--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/maaslin-4450aa4ecc84/src/CreateReadConfigFile.R	Sun Feb 08 23:08:38 2015 -0500
@@ -0,0 +1,63 @@
+#!/usr/bin/env Rscript
+#####################################################################################
+#Copyright (C) <2012>
+#
+#Permission is hereby granted, free of charge, to any person obtaining a copy of
+#this software and associated documentation files (the "Software"), to deal in the
+#Software without restriction, including without limitation the rights to use, copy,
+#modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
+#and to permit persons to whom the Software is furnished to do so, subject to
+#the following conditions:
+#
+#The above copyright notice and this permission notice shall be included in all copies
+#or substantial portions of the Software.
+#
+#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+#INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+#PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+#OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+#SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# This file is a component of the MaAsLin (Multivariate Associations Using Linear Models), 
+# authored by the Huttenhower lab at the Harvard School of Public Health
+# (contact Timothy Tickle, ttickle@hsph.harvard.edu).
+#####################################################################################
+
+inlinedocs <- function(
+##author<< Curtis Huttenhower <chuttenh@hsph.harvard.edu> and Timothy Tickle <ttickle@hsph.harvard.edu>
+##description<< Allows read config files to be created.
+) { return( pArgs ) }
+
+### Logging class
+suppressMessages(library( logging, warn.conflicts=FALSE, quietly=TRUE, verbose=FALSE))
+### Class for commandline argument processing
+suppressMessages(library( optparse, warn.conflicts=FALSE, quietly=TRUE, verbose=FALSE))
+
+### Source the IO.R for the script
+source(file.path("src","lib","IO.R"))
+source(file.path("src","lib","Constants.R"))
+
+### Create command line argument parser
+### The TSV (tab seperated value (column major, samples are rows) file that will be read in
+### The column that is the last metadata name
+### The read.config file that will be used to read in the TSV file
+pArgs <- OptionParser( usage = "%prog [optional] <strOutputRC> <strMatrixName>" )
+# Settings for Read config
+## row indices
+pArgs <- add_option( pArgs, c("-r", "--rows"), type="character", action="store", dest="strRows", default=NA, metavar="row_indices", help="Rows to read by index starting with 1.")
+## column indices
+pArgs <- add_option( pArgs, c("-c", "--columns"), type="character", action="store", dest="strColumns", default=NA, metavar="column_indices", help="Columns to read in by index starting with 1.")
+## delimiter
+pArgs <- add_option( pArgs, c("-d", "--delimiter"), type="character", action="store", dest="charDelimiter", default="\t", metavar="delimiter", help="Delimiter to read the matrix.")
+## append to current file
+pArgs <- add_option( pArgs, c("-a", "--append"), type="logical", action="store_true", dest="fAppend", default=FALSE, metavar="append", help="Append to existing data. Default no append.")
+### Parse arguments
+lsArgs <- parse_args( pArgs, positional_arguments = TRUE )
+
+#Get positional arguments
+if( !(length( lsArgs$args ) == 2) ) { stop( print_help( pArgs ) ) }
+
+### Write to file the read config script
+funcWriteMatrixToReadConfigFile(strConfigureFileName=lsArgs$args[1], strMatrixName=lsArgs$args[2], strRowIndices=lsArgs$options$strRows,
+  strColIndices=lsArgs$options$strColumns,acharDelimiter=lsArgs$options$charDelimiter,fAppend=lsArgs$options$fAppend)