LBMC » CacheCache

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Readme / Documentation for `cachecache`

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`cachecache` offers Python API and R package allowing to perform 

direct qtl detection from raw sequence reads of yeast populations under selection.

License

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Copyright CNRS 2012-2013                                                 

- Florent CHUFFART                                                         

- Gael YVERT                                                               

This software is a computer program which purpose is to perform direct qtl 

detection from raw sequence reads of yeast populations under selection.

The Software is provided "as is" without warranty of any kind, either express or 

implied, including without limitation any implied warranties of condition, 

uninterrupted use, merchantability, fitness for a particular purpose, or 

non-infringement. You use this software at your own risk.

This software is governed by the CeCILL license under French law and     

abiding by the rules of distribution of free software.  You can  use,    

modify and/ or redistribute the software under the terms of the CeCILL   

license as circulated by CEA, CNRS and INRIA at the following URL        

"http://www.cecill.info".                                                

As a counterpart to the access to the source code and  rights to copy,   

modify and redistribute granted by the license, users are provided only  

with a limited warranty  and the software's author,  the holder of the   

economic rights,  and the successive licensors  have only  limited       

liability.                                                               

In this respect, the user's attention is drawn to the risks associated   

with loading,  using,  modifying and/or developing or reproducing the    

software by the user in light of its specific status of free software,   

that may mean  that it is complicated to manipulate,  and  that  also    

therefore means  that it is reserved for developers  and  experienced    

professionals having in-depth computer knowledge. Users are therefore    

encouraged to load and test the software's suitability as regards their  

requirements in conditions enabling the security of their systems and/or 

data to be ensured and,  more generally, to use and operate it in the    

same conditions as regards security.                                     

The fact that you are presently reading this means that you have had     

knowledge of the CeCILL license and that you accept its terms.           

Installation Instructions

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Links

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`cachecache` home page: https://forge.cbp.ens-lyon.fr/redmine/projects/cachecache

Package: cachecache

Maintainer: Florent Chuffart <florent.chuffart@ens-lyon.fr>

Author: Florent Chuffart

Version: 0.2

License: CeCILL 

Title: cachecache

Depends: 

Description: cachecache is an R package allowing to reduce disk access by managing a cache. Data on the disk is identified by a path that is also an index in the cache (an R list). this index provide an access to the same data in RAM space. cachecache is used to compute NGS data in the SiGHT project context (ERC-StG2011-281359). For more information on how to use bot, have a look on the examples of the help ?cahecache::get_content.

URL: http://forge.cbp.ens-lyon.fr/redmine/projects/cachecache http://www.ens-lyon.fr/LBMC/gisv/index.php/en/protocols/bioinformatics  http://www.ens-lyon.fr/LBMC/gisv

export(get_content)

get_content = structure( function(## Get content from cached 

### Access to the cached content of a file via the global variable CACHE_CACHE. Load content in CACHE_CACHE if needed.

filename, ##<< The path to the file that contain dataset.

class=NULL, ##<< The class of dataset.

... ##<< Parameters that will be passed to my_read

) {

  if (inherits(try(CACHE_CACHE,TRUE), "try-error") || is.null(CACHE_CACHE)) {

    CACHE_CACHE <<- list()

  }

  obj = list(filename=filename)

  class(obj) = class

  if (is.null(CACHE_CACHE[[obj$filename]])) {

    print(paste("Loading file ",obj$filename, sep=""))

		tmp_content = my_read(obj, ...)

    print("affect it...")

    CACHE_CACHE[[obj$filename]] <<- tmp_content

    print("done.")

  }  

  return(CACHE_CACHE[[obj$filename]])

### Returns the cached content of the current object. 

}, ex=function(){

	# Create a dataframe

	df = data.frame(list(key1 = "value1", key2 = "value2"), stringsAsFactors=FALSE)

	df = rbind(df, list(key1 = "value1'", key2 = "value3'"))

	# Dump it into tmp file

	write.table(df, file="/tmp/tmp.dump.table.tmp")

	# Load it into cache using feature.

	# First time it will be load into cache

	print(get_content("/tmp/tmp.dump.table.tmp", "table", stringsAsFactors=FALSE))

	# Second time not

	print(get_content("/tmp/tmp.dump.table.tmp", "table", stringsAsFactors=FALSE))

})

my_read = function(

### Abstract my_read function.	

	obj, ...) {

  UseMethod("my_read", obj)

}

my_read.default = function(

### Default my_read function.	

	obj, ...){

  stop(paste("ERROR, my_read is not defined for any Objects (file ", obj$filename," )", sep=""))			

}

my_read.table = function(

### my_read function for table files.	

	obj, ...){

	if (rev(unlist(strsplit(obj$filename, ".", fixed=TRUE)))[1] == "gz") {

	  return(read.table(file=gzfile(obj$filename), ...))			

	} else { 

	  return(read.table(file=obj$filename, ...))

	}

}	

my_read.cvs = function(

### my_read function for cvs files.	

	obj, ...){

  return(read.csv(file=obj$filename, ...))

}