getBaseParsers(baseMapType, db=FALSE)
fileMuncher(outName, dataFile, parser, organism)
fileMuncher_DB(dataFile, parser, organism)
writeInput(parser, perlName, organism, dataFile)
writeInputSP(perlName,organism)
writeInputIPI(perlName,organism)
writeInputREFSEQ(perlName,organism)
writeInputBLAST(perlName,organism, dataFile)
writeInputPFAM(perlName,organism)
writeInputINTERPRO(perlName,organism)
writeOutput(parser, perlName)
.callPerl(script, os)
getSrcObjs(srcUrls, organism, built, fromWeb = TRUE)
getBaseData(srcObjs)
splitEntry(dataRow, sep = ";", asNumeric = FALSE)
twoStepSplit(dataRow, entrySep = ";", eleSep = "@", asNumeric = FALSE)
mergeRowByKey(mergeMe, keyCol = 1, sep = ";")getBaseParsers returns the path of parser file.getSrcObjs returns a list of defined the objects of class
"pBase".getBaseData returns a matrix of protein annotation data.splitEntry returns a vector.twoStepSplit returns a vector.mergeRowByKey returns a data frame containing the merged values.
getBaseParsers return a character string of the name of a
parser file based on the given database. Each parser file is a part of
perl script and used to parse relevant data.
fileMuncher produce perl file based on given parser and
additional input files, then perform this perl program via R.
fileMuncher_DB produce perl file based on given parser and
additional input, then perform this perl program via R. Result data are
stored in the relative ouput files. It is designed for the SQLite-based
annotation package.
writeInput write additional information including input files
into the perl script.
writeOutput write information about ouput files into the perl
script.
.callPerl perform perl program via R.
getSrcObjs given url of database and concerned organism,
define objects of class "pBase". pBase is a sub class of "pubRepo", and it
is used for SwissProt, TREMBL, IPI and NCBI RefSeq data.
getBaseData get basic protein annotation data and sequence
data from protein database: SwissProt, TREMBL, IPI, NCBI PefSeq.
splitEntry split multiple entry for a given mapping.
twoStepSplit split multiple entry with two separaters
(e.g. 12345@18;67891@18).
mergeRowByKey merge duplicating values for the same key.