# HG changeset patch
# User nikos
# Date 1415141682 18000
# Node ID 2ae336f19de08104ba4a733760b0d292deede6cb
# Parent  6b9e957d8db1d7f41359c282d3959e48897ac43a
Uploaded

diff -r 6b9e957d8db1 -r 2ae336f19de0 k2n.R
--- a/k2n.R	Tue Nov 04 15:11:36 2014 -0500
+++ b/k2n.R	Tue Nov 04 17:54:42 2014 -0500
@@ -3,35 +3,14 @@
 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
 args <- commandArgs(trailingOnly = TRUE)
 
-#get options, using the spec as defined by the enclosed list.
-#we read the options from the default: commandArgs(TRUE).
-spec = matrix( c(
-  'verbose', 'v', 2, "integer",
-  'help' , 'h', 0, "logical",
-  'merged', 'm', 1, "character",
-  'read_counts', 'c', 1, "character",
-  'max_observed', 'b', 1, "integer",
-  'barcode_length', 'l', 1, "integer",
-  'output', 'o', 1, "character"
-  ), byrow = TRUE, ncol = 4 );
-
-opt = getopt( spec );
-
-# if help was asked for print a friendly message
-# and exit with a non-zero error code
-if ( !is.null( opt$help ) ) {
-    cat( getopt( spec, usage=TRUE ) ) ;
-    q( status = 1 );
-}
-
 # Read inputs
-merged <- read.table( opt$merged )
-read_counts <- read.table( opt$read_counts )
+merged <- read.table( args[1] )
+read_counts <- read.table( args[2] )
 
 barcodes_nt <- merged[ do.call( paste, as.list( merged[ ,1:3 ] ) ) %in% do.call( paste, as.list( read_counts[ ( read_counts[ , 4 ] ) <= summary( read_counts[ , 4 ] )[ 5 ], 1:3 ] ) ) , 4 ]
 
 ##make the matrix with the nucleotide freqs per position:
-nt_counts <- matrix( nrow = 4, ncol = opt$barcode_length )
+nt_counts <- matrix( nrow = 4, ncol = as.numeric(args[4]) )
 for( h in 1:ncol( nt_counts ) ){
     j <- 1
     for( nt_local in c( "A","C","G","T" ) ) {
@@ -59,7 +38,7 @@
 i <- 1
 results[ i ] <- sum( 1 - ( 1 - probs )**i )
 
-while( results[ i ] <= opt$max_observed ) {
+while( results[ i ] <= as.numeric(args[3]) ) {
     i <- i + 1
     results[ i ] <- sum( 1 - ( 1 - probs )**i )   #Mf to Sf
 }
@@ -71,4 +50,4 @@
 Uf_to_Mf[ i ] <- which( difference == min( difference ) ) #if you want to know how many molecules underlie n unique barcodes ask Uf_to_Mf[n]
 }
 
-write( Uf_to_Mf, file = opt$output )
+write( Uf_to_Mf, file = args[5] )
diff -r 6b9e957d8db1 -r 2ae336f19de0 normalize.xml
--- a/normalize.xml	Tue Nov 04 15:11:36 2014 -0500
+++ b/normalize.xml	Tue Nov 04 17:54:42 2014 -0500
@@ -1,5 +1,5 @@
 <tool id="rna_probing_normalize" version="0.1" name="Normalize" force_history_refresh="True">
-    <description>RNA probing data </description>
+    <description>RNA probing signal</description>
     <requirements>
         <requirement type="package" version="3.1.1">R_3_1_1</requirement>
         <requirement type="R-module">RNAprobR</requirement>
diff -r 6b9e957d8db1 -r 2ae336f19de0 summarize_unique_barcodes.sh
--- a/summarize_unique_barcodes.sh	Tue Nov 04 15:11:36 2014 -0500
+++ b/summarize_unique_barcodes.sh	Tue Nov 04 17:54:42 2014 -0500
@@ -210,7 +210,7 @@
 
 if [ "$k2n" == "True" ]; then
     bar_length=$(head -n 1 $barcodes | cut -f 2 | xargs expr length)
-    Rscript $R_SCRIPT_PATH/k2n.R -m merged_temp.gz -c $output_dir/read_counts.txt -b ${max_observed_barcodes} -l $bar_length -o $output_dir/k2n.txt
+    Rscript $R_SCRIPT_PATH/k2n.R merged_temp.gz $output_dir/read_counts.txt ${max_observed_barcodes} $bar_length $output_dir/k2n.txt
 fi
 
 #Remove temp files