rename SelectiveGenomeAmplification

1 files changed, 123 insertions, 0 deletions

diff --git a/SelectiveGenomeAmplification b/SelectiveGenomeAmplification
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+#!/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