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annotate maaslin-4450aa4ecc84/src/CreateReadConfigFile.R @ 1:a87d5a5f2776

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Uploaded the version running on the prod server
author george-weingart
date Sun, 08 Feb 2015 23:08:38 -0500
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1 #!/usr/bin/env Rscript
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2 #####################################################################################
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3 #Copyright (C) <2012>
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4 #
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5 #Permission is hereby granted, free of charge, to any person obtaining a copy of
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6 #this software and associated documentation files (the "Software"), to deal in the
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7 #Software without restriction, including without limitation the rights to use, copy,
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8 #modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
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9 #and to permit persons to whom the Software is furnished to do so, subject to
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10 #the following conditions:
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11 #
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12 #The above copyright notice and this permission notice shall be included in all copies
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13 #or substantial portions of the Software.
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14 #
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15 #THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
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16 #INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
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17 #PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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18 #HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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19 #OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
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20 #SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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21 #
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22 # This file is a component of the MaAsLin (Multivariate Associations Using Linear Models),
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23 # authored by the Huttenhower lab at the Harvard School of Public Health
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24 # (contact Timothy Tickle, ttickle@hsph.harvard.edu).
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25 #####################################################################################
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26
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27 inlinedocs <- function(
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28 ##author<< Curtis Huttenhower <chuttenh@hsph.harvard.edu> and Timothy Tickle <ttickle@hsph.harvard.edu>
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29 ##description<< Allows read config files to be created.
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30 ) { return( pArgs ) }
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31
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32 ### Logging class
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33 suppressMessages(library( logging, warn.conflicts=FALSE, quietly=TRUE, verbose=FALSE))
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34 ### Class for commandline argument processing
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35 suppressMessages(library( optparse, warn.conflicts=FALSE, quietly=TRUE, verbose=FALSE))
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36
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37 ### Source the IO.R for the script
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38 source(file.path("src","lib","IO.R"))
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39 source(file.path("src","lib","Constants.R"))
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40
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41 ### Create command line argument parser
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42 ### The TSV (tab seperated value (column major, samples are rows) file that will be read in
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43 ### The column that is the last metadata name
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44 ### The read.config file that will be used to read in the TSV file
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45 pArgs <- OptionParser( usage = "%prog [optional] <strOutputRC> <strMatrixName>" )
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46 # Settings for Read config
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47 ## row indices
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48 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.")
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49 ## column indices
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50 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.")
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51 ## delimiter
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52 pArgs <- add_option( pArgs, c("-d", "--delimiter"), type="character", action="store", dest="charDelimiter", default="\t", metavar="delimiter", help="Delimiter to read the matrix.")
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53 ## append to current file
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54 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.")
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55 ### Parse arguments
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56 lsArgs <- parse_args( pArgs, positional_arguments = TRUE )
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57
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58 #Get positional arguments
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59 if( !(length( lsArgs$args ) == 2) ) { stop( print_help( pArgs ) ) }
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60
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61 ### Write to file the read config script
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62 funcWriteMatrixToReadConfigFile(strConfigureFileName=lsArgs$args[1], strMatrixName=lsArgs$args[2], strRowIndices=lsArgs$options$strRows,
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63 strColIndices=lsArgs$options$strColumns,acharDelimiter=lsArgs$options$charDelimiter,fAppend=lsArgs$options$fAppend)