From 6a7295a258932a78c616ea4f8f591eb5f0191da4 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Wed, 8 Jan 2014 11:20:39 -0500
Subject: initial commit

---
 select_kmers.sh | 86 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 86 insertions(+)
 create mode 100755 select_kmers.sh

(limited to 'select_kmers.sh')

diff --git a/select_kmers.sh b/select_kmers.sh
new file mode 100755
index 0000000..11ee124
--- /dev/null
+++ b/select_kmers.sh
@@ -0,0 +1,86 @@
+#!/bin/bash
+# range of mers, min and max 
+: ${min_mer_range=6}
+: ${max_mer_range=10}
+# directory to store our counts and sorted counts
+: ${counts_directory=$PWD/counts}
+# temp directory 
+: ${tmp_directory=$PWD/tmp}
+# maximum kmer melting point
+: ${max_melting_temp=20}
+# minimum mer count
+# ! you can supply either a percentage like this .5
+# ! or you can supply a raw number (100)
+: ${min_mer_count=1000}
+# maximum mers to pick
+: ${max_select=15}
+
+export min_mer_range
+export max_mer_range
+export max_select
+export min_mer_count
+
+
+if [ ! -d $counts_directory ]; then
+	mkdir $counts_directory
+fi
+
+if [ ! -d $tmp_directory ]; then
+	mkdir $tmp_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)
+
+echo "checking if mers are below melting temperature in the foreground"
+
+rm $fg_counts-fg-non-melting
+
+python below_melting_temperature.py $max_melting_temp < $fg_counts > $fg_counts-fg-non-melting
+
+python ./select_mers.py $fg_counts-fg-non-melting $fg_tmp $bg_counts $bg_tmp # > $(basename $foreground)_$(basename $background)_final_mers
-- 
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