fileMuncher {AnnBuilder}R Documentation

Dynamically create a Perl script to parse a source file base on user specifications

Description

This function takes a base file, a source file, and a segment of Perl script specifying how the source file will be parsed and the generates a fully executable Perl script that is going to be called to parse the source file.

Usage

fileMuncher(outName, baseFile, dataFile, parser, isDir = FALSE)
mergeRowByKey(mergeMe, keyCol = 1, sep = ";")

Arguments

outName outName a character string for the name of the file where the parsed data will be stored
baseFile baseFile a character string for the name of the file that is going to be used as the base to process the source file. Only data that are corresponding to the ids defined in the base file will be processed and mapped
dataFile dataFile a character string for the name of the source data file
parser parser a character string for the name of the file containing a segment of a Perl script for parsing the source file. An output connection to OUT that is for storing parsed data, an input connection to BASE for importing base file, and an input connection to DATA for reading the source data file are assumed to be open. parser should define how BASE and DATA will be used to extract data and then store them in OUT
isDir isDir a boolean indicating whether dataFile is a name of a directory (TRUE) or not (FALSE)
mergeMe mergeMe a data matrix that is going to be processed to merge rows with duplicating keys
keyCol keyCol an integer for the index of the column containing keys based on which entries will be merged
sep sep a character string for the separator used to separate multiple values

Details

The system is assumed to be able to run Perl. Perl scripts generated dynamically will also be removed after execution.

mergeRowByKey merges data based on common keys. Keys multiple values for a given key will be separated by "sep".

Value

fileMuncher returns a character string for the name of the output file
mergeRowByKey returns a matrix with merged data.

Note

This function is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R

Author(s)

Jianhua Zhang

See Also

resolveMaps

Examples

if(interactive()){
path <- file.path(.path.package("AnnBuilder"), "scripts")
temp <- matrix(c("32469_f_at", "D90278", "32469_at", "L00693", "33825_at",
"X68733", "35730_at", "X03350", "38912_at", "D90042", "38936_at",
"M16652"), ncol = 2, byrow = TRUE)
write.table(temp, "tempBase", sep = "\t", quote = FALSE,
row.names = FALSE, col.names = FALSE)
# Parse a truncated version of LL\_tmpl.gz from Bioconductor
srcFile <-
loadFromUrl("http://www.bioconductor.org/datafiles/wwwsources/Tll_tmpl.gz")  
fileMuncher(outName = "temp", baseFile = "tempBase", dataFile = srcFile,
parser =  file.path(path, "gbLLParser"), isDir = FALSE)
# Show the parsed data
read.table(file = "temp", sep = "\t", header = FALSE)
unlink("tempBase")
unlink("temp")
}

[Package AnnBuilder version 1.4.21 Index]