcolname="children_id"
)
)
),
list(
objName="PDB2CL",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="pdb",
Lcolname="pdb_id",
Rcolname="pdb_chain",
Rattribnames=c(cl="{cl}")
)
)
),
list(
objName="PDB2CF",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="pdb",
Lcolname="pdb_id",
Rcolname="pdb_chain",
Rattribnames=c(cf="{cf}")
)
)
),
list(
objName="PDB2SF",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="pdb",
Lcolname="pdb_id",
Rcolname="pdb_chain",
Rattribnames=c(sf="{sf}")
)
)
),
list(
objName="PDB2FA",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="pdb",
Lcolname="pdb_id",
Rcolname="pdb_chain",
Rattribnames=c(fa="{fa}")
)
)
),
list(
objName="PDB2DM",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="pdb",
Lcolname="pdb_id",
Rcolname="pdb_chain",
Rattribnames=c(dm="{dm}")
)
)
),
list(
objName="PDB2SP",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="pdb",
Lcolname="pdb_id",
Rcolname="pdb_chain",
Rattribnames=c(sp="{sp}")
)
)
),
list(
objName="PDB2PX",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="pdb",
Lcolname="pdb_id",
Rcolname="pdb_chain",
Rattribnames=c(px="{px}")
)
)
)
)),
GENEINT = return(list(
list(
objName="GGI",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="geneint",
Lcolname="gene_id_a",
Rcolname="gene_id_b"
)
)
),
list(
objName="TAXID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="tax",
Lcolname="gene_id",
Rcolname="tax_id"
)
)
)
)),
INTACT = return(list(
list(
objName="PPI",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="intact",
Lcolname="up_ac_a",
Rcolname="up_ac_b"
)
)
),
list(
objName="TAXID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="tax",
Lcolname="up_ac",
Rcolname="tax_id"
)
)
)
)),
MPPI = return(list(
list(
objName="PPI",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="mppi",
Lcolname="up_ac_a",
Rcolname="up_ac_b"
)
)
)
)),
"3DID" = return(list(
list(
objName="DDI",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="did",
Lcolname="pfam_a",
Rcolname="pfam_b"
)
)
)
)),
DOMINE = return(list(
list(
objName="DDI",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="domine",
Lcolname="pfam_a",
Rcolname="method",
Rattribnames=c(pfam_b="{pfam_b}")
)
)
),
list(
objName="METHOD",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="method",
Lcolname="method",
Rcolname="method_de"
)
)
)
)),
BACELLO = return(list(
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="seq",
Lcolname="sp_id",
Rcolname="seq"
)
)
),
list(
objName="SUBCELL",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="bacello",
Lcolname="sp_id",
Rcolname="subcell"
)
)
)
)),
DBSUBLOC = return(list(
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="dbsubloc",
Lcolname="sp_ac",
Rcolname="seq"
)
)
),
list(
objName="SUBCELL",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="dbsubloc",
Lcolname="sp_ac",
Rcolname="subcell"
)
)
),
list(
objName="ORGANISM",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="dbsubloc",
Lcolname="sp_ac",
Rcolname="organism"
)
)
),
list(
objName="DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="dbsubloc",
Lcolname="sp_ac",
Rcolname="de"
)
)
)
)),
GOA = return(list(
list(
objName="GO",
Class="GoAnnDbBimap",
L2Rchain=list(
list(
tablename="go",
Lcolname="sp_ac",
tagname=c(Evidence="{evidence}"),
Rcolname="go_id",
Rattribnames=c(Ontology="{ontology}")
)
)
),
list(
objName="DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="de",
Lcolname="sp_ac",
Rcolname="de"
)
)
),
list(
objName="SPID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="id",
Lcolname="sp_ac",
Rcolname="sp_id"
)
)
)
)),
HOMOLOGENE = return(list(
list(
objName="HOMOLOG",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="homolog",
Lcolname="gene_id",
Rcolname="homolog_id"
)
)
),
list(
objName="HOMOLOG2GI",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="homolog",
Lcolname="homolog_id",
Rcolname="gi"
)
)
),
list(
objName="HOMOLOG2AC",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="homolog",
Lcolname="homolog_id",
Rcolname="ncbi_ac"
)
)
),
list(
objName="SYMBOL",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="homolog",
Lcolname="gene_id",
Rcolname="symbol"
)
)
),
list(
objName="TAXID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="homolog",
Lcolname="gene_id",
Rcolname="tax_id"
)
)
),
list(
objName="ORGANISM",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="tax",
Lcolname="tax_id",
Rcolname="organism"
)
)
)
)),
INPARANOID = return(list(
list(
objName="ORTHOLOG",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="ortholog",
Lcolname="protein_id",
Rcolname="ortholog_id"
)
)
),
list(
objName="ORGANISM",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="ortholog",
Lcolname="protein_id",
Rcolname="organism"
)
)
),
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="seq",
Lcolname="protein_id",
Rcolname="seq"
)
)
)
)),
PEPTIDEATLAS = return(list(
list(
objName="PEP2PROTEIN",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="pep2protein",
Lcolname="peptide_id",
Rcolname="protein_position"
)
)
),
list(
objName="PEP2CHR",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="pep2chr",
Lcolname="peptide_id",
Rcolname="chr_position"
)
)
),
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="seq",
Lcolname="peptide_id",
Rcolname="seq"
)
)
)
)),
DNAME = return(list(
list(
objName="GO2NAME",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="go",
Lcolname="go_id",
Rcolname="go_name"
)
)
),
list(
objName="PATH2DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="kegg",
Lcolname="path_id",
Rcolname="path_de"
)
)
),
list(
objName="PFAM2DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="pfam",
Lcolname="pfam_id",
Rcolname="pfam_de"
)
)
),
list(
objName="PFAM2NAME",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="pfam",
Lcolname="pfam_id",
Rcolname="pfam_name"
)
)
),
list(
objName="PROSITE2DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="prosite",
Lcolname="prosite_id",
Rcolname="prosite_de"
)
)
),
list(
objName="INTERPRO2NAME",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="interpro",
Lcolname="interpro_id",
Rcolname="interpro_name"
)
)
),
list(
objName="TAXID2NAME",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="tax",
Lcolname="tax_id",
Rcolname="tax_name"
)
)
)
)),
CROSS = return(list(
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="seq",
Lcolname="protein_id",
Rcolname="seq"
)
)
),
list(
objName="MATCH",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="match",
Lcolname="query",
Rcolname="subject"
)
)
)
))
)
}
createAnnObjs <- function(type, prefix, datacache, dbconn)
{
seeds <- createSeeds(type)
## AnnDbBimap objects
seed0 <- list(
datacache=datacache
)
ann_objs <- AnnotationDbi:::createAnnDbBimaps(seeds, seed0)
ann_objs <- switch(type,
"SP" = createAnnObjs.SP(ann_objs),
"IPI" = createAnnObjs.IPI(ann_objs),
"REFSEQ" = createAnnObjs.REFSEQ(ann_objs),
"BACELLO" = createAnnObjs.BACELLO(ann_objs),
"DBSUBLOC" = createAnnObjs.DBSUBLOC(ann_objs),
"GOA" = createAnnObjs.GOA(ann_objs),
"HOMOLOGENE" = createAnnObjs.HOMOLOGENE(ann_objs),
"SYSPTM" = createAnnObjs.SYSPTM(ann_objs),
"SYSBODYFLUID" = createAnnObjs.SYSBODYFLUID(ann_objs),
"INPARANOID" = createAnnObjs.INPARANOID(ann_objs),
ann_objs
)
if( !dbExistsTable(dbconn,"map_counts") ){
tmp <- sapply(ls(ann_objs), function(x){count.mappedkeys(base:::get(x,envir=ann_objs))} )
tmp <- data.frame(names(tmp),tmp)
colnames(tmp) <- c("map_name","count")
dbWriteTable(dbconn, "map_counts", tmp, row.names=F)
}
ann_objs$MAPCOUNTS <- createMAPCOUNTS(dbconn, prefix)
AnnotationDbi:::prefixAnnObjNames(ann_objs, prefix)
}
createAnnObjs.SP <- function(ann_objs){
ann_objs$GO2SPID <- revmap(ann_objs$GO, objName="GO2SPID")
ann_objs$PATH2SPID <- revmap(ann_objs$PATH, objName="PATH2SPID")
ann_objs$REFSEQ2SPID <- revmap(ann_objs$REFSEQ, objName="REFSEQ2SPID")
ann_objs
}
createAnnObjs.REFSEQ <- function(ann_objs){
ann_objs$GO2GI <- revmap(ann_objs$GO, objName="GO2GI")
ann_objs$PATH2GI <- revmap(ann_objs$PATH, objName="PATH2GI")
ann_objs$REFSEQ2GI <- revmap(ann_objs$REFSEQ, objName="REFSEQ2GI")
ann_objs
}
createAnnObjs.IPI <- function(ann_objs){
ann_objs$GO2IPIID <- revmap(ann_objs$GO, objName="GO2IPIID")
ann_objs$PATH2IPIID <- revmap(ann_objs$PATH, objName="PATH2IPIID")
ann_objs$IPIAC2IPIID <- revmap(ann_objs$IPIACs, objName="IPIAC2IPIID")
ann_objs$SPID2IPIID <- revmap(ann_objs$SPID, objName="SPID2IPIID")
ann_objs$SPAC2IPIID <- revmap(ann_objs$SPAC, objName="SPAC2IPIID")
ann_objs$REFSEQ2IPIID <- revmap(ann_objs$REFSEQ, objName="REFSEQ2IPIID")
ann_objs
}
createAnnObjs.BACELLO <- function(ann_objs){
ann_objs$SUBCELL2SPID <- revmap(ann_objs$SUBCELL, objName="SUBCELL2SPID")
ann_objs
}
createAnnObjs.DBSUBLOC <- function(ann_objs){
ann_objs$SUBCELL2SPAC <- revmap(ann_objs$SUBCELL, objName="SUBCELL2SPAC")
ann_objs
}
createAnnObjs.GOA <- function(ann_objs){
ann_objs$GO2SPAC <- revmap(ann_objs$GO, objName="GO2SPAC")
ann_objs$SPID2SPAC <- revmap(ann_objs$SPID, objName="SPID2SPAC")
ann_objs
}
createAnnObjs.SYSBODYFLUID <- function(ann_objs){
ann_objs$BF2PMID <- revmap(ann_objs$PMID2BF, objName="BF2PMID")
ann_objs
}
createAnnObjs.HOMOLOGENE <- function(ann_objs){
ann_objs$HOMOLOG2GENEID <- revmap(ann_objs$HOMOLOG, objName="HOMOLOG2GENEID")
ann_objs
}
createAnnObjs.INPARANOID <- function(ann_objs){
ann_objs$ORTHOLOG2PROTEIN <- revmap(ann_objs$ORTHOLOG, objName="ORTHOLOG2PROTEIN")
ann_objs
}
createAnnObjs.SYSPTM <- function(ann_objs){
ann_objs$PTMTYPE2SITE <- revmap(ann_objs$PTMTYPE, objName="PTMTYPE2SITE")
ann_objs
}
Try the PAnnBuilder package in your browser
Any scripts or data that you put into this service are public.
PAnnBuilder documentation built on May 2, 2018, 4:07 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions dbGetTable createMAPCOUNTS createSeeds createAnnObjs createAnnObjs.SP createAnnObjs.REFSEQ createAnnObjs.IPI createAnnObjs.BACELLO createAnnObjs.DBSUBLOC createAnnObjs.GOA createAnnObjs.SYSBODYFLUID createAnnObjs.HOMOLOGENE createAnnObjs.INPARANOID createAnnObjs.SYSPTM
Documented in createAnnObjs createSeeds
## dbschema is from "AnnotationDbi" package.
setMethod("dbschema", "DBIConnection",
function(x, file="", show.indices=FALSE)
{
schema <- dbmeta(x, "DBSCHEMA")
version <- dbmeta(x, "DBSCHEMAVERSION")
file <- system.file("DBschemas",
paste("schemas_", version, sep=""),
paste(schema, ".sql", sep=""),
package="PAnnBuilder")
lines <- readLines(file)
if (!show.indices) {
## Remove the CREATE INDEX lines
createIndexStart <- "CREATE INDEX"
createIndexEnd <- ";"
ii <- which(substr(lines, 1, nchar(createIndexStart)) == createIndexStart
& substr(lines, nchar(lines)-nchar(createIndexEnd)+1, nchar(lines)) == createIndexEnd)
ii <- setdiff(ii, grep(createIndexEnd, substr(lines, 1, nchar(lines)-nchar(createIndexEnd)), fixed=TRUE))
if( length(ii)>0 ){
## Remove comments preceding the CREATE INDEX blocks
beforeLastBlock <- function(ii, i)
{
while ((i >= 1) && !(i %in% ii))
i <- i - 1
while ((i >= 1) && (i %in% ii))
i <- i - 1
i
}
i <- max(ii)
while (i >= 1) {
i <- beforeLastBlock(ii, i)
while (i >= 1) {
if (substr(lines[i], 1, 2) != "--")
break
ii <- c(i, ii)
i <- i - 1
}
}
lines <- lines[-ii]
}
}
## Remove empty trailing lines
ii <- integer(0)
i <- length(lines)
while ((i >= 1) && (lines[i] == "")) {
ii <- c(i, ii)
i <- i - 1
}
lines <- lines[-ii]
cat(lines, sep="\n")
}
)
setMethod("dbschema", "environment",
function(x, file="", show.indices=FALSE)
dbschema(dbconn(x), file=file, show.indices=show.indices))
setMethod("dbschema", "AnnDbObj",
function(x, file="", show.indices=FALSE)
dbschema(x@datacache, file=file, show.indices=show.indices))
## dbGetTable is from "AnnotationDbi" package, and modified by Hong Li.
dbGetTable <- function (conn, tablename, extra.SQL = NULL)
{
SQL <- paste("SELECT * FROM ", tablename, sep = "")
if (!is.null(extra.SQL))
SQL <- paste(SQL, extra.SQL)
dbGetQuery(conn, SQL)
}
## createMAPCOUNTS is from "AnnotationDbi" package, and modified by Hong Li.
createMAPCOUNTS <- function (dbconn, prefix){
data <- dbGetTable(dbconn, "map_counts", "WHERE map_name != 'TOTAL' ORDER BY map_name")
MAPCOUNTS <- data[[2]]
names(MAPCOUNTS) <- paste(prefix, data[["map_name"]], sep = "")
MAPCOUNTS
}
createSeeds <- function(type){
type = toupper(type)
switch(type,
SP = return(list(
list(
objName="SPAC",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="sp_ac"
)
)
),
list(
objName="LEN",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="len"
)
)
),
list(
objName="MW",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="mw"
)
)
),
list(
objName="DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="de",
Lcolname="sp_id",
Rcolname="de"
)
)
),
list(
objName="SYMBOL",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="symbol"
)
)
),
list(
objName="UNIGENE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="unigene_id"
)
)
),
list(
objName="KEGG",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="kegg",
Lcolname="sp_id",
Rcolname="kegg_id"
)
)
),
list(
objName="FUNCTION",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="functions"
)
)
),
list(
objName="SUBCELL",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="subcelluar"
)
)
),
list(
objName="TISSUE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="tissue"
)
)
),
list(
objName="DISEASE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sp_id",
Rcolname="disease"
)
)
),
list(
objName="SPACs",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="spac",
Lcolname="sp_id",
Rcolname="sp_acs"
)
)
),
list(
objName="PMID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="pubmed",
Lcolname="sp_id",
Rcolname="pubmed_id"
)
)
),
list(
objName="REFSEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="refseq",
Lcolname="sp_id",
Rcolname="ref_id"
)
)
),
list(
objName="GENEID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="geneid",
Lcolname="sp_id",
Rcolname="gene_id"
)
)
),
list(
objName="PDB",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="pdb",
Lcolname="sp_id",
Rcolname="pdb_id"
)
)
),
list(
objName="GN",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="alias",
Lcolname="sp_id",
Rcolname="alias_symbol"
)
)
),
list(
objName="INT",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="int",
Lcolname="sp_id",
Rcolname="sp_ac_b"
)
)
),
list(
objName="PATH",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="path",
Lcolname="sp_id",
Rcolname="path_id"
)
)
),
list(
objName="INTERPRO",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="interpro",
Lcolname="sp_id",
Rcolname="interpro_id"
)
)
),
list(
objName="PFAM",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="pfam",
Lcolname="sp_id",
Rcolname="pfam_id"
)
)
),
list(
objName="PROSITE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="prosite",
Lcolname="sp_id",
Rcolname="prosite_id"
)
)
),
list(
objName="GO",
Class="GoAnnDbBimap",
L2Rchain=list(
list(
tablename="go", # no rightmost table for a Go3AnnDbBimap
Lcolname="sp_id",
tagname=c(Evidence="{evidence}"),
Rcolname="go_id",
Rattribnames=c(Ontology="{ontology}")
)
)
),
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="seq",
Lcolname="sp_id",
Rcolname="seq"
)
)
)
)),
IPI = return(list(
list(
objName="IPIAC",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="ipi_ac"
)
)
),
list(
objName="IPIACs",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="ipiac",
Lcolname="ipi_id",
Rcolname="ipi_acs"
)
)
),
list(
objName="LEN",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="len"
)
)
),
list(
objName="MW",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="mw"
)
)
),
list(
objName="DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="de"
)
)
),
list(
objName="SYMBOL",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="symbol"
)
)
),
list(
objName="SPAC",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="sp_ac"
)
)
),
list(
objName="SPID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="sp_id"
)
)
),
list(
objName="REFSEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="ref_id"
)
)
),
list(
objName="GI",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="gi"
)
)
),
list(
objName="GENEID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="gene_id"
)
)
),
list(
objName="UNIGENE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="unigene_id"
)
)
),
list(
objName="KEGG",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="ipi_id",
Rcolname="kegg_id"
)
)
),
list(
objName="PATH",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="path",
Lcolname="ipi_id",
Rcolname="path_id"
)
)
),
list(
objName="INTERPRO",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="interpro",
Lcolname="ipi_id",
Rcolname="interpro_id"
)
)
),
list(
objName="PFAM",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="pfam",
Lcolname="ipi_id",
Rcolname="pfam_id"
)
)
),
list(
objName="PROSITE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="prosite",
Lcolname="ipi_id",
Rcolname="prosite_id"
)
)
),
list(
objName="GO",
Class="GoAnnDbBimap",
L2Rchain=list(
list(
tablename="go", # no rightmost table for a Go3AnnDbBimap
Lcolname="ipi_id",
tagname=c(Evidence="{evidence}"),
Rcolname="go_id",
Rattribnames=c(Ontology="{ontology}")
)
)
),
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="seq",
Lcolname="ipi_id",
Rcolname="seq"
)
)
)
)),
REFSEQ = return(list(
list(
objName="REFSEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="gi",
Rcolname="ref_id"
)
)
),
list(
objName="GENEID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="gi",
Rcolname="gene_id"
)
)
),
list(
objName="SYMBOL",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="gi",
Rcolname="symbol"
)
)
),
list(
objName="DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="gi",
Rcolname="de"
)
)
),
list(
objName="KEGG",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="gi",
Rcolname="kegg_id"
)
)
),
list(
objName="PATH",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="path",
Lcolname="gi",
Rcolname="path_id"
)
)
),
list(
objName="GO",
Class="GoAnnDbBimap",
L2Rchain=list(
list(
tablename="go", # no rightmost table for a Go3AnnDbBimap
Lcolname="gi",
tagname=c(Evidence="{evidence}"),
Rcolname="go_id",
Rattribnames=c(Ontology="{ontology}")
)
)
),
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="seq",
Lcolname="gi",
Rcolname="seq"
)
)
)
)),
SYSBODYFLUID = return(list(
list(
objName="BF",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="sysbodyfluid",
Lcolname="ipi_id",
Rcolname="pubmed_id",
Rattribnames=c(BF="{body_fluid}")
)
)
),
list(
objName="BF2IPI",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="sysbodyfluid",
Lcolname="body_fluid",
Rcolname="pubmed_id",
Rattribnames=c(IPIID="{ipi_id}")
)
)
),
list(
objName="PMID2TITLE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="paper",
Lcolname="pubmed_id",
Rcolname="title"
)
)
),
list(
objName="PMID2PLATFORM",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="paper",
Lcolname="pubmed_id",
Rcolname="platform"
)
)
),
list(
objName="PMID2BF",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="paper",
Lcolname="pubmed_id",
Rcolname="body_fluid"
)
)
),
list(
objName="PMID2ENGINE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="paper",
Lcolname="pubmed_id",
Rcolname="search_engine"
)
)
),
list(
objName="PMID2SAMPLE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="paper",
Lcolname="pubmed_id",
Rcolname="sample"
)
)
)
)),
SYSPTM = return(list(
list(
objName="PTMTYPE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="sysptm",
Lcolname="ptm_site",
Rcolname="ptm_type"
)
)
),
list(
objName="ORGANISM",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sysptm_id",
Rcolname="organism"
)
)
),
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sysptm_id",
Rcolname="seq"
)
)
),
list(
objName="GENEID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="basic",
Lcolname="sysptm_id",
Rcolname="gene_id"
)
)
),
list(
objName="DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="de",
Lcolname="sysptm_id",
Rcolname="de"
)
)
),
list(
objName="GN",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="alias",
Lcolname="sysptm_id",
Rcolname="alias_symbol"
)
)
),
list(
objName="IDs",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="xref",
Lcolname="sysptm_id",
Rcolname="database",
Rattribnames=c(IDs="{protein_id}")
)
)
)
)),
SCOP = return(list(
list(
objName="TYPE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="des",
Lcolname="scop_id",
Rcolname="type"
)
)
),
list(
objName="CLASSIFICATION",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="des",
Lcolname="scop_id",
Rcolname="class"
)
)
),
list(
objName="NAME",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="des",
Lcolname="scop_id",
Rcolname="name"
)
)
),
list(
objName="DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="des",
Lcolname="scop_id",
Rcolname="de"
)
)
),
list(
objName="PARENT",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="parent",
Lcolname="scop_id",
Rcolname="parent_id"
)
)
),
list(
objName="CHILDREN",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="children",
Lcolname="scop_id",
Rcolname="children_id"
)
)
),
list(
objName="PDB2CL",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="pdb",
Lcolname="pdb_id",
Rcolname="pdb_chain",
Rattribnames=c(cl="{cl}")
)
)
),
list(
objName="PDB2CF",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="pdb",
Lcolname="pdb_id",
Rcolname="pdb_chain",
Rattribnames=c(cf="{cf}")
)
)
),
list(
objName="PDB2SF",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="pdb",
Lcolname="pdb_id",
Rcolname="pdb_chain",
Rattribnames=c(sf="{sf}")
)
)
),
list(
objName="PDB2FA",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="pdb",
Lcolname="pdb_id",
Rcolname="pdb_chain",
Rattribnames=c(fa="{fa}")
)
)
),
list(
objName="PDB2DM",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="pdb",
Lcolname="pdb_id",
Rcolname="pdb_chain",
Rattribnames=c(dm="{dm}")
)
)
),
list(
objName="PDB2SP",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="pdb",
Lcolname="pdb_id",
Rcolname="pdb_chain",
Rattribnames=c(sp="{sp}")
)
)
),
list(
objName="PDB2PX",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="pdb",
Lcolname="pdb_id",
Rcolname="pdb_chain",
Rattribnames=c(px="{px}")
)
)
)
)),
GENEINT = return(list(
list(
objName="GGI",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="geneint",
Lcolname="gene_id_a",
Rcolname="gene_id_b"
)
)
),
list(
objName="TAXID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="tax",
Lcolname="gene_id",
Rcolname="tax_id"
)
)
)
)),
INTACT = return(list(
list(
objName="PPI",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="intact",
Lcolname="up_ac_a",
Rcolname="up_ac_b"
)
)
),
list(
objName="TAXID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="tax",
Lcolname="up_ac",
Rcolname="tax_id"
)
)
)
)),
MPPI = return(list(
list(
objName="PPI",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="mppi",
Lcolname="up_ac_a",
Rcolname="up_ac_b"
)
)
)
)),
"3DID" = return(list(
list(
objName="DDI",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="did",
Lcolname="pfam_a",
Rcolname="pfam_b"
)
)
)
)),
DOMINE = return(list(
list(
objName="DDI",
Class="IpiAnnDbMap",
L2Rchain=list(
list(
tablename="domine",
Lcolname="pfam_a",
Rcolname="method",
Rattribnames=c(pfam_b="{pfam_b}")
)
)
),
list(
objName="METHOD",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="method",
Lcolname="method",
Rcolname="method_de"
)
)
)
)),
BACELLO = return(list(
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="seq",
Lcolname="sp_id",
Rcolname="seq"
)
)
),
list(
objName="SUBCELL",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="bacello",
Lcolname="sp_id",
Rcolname="subcell"
)
)
)
)),
DBSUBLOC = return(list(
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="dbsubloc",
Lcolname="sp_ac",
Rcolname="seq"
)
)
),
list(
objName="SUBCELL",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="dbsubloc",
Lcolname="sp_ac",
Rcolname="subcell"
)
)
),
list(
objName="ORGANISM",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="dbsubloc",
Lcolname="sp_ac",
Rcolname="organism"
)
)
),
list(
objName="DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="dbsubloc",
Lcolname="sp_ac",
Rcolname="de"
)
)
)
)),
GOA = return(list(
list(
objName="GO",
Class="GoAnnDbBimap",
L2Rchain=list(
list(
tablename="go",
Lcolname="sp_ac",
tagname=c(Evidence="{evidence}"),
Rcolname="go_id",
Rattribnames=c(Ontology="{ontology}")
)
)
),
list(
objName="DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="de",
Lcolname="sp_ac",
Rcolname="de"
)
)
),
list(
objName="SPID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="id",
Lcolname="sp_ac",
Rcolname="sp_id"
)
)
)
)),
HOMOLOGENE = return(list(
list(
objName="HOMOLOG",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="homolog",
Lcolname="gene_id",
Rcolname="homolog_id"
)
)
),
list(
objName="HOMOLOG2GI",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="homolog",
Lcolname="homolog_id",
Rcolname="gi"
)
)
),
list(
objName="HOMOLOG2AC",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="homolog",
Lcolname="homolog_id",
Rcolname="ncbi_ac"
)
)
),
list(
objName="SYMBOL",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="homolog",
Lcolname="gene_id",
Rcolname="symbol"
)
)
),
list(
objName="TAXID",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="homolog",
Lcolname="gene_id",
Rcolname="tax_id"
)
)
),
list(
objName="ORGANISM",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="tax",
Lcolname="tax_id",
Rcolname="organism"
)
)
)
)),
INPARANOID = return(list(
list(
objName="ORTHOLOG",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="ortholog",
Lcolname="protein_id",
Rcolname="ortholog_id"
)
)
),
list(
objName="ORGANISM",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="ortholog",
Lcolname="protein_id",
Rcolname="organism"
)
)
),
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="seq",
Lcolname="protein_id",
Rcolname="seq"
)
)
)
)),
PEPTIDEATLAS = return(list(
list(
objName="PEP2PROTEIN",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="pep2protein",
Lcolname="peptide_id",
Rcolname="protein_position"
)
)
),
list(
objName="PEP2CHR",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="pep2chr",
Lcolname="peptide_id",
Rcolname="chr_position"
)
)
),
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="seq",
Lcolname="peptide_id",
Rcolname="seq"
)
)
)
)),
DNAME = return(list(
list(
objName="GO2NAME",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="go",
Lcolname="go_id",
Rcolname="go_name"
)
)
),
list(
objName="PATH2DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="kegg",
Lcolname="path_id",
Rcolname="path_de"
)
)
),
list(
objName="PFAM2DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="pfam",
Lcolname="pfam_id",
Rcolname="pfam_de"
)
)
),
list(
objName="PFAM2NAME",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="pfam",
Lcolname="pfam_id",
Rcolname="pfam_name"
)
)
),
list(
objName="PROSITE2DE",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="prosite",
Lcolname="prosite_id",
Rcolname="prosite_de"
)
)
),
list(
objName="INTERPRO2NAME",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="interpro",
Lcolname="interpro_id",
Rcolname="interpro_name"
)
)
),
list(
objName="TAXID2NAME",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="tax",
Lcolname="tax_id",
Rcolname="tax_name"
)
)
)
)),
CROSS = return(list(
list(
objName="SEQ",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="seq",
Lcolname="protein_id",
Rcolname="seq"
)
)
),
list(
objName="MATCH",
Class="AnnDbBimap",
L2Rchain=list(
list(
tablename="match",
Lcolname="query",
Rcolname="subject"
)
)
)
))
)
}
createAnnObjs <- function(type, prefix, datacache, dbconn)
{
seeds <- createSeeds(type)
## AnnDbBimap objects
seed0 <- list(
datacache=datacache
)
ann_objs <- AnnotationDbi:::createAnnDbBimaps(seeds, seed0)
ann_objs <- switch(type,
"SP" = createAnnObjs.SP(ann_objs),
"IPI" = createAnnObjs.IPI(ann_objs),
"REFSEQ" = createAnnObjs.REFSEQ(ann_objs),
"BACELLO" = createAnnObjs.BACELLO(ann_objs),
"DBSUBLOC" = createAnnObjs.DBSUBLOC(ann_objs),
"GOA" = createAnnObjs.GOA(ann_objs),
"HOMOLOGENE" = createAnnObjs.HOMOLOGENE(ann_objs),
"SYSPTM" = createAnnObjs.SYSPTM(ann_objs),
"SYSBODYFLUID" = createAnnObjs.SYSBODYFLUID(ann_objs),
"INPARANOID" = createAnnObjs.INPARANOID(ann_objs),
ann_objs
)
if( !dbExistsTable(dbconn,"map_counts") ){
tmp <- sapply(ls(ann_objs), function(x){count.mappedkeys(base:::get(x,envir=ann_objs))} )
tmp <- data.frame(names(tmp),tmp)
colnames(tmp) <- c("map_name","count")
dbWriteTable(dbconn, "map_counts", tmp, row.names=F)
}
ann_objs$MAPCOUNTS <- createMAPCOUNTS(dbconn, prefix)
AnnotationDbi:::prefixAnnObjNames(ann_objs, prefix)
}
createAnnObjs.SP <- function(ann_objs){
ann_objs$GO2SPID <- revmap(ann_objs$GO, objName="GO2SPID")
ann_objs$PATH2SPID <- revmap(ann_objs$PATH, objName="PATH2SPID")
ann_objs$REFSEQ2SPID <- revmap(ann_objs$REFSEQ, objName="REFSEQ2SPID")
ann_objs
}
createAnnObjs.REFSEQ <- function(ann_objs){
ann_objs$GO2GI <- revmap(ann_objs$GO, objName="GO2GI")
ann_objs$PATH2GI <- revmap(ann_objs$PATH, objName="PATH2GI")
ann_objs$REFSEQ2GI <- revmap(ann_objs$REFSEQ, objName="REFSEQ2GI")
ann_objs
}
createAnnObjs.IPI <- function(ann_objs){
ann_objs$GO2IPIID <- revmap(ann_objs$GO, objName="GO2IPIID")
ann_objs$PATH2IPIID <- revmap(ann_objs$PATH, objName="PATH2IPIID")
ann_objs$IPIAC2IPIID <- revmap(ann_objs$IPIACs, objName="IPIAC2IPIID")
ann_objs$SPID2IPIID <- revmap(ann_objs$SPID, objName="SPID2IPIID")
ann_objs$SPAC2IPIID <- revmap(ann_objs$SPAC, objName="SPAC2IPIID")
ann_objs$REFSEQ2IPIID <- revmap(ann_objs$REFSEQ, objName="REFSEQ2IPIID")
ann_objs
}
createAnnObjs.BACELLO <- function(ann_objs){
ann_objs$SUBCELL2SPID <- revmap(ann_objs$SUBCELL, objName="SUBCELL2SPID")
ann_objs
}
createAnnObjs.DBSUBLOC <- function(ann_objs){
ann_objs$SUBCELL2SPAC <- revmap(ann_objs$SUBCELL, objName="SUBCELL2SPAC")
ann_objs
}
createAnnObjs.GOA <- function(ann_objs){
ann_objs$GO2SPAC <- revmap(ann_objs$GO, objName="GO2SPAC")
ann_objs$SPID2SPAC <- revmap(ann_objs$SPID, objName="SPID2SPAC")
ann_objs
}
createAnnObjs.SYSBODYFLUID <- function(ann_objs){
ann_objs$BF2PMID <- revmap(ann_objs$PMID2BF, objName="BF2PMID")
ann_objs
}
createAnnObjs.HOMOLOGENE <- function(ann_objs){
ann_objs$HOMOLOG2GENEID <- revmap(ann_objs$HOMOLOG, objName="HOMOLOG2GENEID")
ann_objs
}
createAnnObjs.INPARANOID <- function(ann_objs){
ann_objs$ORTHOLOG2PROTEIN <- revmap(ann_objs$ORTHOLOG, objName="ORTHOLOG2PROTEIN")
ann_objs
}
createAnnObjs.SYSPTM <- function(ann_objs){
ann_objs$PTMTYPE2SITE <- revmap(ann_objs$PTMTYPE, objName="PTMTYPE2SITE")
ann_objs
}
Try the PAnnBuilder package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.