--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aggregate.py	Thu Aug 11 18:30:23 2016 -0400
@@ -0,0 +1,324 @@
+# A translation of aggregate.pl into python! For analysis of Tn-Seq.
+# This script requires BioPython just like calc_fitness.py, so you need it installed along with its dependencies if you want to run these scripts on your own.
+# How to install BioPython and a list of its dependencies can be found here: http://biopython.org/DIST/docs/install/Installation.html
+
+
+
+
+
+
+
+
+
+
+##### ARGUMENTS #####
+
+# Prints basic instructions on / options for using this code; called when the user forgets to enter an output file or fitness file(s)
+
+def print_usage():
+	print "Aggregate.py's usage is as follows:" + "\n\n"
+	print "\033[1m" + "Required" + "\033[0m" + "\n"
+	print "-o" + "\t\t" + "Output file for aggregated data." + "\n"
+	print "\n"
+	print "\033[1m" + "Optional" + "\033[0m" + "\n"
+	print "-c" + "\t\t" + "Check for missing genes in the data set - provide a reference genome in genbank format. Missing genes will be sent to stdout." + "\n"
+	print "-m" + "\t\t" + "Place a mark in an extra column for this set of genes. Provide a file with a list of genes seperated by newlines." + "\n"
+	print "-x" + "\t\t" + "Cutoff: Don't include fitness scores with average counts (c1+c2)/2 < x (default: 0)" + "\n"
+	print "-b" + "\t\t" + "Blanks: Exclude -b % of blank fitness scores (scores where c2 = 0) (default: 0 = 0%)" + "\n"
+	print "-w" + "\t\t" + "Use weighted algorithm to calculate averages, variance, sd, se" + "\n"
+	print "-l" + "\t\t" + "Weight ceiling: maximum value to use as a weight (default: 999,999)" + "\n"
+	print "\n"
+	print "All remainder arguements will be treated as fitness files (those files created by calc_fitness.py)" + "\n"
+	print "\n"
+	
+# Turns the arguments entered in the command line into variables so that they can actually be called. 
+
+import argparse 
+parser = argparse.ArgumentParser()
+parser.add_argument("-o", action="store", dest="summary")
+parser.add_argument("-c", action="store", dest="find_missing")
+parser.add_argument("-m", action="store", dest="marked")
+parser.add_argument("-x", action="store", dest="cutoff")
+parser.add_argument("-b", action="store", dest="blank_pc")
+parser.add_argument("-w", action="store", dest="weighted")
+parser.add_argument("-l", action="store", dest="weight_ceiling")
+parser.add_argument("fitnessfiles", nargs=argparse.REMAINDER)
+
+#Shortens the names of those variables created from the arguments - from parser.parse_args().ref_genome to arguments.ref_genome, for example.
+
+arguments = parser.parse_args()
+
+#Checks that the required arguments have been entered; if not informs the user they need to provide a name for the output file / the fitness file(s) and print's aggregate.py's usage
+
+if not arguments.summary:
+	print "\n" + "You are missing a value for the -o flag. "
+	print_usage() 
+	quit()
+
+if not arguments.fitnessfiles:
+	print "\n" + "You are missing fitness file(s); these should be entered immediately after all the flags. "
+	print_usage() 
+	quit()
+	
+#Sets the maximum weight of a fitness value, if that wasn't specified in the command line. 
+	
+if (not arguments.weight_ceiling):
+	arguments.max_weight = 999999
+	
+#Sets the cutoff to a default value of 0 if it wasn't specified in the command line.
+#Cutoff exists to discard positions with a low number of counted transcripts, because their fitness may not be as accurate - for the same reasoning that studies with low sample sizes can be innacurate. 
+	
+if (not arguments.cutoff):
+	arguments.cutoff = 0
+
+#Sets the % of blank fitness values to exclude to a default value of 0 if it wasn't specified in the command line. This can be found in the 2nd output of calc_fitness.
+
+if (not arguments.blank_pc):
+	arguments.blank_pc = 0
+
+# gets blank_pc from the output file of calc_fit / consol
+
+if arguments.blank_pc:
+	with open(arguments.blank_pc) as file:
+		blank_pc = file.read().splitlines()
+		arguments.blank_pc = float(blank_pc[1].split()[1])
+
+
+
+
+
+
+
+##### SUBROUTINES #####
+
+#A subroutine that calculates the average, variance, standard deviation (sd), and standard error (se) of a group of scores; for use when aggregating scores by gene later on
+
+import math
+def average(scores):
+	sum = 0
+	num = 0
+	
+#Finds the average of the scores
+	
+	for i in scores:
+		sum += i
+		num += 1
+	average = sum/num
+	
+#Finds the variance of the scores
+
+	xminusxbars = 0
+	for i in scores:
+		xminusxbars += (i - average)**2
+	variance = xminusxbars/(num-1)
+	
+#Finds the standard deviation and standard error of the scores; then the average / variance / standard deviation / standard error are returned
+
+	sd = math.sqrt(variance)
+	se = sd / math.sqrt(num)
+	return (average, variance, sd, se)
+
+#A subroutine that calculates the weighted average, variance, standard deviation (sd), and standard error (se) of a group of scores; the weights come from the number of reads each insertion location has
+#For use when aggregating scores by gene later on, if the weighted argument is called
+
+def weighted_average(scores,weights):
+	sum = 0
+	weighted_average = 0
+	weighted_variance = 0
+	top = 0
+	bottom = 0
+	i = 0
+	
+#Finds weighted average of the scores
+	
+	while i < len(weights):
+		if not scores[i]:
+			scores[i] = 0.0
+		top += float(weights[i])*float(scores[i])
+		bottom += float(weights[i])
+		i += 1
+	if bottom == 0:
+		return 0
+	weighted_average = top/bottom
+	
+#Finds weighted variance of the scores
+
+	top = 0
+	bottom = 0
+	i = 0
+	while i < len(weights):
+		top += float(weights[i]) * (float(scores[i]) - weighted_average)**2
+		bottom += float(weights[i])
+		i += 1
+	weighted_variance = top/bottom
+    
+#Finds weighted standard deviation and standard error of the scores; then the weighted average / variance / standard deviation / standard error are returned
+    
+	weighted_stdev = math.sqrt(weighted_variance)
+	weighted_stder = weighted_stdev/math.sqrt(len(scores))
+	return (weighted_average, weighted_variance, weighted_stdev, weighted_stder)
+
+
+
+
+
+
+
+
+
+
+##### AGGREGATION / CALCULATIONS #####
+
+#Reads the genes which should be marked in the final aggregate file into an array
+
+import os.path
+if arguments.marked:
+	with open(arguments.marked) as file:
+		marked_set = file.read().splitlines()
+
+#Creates a dictionary of dictionaries to contain a summary of all genes and their fitness values
+#Each gene is its own dictionary with w and s as keys for the various fitnesses and weights of the insertion locations within those genes respectively
+#The fitness values and weights match up, so that the weight of gene_summary[locus]["w"][2] would be gene_summary[locus]["s"][2]
+
+import csv
+gene_summary = {}
+for eachfile in arguments.fitnessfiles:
+	with open(eachfile) as csvfile:
+		lines = csv.reader(csvfile)
+		for line in lines:
+			locus = line[9]
+			w = line[12]
+			if w == 'nW':
+				continue
+			if not w:
+				w == 0
+			c1 = float(line[2])
+			c2 = float(line[3])
+			avg = (c1+c2)/2
+			if avg < float(arguments.cutoff):
+				continue
+			if avg > float(arguments.weight_ceiling):
+				avg = arguments.weight_ceiling
+			if locus not in gene_summary:
+				gene_summary[locus] = {"w" : [], "s": []}
+			gene_summary[locus]["w"].append(w)
+			gene_summary[locus]["s"].append(avg)
+
+#If finding any missing gene loci is requested in the arguments, starts out by loading all the known features from a genbank file
+
+from Bio import SeqIO
+if (arguments.find_missing):
+	output = [["locus","mean","var","sd","se","gene","Total","Blank","Not Blank","Blank Removed","M\n"]]
+	handle = open(arguments.find_missing, "rU")
+	for record in SeqIO.parse(handle, "genbank"):
+		refname = record.id
+		features = record.features
+	handle.close()
+	
+#Goes through the features to find which are genes
+	
+	for feature in features:
+		gene = ""
+		if feature.type == "gene":
+			locus = "".join(feature.qualifiers["locus_tag"])
+			if "gene" in feature.qualifiers:
+				gene = "".join(feature.qualifiers["gene"])
+		else:
+			continue
+			
+#Goes through the fitness scores of insertions within each gene, and removes whatever % of blank fitness scores were requested along with their corresponding weights
+
+		sum = 0
+		num = 0
+		avgsum = 0
+		blank_ws = 0
+		i = 0
+		if locus in gene_summary.keys():
+			for w in gene_summary[locus]["w"]:
+				if float(w) == 0:
+					blank_ws += 1
+				else:
+					sum += float(w)
+					num += 1
+			count = num + blank_ws		
+			removed = 0
+			to_remove = int(float(arguments.blank_pc)*count)
+			if blank_ws > 0:
+				i = 0
+				while i < len(gene_summary[locus]["w"]):
+					if removed == to_remove:
+						break
+					if not w:
+						del gene_summary[locus]["w"][i]
+						del gene_summary[locus]["s"][i]
+						removed += 1
+						i -= 1
+					i += 1
+
+#If all the fitness values within a gene are empty, sets mean/var to 0.10 and Xs out sd/se; marks the gene if that's requested
+
+			if num == 0:	
+				if (arguments.marked and locus in marked_set):
+					output.append([locus, "0.10", "0.10", "X", "X", gene, count, blank_ws, num, removed, "M", "\n"])
+				else:
+					output.append([locus, "0.10", "0.10", "X", "X", gene, count, blank_ws, num, removed, "\n"])
+
+#Otherwise calls average() or weighted_average() to find the aggregate w / count / standard deviation / standard error of the insertions within each gene; marks the gene if that's requested
+
+			else:
+				if not arguments.weighted:
+					(average, variance, stdev, stderr) = average(gene_summary[locus]["w"])
+				else:
+					(average, variance, stdev, stderr) = weighted_average(gene_summary[locus]["w"],gene_summary[locus]["s"])
+				if (arguments.marked and locus in marked_set):
+					output.append([locus, average, variance, stdev, stderr, gene, count, blank_ws, num, removed, "M", "\n"])
+				else:
+					output.append([locus, average, variance, stdev, stderr, gene, count, blank_ws, num, removed, "\n"])
+		
+#If a gene doesn't have any insertions, sets mean/var to 0.10 and Xs out sd/se, plus leaves count through removed blank because there were no reads.
+
+		else:
+			if (arguments.marked and locus in marked_set):
+				output.append([locus, "0.10", "0.10", "X", "X", gene, "", "", "", "", "M", "\n"])
+			else:
+				output.append([locus, "0.10", "0.10", "X", "X", gene, "", "", "", "", "\n"])
+
+#Writes the aggregated fitness file
+
+	with open(arguments.summary, "wb") as csvfile:
+		writer = csv.writer(csvfile)
+		writer.writerows(output)
+
+#If finding missing genes is not requested, just finds the aggregate w / count / standard deviation / standard error of the insertions within each gene, and writes them to a file, plus marks the genes requested
+#This is never called through Galaxy since finding missing genes is better than not finding them.
+
+else:
+	output = [["Locus","W","Count","SD","SE","M\n"]]
+	for gene in gene_summary.keys():
+		sum = 0
+		num = 0
+		average = 0
+		if "w" not in gene_summary[gene]:
+			continue
+		for i in gene_summary[gene]["w"]:
+			sum += i
+			num += 1
+		average = sum/num
+		xminusxbars = 0
+		for i in w:
+			xminusxbars += (i-average)**2
+		if num > 1:
+			sd = math.sqrt(xminusxbars/(num-1))
+			se = sd / math.sqrt(num)
+		if (arguments.marked and locus in marked_set):
+			output.append([gene, average, num, sd, se, "M", "\n"])
+		else:
+			output.append([gene, average, num, sd, se, "\n"])
+	with open(arguments.summary, "wb") as csvfile:
+		writer = csv.writer(csvfile)
+		writer.writerows(output)
+
+
+#Test: python ../script/aggregate.py -m tigr4_normal.txt -w 1 -x 10 -l 50 -b 0 -c NC_003028b2.gbk -o aggregates/L3_2394eVI_GlucTEST.csv results/L3_2394eVI_Gluc.csv
+
+#Perl Test: perl ../script/aggregate.pl -m tigr4_normal.txt -w 1 -x 10 -l 50 -b 0 -c NC_003028b2.gbk -o aggregates/L3_2394eVI_Gluc.csv results/L3_2394eVI_Gluc.csv
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