From be091dd9ca7dbdb8c9791003a67d13616621ff68 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Fri, 17 Jan 2014 14:44:09 -0500
Subject: rename SelectiveGenomeAmplification

---
 Makefile                        |   4 ++
 SelectiveGenomeAmplification    | 123 ++++++++++++++++++++++++++++++++++++++++
 SelectiveGenomeAmplification.sh | 123 ----------------------------------------
 3 files changed, 127 insertions(+), 123 deletions(-)
 create mode 100755 SelectiveGenomeAmplification
 delete mode 100755 SelectiveGenomeAmplification.sh

diff --git a/Makefile b/Makefile
index 38b2b3d..6921d3f 100644
--- a/Makefile
+++ b/Makefile
@@ -17,3 +17,7 @@ $(BIN)/melting_range: $(SRC)/melting_range.c
 
 clean:
 	rm -vf $(BIN)/strstream $(BIN)/melting_range $(BIN)/strstreamone
+
+install: all
+	install -c $(BIN)/strstream $(BIN)/melting_range $(BIN)/strstreamone SelectiveGenomeAmplification select_mers.py $(dest)
+
diff --git a/SelectiveGenomeAmplification b/SelectiveGenomeAmplification
new file mode 100755
index 0000000..0bff2ca
--- /dev/null
+++ b/SelectiveGenomeAmplification
@@ -0,0 +1,123 @@
+#!/usr/bin/env bash
+# range of mers, min and max 
+: ${min_mer_range=6}
+: ${max_mer_range=10}
+# max mer distance, the distance between two mers in our selected outputs
+: ${max_mer_distance=5000}
+# directory to store our counts and sorted counts
+: ${counts_directory=$PWD/counts}
+# temp directory 
+: ${tmp_directory=$PWD/tmp}
+# output directory 
+: ${output_directory=$PWD/outputs}
+# min/maximum kmer melting point
+: ${max_melting_temp=30}
+: ${min_melting_temp=0}
+# minimum mer count
+: ${min_mer_count=0}
+# maximum mers to pick
+: ${max_select=15}
+# mers to specifically IGNORE, space delimited
+: ${ignore_mers=''}
+
+export ignore_mers
+export min_mer_range
+export max_mer_range
+
+export max_select
+
+export min_mer_count
+export max_mer_distance
+
+export max_melting_temp 
+export min_melting_temp 
+
+PATH=$PATH:$PWD
+
+# Make our counts directory
+if [ ! -d $counts_directory ]; then
+	mkdir $counts_directory
+fi
+
+# Make our temporary directory
+if [ ! -d $tmp_directory ]; then
+	mkdir $tmp_directory
+fi
+
+# Make our output directory
+if [ ! -d $output_directory ]; then
+	mkdir $output_directory
+fi
+
+foreground=$1
+background=$2
+
+if [[ ! -f $foreground ]]; then
+	echo "Could not open $foreground."
+	exit 1
+fi
+
+if [[ ! -f $background ]]; then
+	echo "Could not open $background."
+	exit 1
+fi
+
+for fasta_file in $foreground $background; do
+
+	counts=$counts_directory/$(basename $fasta_file)
+	tmp=$tmp_directory/$(basename $fasta_file)
+
+	echo pre-processing $fasta_file
+
+	# check if our preprocessed file exists
+	if [[ ! -f $tmp ]]; then
+		echo "> pre processed $fasta_file" >> $tmp
+		cat $fasta_file | grep -v "^>" | tr -d '\n' >> $tmp
+	fi
+
+	# run counts if they haven't been created 
+	rm $counts-counts
+	for mer in `seq $min_mer_range $max_mer_range`;	do 
+		if [ ! -e $counts-counts-$mer ]; then
+			echo checking $mer mers for $fasta_file
+			kmer_total_count -i $tmp -k $mer -l -n >> $counts-counts-$mer
+		else 
+			echo "$mer mers already done for $fasta_file"
+		fi
+		
+		cat $counts-counts-$mer >> $counts-counts
+	
+	done
+done
+
+
+fg_counts=$counts_directory/$(basename $foreground)-counts
+bg_counts=$counts_directory/$(basename $background)-counts
+
+fg_tmp=$tmp_directory/$(basename $foreground)
+bg_tmp=$tmp_directory/$(basename $background)
+
+# remove ignored mers
+if [ "$ignore_mers" ]; then
+	echo "removing ignored mers: " + $ignore_mers
+	for mer in $ignore_mers; do
+		sed -i '/^'$mer'\t/d' $fg_counts
+		sed -i '/^'$mer'\t/d' $bg_counts
+	done
+fi
+
+
+echo "checking if mers are below melting temperature in the foreground"
+rm $fg_counts-fg-non-melting
+melting_range $min_melting_temp $max_melting_temp < $fg_counts > $fg_counts-fg-non-melting &
+
+echo "checking if mers are below melting temperature in the background"
+rm $bg_counts-bg-non-melting
+melting_range $min_melting_temp $max_melting_temp < $bg_counts > $bg_counts-bg-non-melting
+
+# echo "scoring mer selectivity"
+# python ./mer_selectivity.py $fg_counts-fg-non-melting $bg_counts-bg-non-melting
+
+echo ""
+echo "scoring mers"
+python ./select_mers.py $fg_counts-fg-non-melting $fg_tmp $bg_counts-bg-non-melting $bg_tmp # > $(basename $foreground)_$(basename $background)_final_mers 
diff --git a/SelectiveGenomeAmplification.sh b/SelectiveGenomeAmplification.sh
deleted file mode 100755
index e46d9ea..0000000
--- a/SelectiveGenomeAmplification.sh
+++ /dev/null
@@ -1,123 +0,0 @@
-#!/bin/bash
-# range of mers, min and max 
-: ${min_mer_range=6}
-: ${max_mer_range=10}
-# max mer distance, the distance between two mers in our selected outputs
-: ${max_mer_distance=5000}
-# directory to store our counts and sorted counts
-: ${counts_directory=$PWD/counts}
-# temp directory 
-: ${tmp_directory=$PWD/tmp}
-# output directory 
-: ${output_directory=$PWD/outputs}
-# min/maximum kmer melting point
-: ${max_melting_temp=30}
-: ${min_melting_temp=0}
-# minimum mer count
-: ${min_mer_count=0}
-# maximum mers to pick
-: ${max_select=15}
-# mers to specifically IGNORE, space delimited
-: ${ignore_mers=''}
-
-export ignore_mers
-export min_mer_range
-export max_mer_range
-
-export max_select
-
-export min_mer_count
-export max_mer_distance
-
-export max_melting_temp 
-export min_melting_temp 
-
-PATH=$PATH:$PWD
-
-# Make our counts directory
-if [ ! -d $counts_directory ]; then
-	mkdir $counts_directory
-fi
-
-# Make our temporary directory
-if [ ! -d $tmp_directory ]; then
-	mkdir $tmp_directory
-fi
-
-# Make our output directory
-if [ ! -d $output_directory ]; then
-	mkdir $output_directory
-fi
-
-foreground=$1
-background=$2
-
-if [[ ! -f $foreground ]]; then
-	echo "Could not open $foreground."
-	exit 1
-fi
-
-if [[ ! -f $background ]]; then
-	echo "Could not open $background."
-	exit 1
-fi
-
-for fasta_file in $foreground $background; do
-
-	counts=$counts_directory/$(basename $fasta_file)
-	tmp=$tmp_directory/$(basename $fasta_file)
-
-	echo pre-processing $fasta_file
-
-	# check if our preprocessed file exists
-	if [[ ! -f $tmp ]]; then
-		echo "> pre processed $fasta_file" >> $tmp
-		cat $fasta_file | grep -v "^>" | tr -d '\n' >> $tmp
-	fi
-
-	# run counts if they haven't been created 
-	rm $counts-counts
-	for mer in `seq $min_mer_range $max_mer_range`;	do 
-		if [ ! -e $counts-counts-$mer ]; then
-			echo checking $mer mers for $fasta_file
-			kmer_total_count -i $tmp -k $mer -l -n >> $counts-counts-$mer
-		else 
-			echo "$mer mers already done for $fasta_file"
-		fi
-		
-		cat $counts-counts-$mer >> $counts-counts
-	
-	done
-done
-
-
-fg_counts=$counts_directory/$(basename $foreground)-counts
-bg_counts=$counts_directory/$(basename $background)-counts
-
-fg_tmp=$tmp_directory/$(basename $foreground)
-bg_tmp=$tmp_directory/$(basename $background)
-
-# remove ignored mers
-if [ "$ignore_mers" ]; then
-	echo "removing ignored mers: " + $ignore_mers
-	for mer in $ignore_mers; do
-		sed -i '/^'$mer'\t/d' $fg_counts
-		sed -i '/^'$mer'\t/d' $bg_counts
-	done
-fi
-
-
-echo "checking if mers are below melting temperature in the foreground"
-rm $fg_counts-fg-non-melting
-melting_range $min_melting_temp $max_melting_temp < $fg_counts > $fg_counts-fg-non-melting &
-
-echo "checking if mers are below melting temperature in the background"
-rm $bg_counts-bg-non-melting
-melting_range $min_melting_temp $max_melting_temp < $bg_counts > $bg_counts-bg-non-melting
-
-# echo "scoring mer selectivity"
-# python ./mer_selectivity.py $fg_counts-fg-non-melting $bg_counts-bg-non-melting
-
-echo ""
-echo "scoring mers"
-python ./select_mers.py $fg_counts-fg-non-melting $fg_tmp $bg_counts-bg-non-melting $bg_tmp # > $(basename $foreground)_$(basename $background)_final_mers 
-- 
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