Rename!

1 files changed, 0 insertions, 343 deletions

diff --git a/SelectiveGenomeAmplification b/SelectiveGenomeAmplification
deleted file mode 100755
index e778cbd..0000000
--- a/SelectiveGenomeAmplification
+++ /dev/null
@@ -1,343 +0,0 @@
-#!/usr/bin/env bash
-
-set -e
-# arguments:
-
-# check_non_empty
-check_non_empty() {
-	if [[ ! -s $1 ]]; then
-		echo "Warning: no mers remain after the '$2' filter!"
-		echo "Exiting..."
-		exit 1
-	fi
-}
-# check_mers filename
-check_mers() {
-
-	local fasta_file="$1"
-	local counts="$2"
-	local mer=0
-
-	echo "  counting mers in $fasta_file"
-
-	#  remove the counts file so we can concatenate
-	if [[ -e "$counts"-counts ]]; then
-		echo "    removing $counts-counts"
-		rm "$counts"-counts
-	fi
-
-	# check each mer size and process if not already run
-	for (( mer = min_mer_range; mer <= max_mer_range; mer++)) ; do 
-		if [[ ! -e "$counts"-counts-"$mer" ]]; then
-			echo "    checking $mer mers for $fasta_file"
-			kmer_continuous_count -c -i "$fasta_file" -k "$mer" -l -n > "$counts"-counts-"$mer" || exit 1
-		else 
-			echo "    $mer-mers already done for $fasta_file (assuming no change)"
-		fi
-		
-		# concatentate 
-		cat "$counts"-counts-"$mer" >> "$counts"-counts
-
-	done
-
-}
-
-all=run
-# Parse in our arguments
-if [[ -z "$foreground" ]] && [[ -z "$background" ]]; then 
-	if (( $# < 2 )); then  
-		echo "please supply two genomes, foreground and background"
-		exit 1
-	fi;
-
-	: ${foreground=$1}
-	: ${background=$2}
-	start=3
-else
-	start=1
-fi
-
-if (( $# > 2 )); then
-	unset all
-
-	for i in "${@:$start}"; do 
-		if [[ "$i" = "1" ]] || [[ "$i" = "count" ]]; then
-			step=1;	step_mers=1
-		fi
-
-		if [[ "$i" = "2" ]] || [[ "$i" = "filter" ]]; then
-			step=1;	step_filters=1
-		fi
-
-		if [[ "$i" = "3" ]] || [[ "$i" = "select" ]]; then
-			step=1;	step_select=1
-		fi
-
-		if [[ "$i" = "4" ]] || [[ "$i" = "score" ]]; then
-			step=1; step_score=1
-		fi
-
-		if [[ $step ]] && [[ ! "$current_run" ]] && [[ ! $step_mers ]]; then
-			echo "Error: If you are going to step through your program, and aren't starting" \
-			"at the first step, you better specify what previous run you want to use" \
-			"as your base"
-			exit
-		fi
-
-		done;
-fi;
-
-if [[ -n "$step" ]] && [[ -z "$step_mers" ]] &&  [[ -z "$step_filters" ]] && [[ -z $step_select ]] && [[ -z "$step_score" ]]; then
-	echo "Error: you need to select at least one step to run."
-	exit 
-fi
-
-echo 
-echo "Planning on running these steps:"
-for var in step_mers step_filters step_select step_score all; do
-	if [[ -n "${!var}" ]]; then
-		echo '  '$var
-	fi
-done
-
-# output directory 
-: ${output_directory=$(basename "$foreground")_$(basename "$background")}
-
-# temp directory 
-: ${tmp_directory="$output_directory"/.tmp}
-
-# directory to store our counts and sorted counts
-: ${counts_directory="$tmp_directory"}
-
-# range of mers, min and max 
-: ${min_mer_range=6}
-: ${max_mer_range=12}
-
-# max mer distance, the distance between two mers in our selected outputs
-: ${max_mer_distance=5000}
-
-# min/maximum kmer meling point
-: ${max_melting_temp=30}
-: ${min_melting_temp=0}
-
-# minimum average binding distance in the foreground
-: ${min_foreground_binding_average=50000}
-
-# maximum mers to pick
-: ${max_select=15}
-
-# maximum mers to check
-: ${max_check=35}
-
-# mers to specifically IGNORE, space delimited
-: ${ignore_mers=''}
-
-# IGNORE all mers that are in these files, space delimited
-: ${ignore_all_mers_from_files}
-
-# maximum number of mers that are consecutively binding
-: ${max_consecutive_binding=4}
-
-# fg_weight, how much to weight to give the higher bindnig primers
-: ${fg_weight=0}
-
-# primer_weight, how much weight to give to sets with a higher number of primers. (between 0 and 1)
-: ${primer_weight=0}
-
-# output_top_nb, How many scored sets would you like in the top_scored_sets output file (Default = 10000)?
-: ${output_top_nb=10000}
-
-# score_func: A custom scoring function. disable by default. See README.md
-: ${score_func="(nb_primers**primer_weight) * (fg_mean_dist * fg_std_dist) / bg_ratio"}
-
-# sort score by the minimum or maximum value. acceptable parameters are min or max.
-: ${sort_by="min"}
-
-export ignore_mers
-export min_mer_range
-export max_mer_range
-
-export max_select
-
-export min_foreground_binding_average
-export max_mer_distance
-
-export max_melting_temp 
-export min_melting_temp 
-
-export fg_weight
-export primer_weight
-
-
-echo
-# check foreground and background
-if [[ ! -f "$foreground" ]]; then
-	echo "Error: could not open $foreground"
-	exit 1
-fi
-
-if [[ ! -f "$background" ]]; then
-	echo "Error: could not open $background"
-	exit 1
-fi
-
-
-if [[ -n "$current_run" ]] && [[ ! -d "$output_directory/$current_run" ]]; then
-	echo -n "run $current_run was not found, it should be a folder here: "
-	echo "$output_directory/$current_run"
-	exit
-fi
-
-if [[ "$sort_by" = "min" ]]; then
-	sort=''
-elif [[ "$sort_by" = "max" ]]; then
-	sort="-r"
-else
-	echo "Error: \$sort_by must either be set to max or min"
-	exit
-fi
-
-num=1
-if [[ -z "$current_run" ]]; then 
-	while [[ -d $output_directory/run_$num ]] ; do
-		let num++
-	done
-	current_run=run_$num
-fi
-
-fg_basename=$(basename "$foreground")
-bg_basename=$(basename "$background")
-
-fg_counts=$counts_directory/$fg_basename-counts
-bg_counts=$counts_directory/$bg_basename-counts
-
-final_fg_counts=$output_directory/$current_run/$fg_basename-filtered-counts
-selected=$output_directory/$current_run/selected-mers
-
-ignore_mers_counts="$output_directory/$current_run/passes-filter/1-$fg_basename-ignore-mers"
-ignore_all_mers_counts="$output_directory/$current_run/passes-filter/2-$fg_basename-ignore-all-mers"
-average_binding="$output_directory/$current_run/passes-filter/3-$fg_basename-average-binding"
-non_melting="$output_directory/$current_run/passes-filter/4-$fg_basename-non-melting"
-consecutive_binding="$output_directory/$current_run/passes-filter/5-$fg_basename-consecutive-binding"
-
-# Make our output directory
-if [[ ! -d "$output_directory" ]]; then
-	mkdir "$output_directory"
-fi
-
-# Make our counts directory
-if [[ ! -d "$counts_directory" ]]; then
-	mkdir "$counts_directory"
-fi
-
-# Make our temporary directory
-if [[ ! -d $tmp_directory ]]; then
-	mkdir "$tmp_directory"
-fi
-
-# Make our current run directory 
-if [[ ! -d $output_directory/$current_run ]]; then
-	mkdir "$output_directory"/"$current_run" 
-fi
-
-# Make our filter directory 
-if [[ ! -d "$output_directory/$current_run/passes-filter" ]]; then
-	mkdir "$output_directory/$current_run/passes-filter"
-fi
-
-echo "Outputting current run parameters"
-	for var in score_func ignore_mers ignore_all_mers_from_files min_mer_range max_mer_range max_check cpus max_consecutive_binding max_select min_foreground_binding_average max_mer_distance min_melting_temp max_melting_temp foreground background; do 
-	echo "$var" "${!var}" >> "$output_directory"/"$current_run"/parameters
-done;
-
-echo "current run is: $current_run"
-echo
-
-if [[ -n "$step_mers" ]] || [[ -n "$all" ]]; then
-	# to continue this project you need to use the current run.
-
-	echo "Step 1: counting primers in foreground and background"
-	check_mers "$foreground" "$counts_directory/$(basename "$foreground")"
-	check_mers "$background" "$counts_directory/$(basename "$background")"
-fi
-
-if [[ -n "$step_filters" ]] || [[ -n "$all" ]]; then
-	if [[ ! -f "$fg_counts" ]]; then
-		echo "Error: you need to run your count step before filtration"
-		exit
-	fi
-	echo "Step 2: filtering mers"
-
-
-	cp "$fg_counts" "$ignore_mers_counts"
-	# remove ignored mers
-	if [[ "$ignore_mers" ]]; then
-		echo "  filtering explicitly ignored mers: $ignore_mers"
-		for mer in $ignore_mers; do
-			sed -i '/^'"$mer"'\t/d' "$ignore_mers_counts"
-		done
-	fi
-	check_non_empty "$ignore_mers_counts" "ignore mers" 
-
-	cp "$ignore_mers_counts" "$ignore_all_mers_counts"
-	# remove ignored mers
-	if [[ "$ignore_all_mers_from_files" ]]; then
-		for ignore_file in $ignore_all_mers_from_files; do
-
-			if [[ -f "$ignore_file" ]]; then 
-				echo "  filtering ignored mers from: $ignore_file"
-
-				counts="$counts_directory/ignore-"$(basename "$ignore_file")
-				check_mers "$ignore_file" "$counts"
-
-				while read mer_line; do
-						mer=$(echo "$mer_line" | sed -e 's/\t.*//g')
-						sed -i '/^'"$mer"'\t/d' "$ignore_all_mers_counts"
-					done < "$counts-counts"
-			else 
-				echo "  $ignore_file not found, continuing..."
-			fi
-
-		done
-	fi
-	check_non_empty "$ignore_all_mers_counts" "ignore all mers from file "
-	
-	echo "  filtering mers that appear less frequently than the average binding site distance ($min_foreground_binding_average)"
-	filter_average_binding.py "$ignore_all_mers_counts" "$min_foreground_binding_average" < "$fg_counts"  > "$average_binding" || exit 1
-	check_non_empty "$average_binding" "average binding"
-
-	echo "  filtering mers that are not in the melting range ($min_melting_temp-$max_melting_temp)"
-	filter_melting_temperature.py "$min_melting_temp" "$max_melting_temp" < "$average_binding" > "$non_melting" || exit 1
-	check_non_empty "$non_melting" "melting temperature"
-
-	echo "  filtering mers that have more consecutive binding mers than allowed ($max_consecutive_binding)"
-	filter_max_consecutive_binding.py "$max_consecutive_binding" < "$non_melting" > "$consecutive_binding" || exit 1
-	check_non_empty "$consecutive_binding" "consecutive binding"
-
-	cp $consecutive_binding $final_fg_counts
-fi
-
-if [[ -n "$step_select" ]] || [[ -n "$all" ]]; then
-	if [[ ! -f "$final_fg_counts" ]]; then
-		echo "Error: you need to run your filtration step before selection"
-		exit
-	fi
-	echo "Step 3: Scoring mer selectivity"
-	select_mers.py "$final_fg_counts" "$bg_counts" > "$selected" || exit 1
-fi
-
-if [[ -n "$step_score" ]] || [[ -n "$all" ]]; then
-	if [[ ! -f "$selected" ]]; then
-		echo "Error: you need to run your selection step before you run your scoring"
-		exit
-	fi
-
-	echo "Step 4: Scoring top mers based on selectivity"
-	score_wrapper.sh "$selected" "$foreground" "$background" "$output_directory/$current_run/all-scores" || exit 1
-
-	# output our sorted scores
-	echo "sorting and outputting top $output_top_nb scores"
-	echo "top scores output file: $output_directory/$current_run/top-scores"
-	head -n 3 $output_directory/$current_run/all-scores > $output_directory/$current_run/top-scores
-	tail -n +4 $output_directory/$current_run/all-scores | sort $sort -t $'\t' -nk 3 | head -n $output_top_nb >> $output_directory/$current_run/top-scores
-fi