--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SNP_Mapping.py	Sat Jun 22 18:39:14 2013 -0400
@@ -0,0 +1,440 @@
+#!/usr/bin/python
+
+import re
+import sys
+import optparse
+import csv
+import re
+import pprint
+from decimal import *
+from rpy import *
+
+def main():
+	csv.field_size_limit(1000000000)
+
+	parser = optparse.OptionParser()
+	parser.add_option('-v', '--sample_vcf', dest = 'sample_vcf', action = 'store', type = 'string', default = None, help = "Sample VCF from GATK Unified Genotyper")
+	parser.add_option('-l', '--loess_span', dest = 'loess_span', action = 'store', type = 'float', default = .01, help = "Loess span")
+	parser.add_option('-d', '--d_yaxis', dest = 'd_yaxis', action = 'store', type = 'float', default = .7, help = "y-axis upper limit for dot plot")  
+	parser.add_option('-y', '--h_yaxis', dest = 'h_yaxis', action = 'store', type = 'int', default = 5, help = "y-axis upper limit for histogram plot")   
+	parser.add_option('-c', '--points_color', dest = 'points_color', action = 'store', type = 'string', default = "gray27", help = "Color for data points") 
+	parser.add_option('-k', '--loess_color', dest = 'loess_color', action = 'store', type = 'string', default = "red", help = "Color for loess regression line")        
+	parser.add_option('-z', '--standardize', dest = 'standardize', default= 'true', help = "Standardize X-axis")
+	parser.add_option('-b', '--break_file', dest = 'break_file', action = 'store', type = 'string', default = 'C.elegans', help = "File defining the breaks per chromosome")
+	parser.add_option('-x', '--bin_size', dest = 'bin_size', action = 'store', type = 'int', default = 1000000, help = "Size of histogram bins, default is 1mb")
+	parser.add_option('-n', '--normalize_bins', dest = 'normalize_bins', default= 'true', help = "Normalize histograms")
+
+
+	parser.add_option('-o', '--output', dest = 'output', action = 'store', type = 'string', default = None, help = "Output file name")
+	parser.add_option('-s', '--location_plot_output', dest = 'location_plot_output', action = 'store', type = 'string', default = "SNP_Mapping_Plot.pdf", help = "Output file name of SNP plots by chromosomal location")
+
+	(options, args) = parser.parse_args()
+
+	vcf_info = parse_vcf(sample_vcf = options.sample_vcf)
+
+	output_vcf_info(output = options.output, vcf_info = vcf_info)
+	
+	#output plot with all ratios
+	rounded_bin_size = int(round((float(options.bin_size) / 1000000), 1) * 1000000)
+	
+	normalized_histogram_bins_per_mb = calculate_normalized_histogram_bins_per_xbase(vcf_info = vcf_info, xbase = rounded_bin_size, normalize_bins = options.normalize_bins)
+	normalized_histogram_bins_per_5kb = calculate_normalized_histogram_bins_per_xbase(vcf_info = vcf_info, xbase = (rounded_bin_size / 2), normalize_bins = options.normalize_bins)
+
+	break_dict = parse_breaks(break_file = options.break_file)
+
+	output_scatter_plots_by_location(location_plot_output = options.location_plot_output, vcf_info = vcf_info, loess_span=options.loess_span, d_yaxis=options.d_yaxis, h_yaxis=options.h_yaxis, points_color=options.points_color, loess_color=options.loess_color, standardize =options.standardize, normalized_hist_per_mb = normalized_histogram_bins_per_mb, normalized_hist_per_5kb = normalized_histogram_bins_per_5kb, breaks = break_dict, rounded_bin_size = rounded_bin_size)
+
+
+def skip_headers(reader = None, i_file = None):
+	# count headers
+	comment = 0
+	while reader.next()[0].startswith('#'):
+		comment = comment + 1
+	
+	# skip headers
+	i_file.seek(0)
+	for i in range(0, comment):
+		reader.next()
+
+def parse_breaks(break_file = None):
+	if break_file == 'C.elegans':
+		break_dict = { 'I' : 16 , 'II' : 16,  'III' : 14, 'IV' : 18, 'V' : 21, 'X' : 18 }
+		return break_dict
+	elif break_file == 'Arabidopsis':
+		break_dict = { '1' : 31 , '2' : 20,  '3' : 24, '4' : 19, '5' : 27 }
+		return break_dict
+	else:
+		i_file = open(break_file, 'rU')
+		break_dict = {}
+		reader = csv.reader(i_file, delimiter = '\t')
+		for row in reader:
+			chromosome = row[0].upper()
+			chromosome = re.sub("chr", "", chromosome, flags = re.IGNORECASE)
+			chromosome = re.sub("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE)
+			break_count = row[1]
+			break_dict[chromosome] = int(break_count)
+		return break_dict
+
+
+def location_comparer(location_1, location_2):
+	chr_loc_1 = location_1.split(':')[0]
+	pos_loc_1 = int(location_1.split(':')[1])
+
+	chr_loc_2 = location_2.split(':')[0]
+	pos_loc_2 = int(location_2.split(':')[1])
+
+	if chr_loc_1 == chr_loc_2:
+		if pos_loc_1 < pos_loc_2:
+			return -1
+		elif pos_loc_1 == pos_loc_1:
+			return 0
+		elif pos_loc_1 > pos_loc_2:
+			return 1
+	elif chr_loc_1 < chr_loc_2:
+		return -1
+	elif chr_loc_1 > chr_loc_2:
+		return 1
+
+def output_vcf_info(output = None, vcf_info = None):
+	o_file = open(output, 'wb')
+	writer = csv.writer(o_file, delimiter = '\t')
+
+	writer.writerow(["#Chr\t", "Pos\t", "Alt Count\t", "Ref Count\t", "Read Depth\t", "Ratio\t"])
+
+	location_sorted_vcf_info_keys = sorted(vcf_info.keys(), cmp=location_comparer)
+
+	for location in location_sorted_vcf_info_keys:
+		alt_allele_count, ref_allele_count, read_depth, ratio = vcf_info[location]
+		
+		location_info = location.split(':')
+		chromosome = location_info[0]
+		position = location_info[1]
+
+		writer.writerow([chromosome, position, alt_allele_count, ref_allele_count, read_depth, ratio])
+
+	o_file.close()
+
+def output_scatter_plots_by_location(location_plot_output = None, vcf_info = None, loess_span="", d_yaxis="", h_yaxis="", points_color="", loess_color="", standardize=None, normalized_hist_per_mb = None, normalized_hist_per_5kb = None, breaks = None, rounded_bin_size = 1000000):
+	positions = {}
+	current_chr = ""
+	prev_chr = ""
+
+	x_label = "Location (Mb)"
+	filtered_label = ''
+
+	location_sorted_vcf_info_keys = sorted(vcf_info.keys(), cmp=location_comparer)
+	
+	break_unit = Decimal(rounded_bin_size) / Decimal(1000000)
+	max_breaks = max(breaks.values())
+
+	try:
+		r.pdf(location_plot_output, 8, 8)
+	
+		for location in location_sorted_vcf_info_keys:
+			current_chr = location.split(':')[0]
+			position = location.split(':')[1]
+
+			alt_allele_count, ref_allele_count, read_depth, ratio = vcf_info[location]
+		
+			if prev_chr != current_chr:
+				if prev_chr != "":
+					hist_dict_mb = get_hist_dict_by_chr(normalized_hist_per_xbase = normalized_hist_per_mb, chr = prev_chr)
+					hist_dict_5kb = get_hist_dict_by_chr(normalized_hist_per_xbase = normalized_hist_per_5kb, chr = prev_chr)
+					
+					plot_data(chr_dict = positions, hist_dict_mb = hist_dict_mb, hist_dict_5kb = hist_dict_5kb, chr = prev_chr + filtered_label, x_label = "Location (Mb)", divide_position = True, draw_secondary_grid_lines = True, loess_span=loess_span, d_yaxis=d_yaxis, h_yaxis=h_yaxis, points_color=points_color, loess_color=loess_color, breaks = breaks[prev_chr], standardize=standardize, max_breaks = max_breaks, break_unit = break_unit)
+				
+				prev_chr = current_chr
+				positions = {}
+		
+			positions[position] = ratio
+
+		hist_dict_mb = get_hist_dict_by_chr(normalized_hist_per_xbase = normalized_hist_per_mb, chr = current_chr)
+		hist_dict_5kb = get_hist_dict_by_chr(normalized_hist_per_xbase = normalized_hist_per_5kb, chr = current_chr)
+							
+		plot_data(chr_dict = positions, hist_dict_mb = hist_dict_mb, hist_dict_5kb = hist_dict_5kb, chr = current_chr + filtered_label, x_label = "Location (Mb)", divide_position = True, draw_secondary_grid_lines = True, loess_span=loess_span, d_yaxis=d_yaxis, h_yaxis=h_yaxis, points_color=points_color, loess_color=loess_color, breaks = breaks[current_chr], standardize=standardize, max_breaks = max_breaks, break_unit = break_unit)
+
+		r.dev_off()
+		
+	except Exception as inst:
+        	print inst
+        	print "There was an error creating the location plot pdf... Please try again"
+
+def get_hist_dict_by_chr(normalized_hist_per_xbase = None, chr = ''):
+	hist_dict = {}	
+
+	for location in normalized_hist_per_xbase:
+		chromosome = location.split(':')[0]		
+		if chromosome == chr:
+			position = int(location.split(':')[1])
+			hist_dict[position] = normalized_hist_per_xbase[location]
+	
+	max_location = max(hist_dict.keys(), key=int)
+	for i in range(1, max_location):
+		if i not in hist_dict:
+			hist_dict[i] = 0	
+	
+	return hist_dict	
+
+def plot_data(chr_dict =  None, hist_dict_mb = None, hist_dict_5kb = None, chr = "", x_label = "", divide_position = False, draw_secondary_grid_lines = False, loess_span=None, d_yaxis=None, h_yaxis=None, points_color="", loess_color="", breaks = None, standardize= None, max_breaks = 1, break_unit = 1):
+	ratios = "c("
+	positions = "c("
+	
+	for position in chr_dict:
+		ratio = chr_dict[position]
+		if divide_position:
+		       	position = float(position) / 1000000.0
+	        positions = positions + str(position) + ", "
+		ratios = ratios + str(ratio) + ", "
+
+	if len(ratios) == 2:
+		ratios = ratios + ")"
+	else:
+		ratios = ratios[0:len(ratios) - 2] + ")"
+
+	if len(positions) == 2:
+		positions = positions + ")"
+	else:
+		positions = positions[0:len(positions) - 2] + ")"
+
+	r("x <- " + positions)
+	r("y <- " + ratios)
+
+	hist_mb_values = "c("
+    	for position in sorted(hist_dict_mb):
+		hist_mb_values = hist_mb_values + str(hist_dict_mb[position]) + ", "
+	
+	if len(hist_mb_values) == 2:
+		hist_mb_values = hist_mb_values + ")"
+	else:
+		hist_mb_values = hist_mb_values[0:len(hist_mb_values) - 2] + ")"
+
+	hist_5kb_values = "c("
+	for position in sorted(hist_dict_5kb):
+		hist_5kb_values = hist_5kb_values + str(hist_dict_5kb[position]) + ", "	
+
+	if len(hist_5kb_values) == 2:
+		hist_5kb_values = hist_5kb_values + ")"
+	else:
+		hist_5kb_values = hist_5kb_values[0:len(hist_5kb_values) - 2] + ")"
+
+	r("xz <- " + hist_mb_values)
+	r("yz <- " + hist_5kb_values)
+
+
+	max_break_str = str(max_breaks)
+	break_unit_str = str(Decimal(break_unit)) 	
+	half_break_unit_str = str(Decimal(break_unit) / Decimal(2))
+	break_penta_unit_str = str(Decimal(break_unit) * Decimal(5))
+
+	if (standardize=='true'):  
+		r("plot(x, y, ,cex=0.60, xlim=c(0," + max_break_str + "), main='LG " + chr + " (Hawaiian Variant Mapping)', xlab= '" + x_label + "', ylim = c(0, %f " %d_yaxis + "), ylab='Ratios of mapping strain alleles/total reads (at SNP positions)', pch=10, col='"+ points_color +"')")
+		r("lines(loess.smooth(x, y, span = %f "%loess_span + "), lwd=5, col='"+ loess_color +"')")
+		r("axis(1, at=seq(0, " + max_break_str + ", by=" + break_unit_str + "), labels=FALSE, tcl=-0.5)")
+		r("axis(1, at=seq(0, " + max_break_str + ", by=" + half_break_unit_str + "), labels=FALSE, tcl=-0.25)")
+		r("axis(2, at=seq(floor(min(y)), 1, by=0.1), labels=FALSE, tcl=-0.2)")
+	elif (standardize=='false'):
+		r("plot(x, y, cex=0.60, main='LG " + chr + " (Hawaiian Variant Mapping)', xlab= '" + x_label + "', ylim = c(0, %f " %d_yaxis + "), ylab='Ratios of mapping strain alleles/total reads (at SNP positions)', pch=10, col='"+ points_color +"')")
+		r("lines(loess.smooth(x, y, span = %f "%loess_span + "), lwd=5, col='"+ loess_color +"')")    
+		r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by= " + break_unit_str + "), labels=FALSE, tcl=-0.5)")
+		r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by= " + half_break_unit_str + "), labels=FALSE, tcl=-0.25)")	
+		r("axis(2, at=seq(floor(min(y)), 1, by=0.1), labels=FALSE, tcl=-0.2)")
+
+	if draw_secondary_grid_lines:
+		r("abline(h = seq(floor(min(y)), 1, by=0.1), v = seq(floor(min(x)), length(x), by= 1), col='gray')")
+	else:
+		r("grid(lty = 1, col = 'gray')")
+
+	if (standardize=='true'):
+		r("barplot(xz, xlim=c(0, " + max_break_str + "), ylim = c(0, " + str(h_yaxis) + "), yaxp=c(0, " + str(h_yaxis) + ", 1), space = 0, col='darkgray', width = " + break_unit_str + ", xlab='Location (Mb)', ylab='Normalized frequency of pure parental alleles ', main='LG " + chr + " (Hawaiian Variant Mapping)')")
+		r("barplot(yz, space = 0, add=TRUE, width = " + half_break_unit_str + ", col=rgb(1, 0, 0, 1))")	
+		r("axis(1, hadj = 1, at=seq(0, " + max_break_str + ", by= " + break_unit_str + "), labels=FALSE, tcl=-0.5)")
+		r("axis(1, at=seq(0, " + max_break_str + ", by= " + break_penta_unit_str + "), labels=TRUE, tcl=-0.5)")
+		r("axis(1, at=seq(0, " + max_break_str + ", by= " + half_break_unit_str + "), labels=FALSE, tcl=-0.25)")
+	elif (standardize=='false'):
+		r("barplot(xz, ylim = c(0, " + str(h_yaxis) + "), yaxp=c(0, " + str(h_yaxis) + ", 1), space = 0, col='darkgray', width = 1, xlab='Location (Mb)', ylab='Normalized frequency of pure parental alleles ', main='LG " + chr + " (Hawaiian Variant Mapping)')")
+		r("barplot(yz, space = 0, add=TRUE, width = 0.5, col=rgb(1, 0, 0, 1))")	
+		r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by= " + break_unit_str + "), labels=FALSE, tcl=-0.5)")
+		r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by= " + break_penta_unit_str + "), labels=TRUE, tcl=-0.5)")
+		r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by= " + half_break_unit_str + "), labels=FALSE, tcl=-0.25)")
+
+
+		
+def calculate_normalized_histogram_bins_per_xbase(vcf_info = None, xbase = 1000000, normalize_bins = None):
+	normalized_histogram_bins_per_xbase = {}
+
+	ref_snp_count_per_xbase = get_ref_snp_count_per_xbase(vcf_info = vcf_info, xbase = xbase)
+	#print "ref_snp_count_per_xbase: " + str(ref_snp_count_per_xbase) 
+	mean_zero_snp_count_per_chromosome = get_mean_zero_snp_count_per_chromosome(vcf_info = vcf_info, xbase = xbase)
+	#print "mean_zero_snp_count_per_chromosome: " + str(mean_zero_snp_count_per_chromosome)
+	zero_snp_count_per_xbase = get_zero_snp_count_per_xbase(vcf_info = vcf_info, xbase = xbase)
+	#print "zero_snp_count_per_xbase: " + str(zero_snp_count_per_xbase)
+
+	for location in ref_snp_count_per_xbase:
+		chromosome = location.split(':')[0]
+		mean_zero_snp_count = mean_zero_snp_count_per_chromosome[chromosome]
+		ref_snp_count = ref_snp_count_per_xbase[location]
+
+		zero_snp_count = 0
+		if location in zero_snp_count_per_xbase:
+			zero_snp_count = zero_snp_count_per_xbase[location]	
+
+		if normalize_bins == 'true':							
+			if zero_snp_count == 0 or ref_snp_count == 0:
+				normalized_histogram_bins_per_xbase[location] = 0
+			elif zero_snp_count == ref_snp_count:
+				normalized_histogram_bins_per_xbase[location] = 0					
+			else:				
+				normalized_histogram_bins_per_xbase[location] = (Decimal(zero_snp_count) / (Decimal(ref_snp_count)-Decimal(zero_snp_count))) * Decimal(mean_zero_snp_count)					
+		else:
+			normalized_histogram_bins_per_xbase[location] = zero_snp_count
+
+	return normalized_histogram_bins_per_xbase
+
+
+def get_ref_snp_count_per_xbase(vcf_info = None, xbase = 1000000):
+	ref_snps_per_xbase = {}
+
+	for location in vcf_info:
+		location_info = location.split(':')
+
+		chromosome = location_info[0].upper()
+		chromosome = re.sub("chr", "", chromosome, flags = re.IGNORECASE)
+		chromosome = re.sub("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE)
+
+		position = location_info[1]
+		xbase_position = (int(position) / xbase) + 1
+
+		location = chromosome + ":" + str(xbase_position)
+		if location in ref_snps_per_xbase:
+			ref_snps_per_xbase[location] = ref_snps_per_xbase[location] + 1
+		else:
+			ref_snps_per_xbase[location] = 1
+
+	return ref_snps_per_xbase
+
+
+
+def get_mean_zero_snp_count_per_chromosome(vcf_info, xbase = 1000000):
+	sample_snp_count_per_xbase = {}
+	
+	for location in vcf_info:
+		alt_allele_count, ref_allele_count, read_depth, ratio = vcf_info[location]
+			
+		location_info = location.split(':')
+		chromosome = location_info[0]
+		position = location_info[1]
+		xbase_position = (int(position) / xbase) + 1
+		xbase_location = chromosome + ":" + str(xbase_position)
+		
+		if int(alt_allele_count) == 0:
+			if xbase_location in sample_snp_count_per_xbase:
+				sample_snp_count_per_xbase[xbase_location] = sample_snp_count_per_xbase[xbase_location] + 1
+			else:
+				sample_snp_count_per_xbase[xbase_location] = 1
+
+		elif int(alt_allele_count) != 0 and xbase_location not in sample_snp_count_per_xbase:		
+			sample_snp_count_per_xbase[xbase_location] = 0
+
+	mean_zero_snp_count_per_chromosome = {}
+	for location in sample_snp_count_per_xbase:
+		chromosome = location.split(':')[0]
+		sample_count = sample_snp_count_per_xbase[location]
+		if chromosome in mean_zero_snp_count_per_chromosome:
+			mean_zero_snp_count_per_chromosome[chromosome].append(sample_count)
+		else:
+			mean_zero_snp_count_per_chromosome[chromosome] = [sample_count]
+
+	for chromosome in mean_zero_snp_count_per_chromosome:
+		summa = sum(mean_zero_snp_count_per_chromosome[chromosome])
+		count = len(mean_zero_snp_count_per_chromosome[chromosome])
+
+		mean_zero_snp_count_per_chromosome[chromosome] = Decimal(summa) / Decimal(count)
+
+	return mean_zero_snp_count_per_chromosome
+
+
+def get_zero_snp_count_per_xbase(vcf_info = None, xbase = 1000000):
+	zero_snp_count_per_xbase = {}
+
+	for location in vcf_info:
+		alt_allele_count, ref_allele_count, read_depth, ratio = vcf_info[location]
+			
+		location_info = location.split(':')
+		chromosome = location_info[0]
+		position = location_info[1]
+		xbase_position = (int(position) / xbase) + 1
+		xbase_location = chromosome + ":" + str(xbase_position)
+		
+		if int(alt_allele_count) == 0:
+			if xbase_location in zero_snp_count_per_xbase:
+				zero_snp_count_per_xbase[xbase_location] = zero_snp_count_per_xbase[xbase_location] + 1
+			else:
+				zero_snp_count_per_xbase[xbase_location] = 1
+
+		elif int(alt_allele_count) != 0 and xbase_location not in zero_snp_count_per_xbase:
+			zero_snp_count_per_xbase[xbase_location] = 0
+
+	return zero_snp_count_per_xbase
+
+
+def parse_vcf(sample_vcf = None):
+	i_file = open(sample_vcf, 'rU')
+	reader = csv.reader(i_file, delimiter = '\t', quoting = csv.QUOTE_NONE)	
+
+	skip_headers(reader = reader, i_file = i_file)
+	vcf_info = {}
+
+	for row in reader:
+		chromosome = row[0].upper()
+		chromosome = re.sub("chr", "", chromosome, flags = re.IGNORECASE)
+		chromosome = re.sub("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE)
+
+		if chromosome != 'MTDNA':
+			position = row[1]
+			#ref_allele = row[2]
+			#read_depth = row[3]
+			#read_bases = row[4]
+
+			vcf_format_info = row[8].split(":")
+			vcf_allele_freq_data = row[9] 
+			
+			read_depth_data_index = vcf_format_info.index("DP")
+			read_depth = vcf_allele_freq_data.split(":")[read_depth_data_index]
+
+			ref_and_alt_counts_data_index = vcf_format_info.index("AD")
+			ref_and_alt_counts = vcf_allele_freq_data.split(":")[ref_and_alt_counts_data_index]	
+			ref_allele_count = ref_and_alt_counts.split(",")[0]
+			alt_allele_count = ref_and_alt_counts.split(",")[1]
+
+			location = chromosome + ":" + position
+	
+			if (Decimal(read_depth)!=0):	
+				getcontext().prec = 6	
+				ratio = Decimal(alt_allele_count) / Decimal(read_depth)
+					
+				vcf_info[location] = (alt_allele_count, ref_allele_count, read_depth, ratio)
+			
+				#debug line
+				#print chromosome, position, read_depth, ref_allele_count, alt_allele_count, ratio, id
+
+	i_file.close()
+
+	return vcf_info
+
+def parse_read_bases(read_bases = None, alt_allele = None):
+	read_bases = re.sub('\$', '', read_bases)
+	read_bases = re.sub('\^[^\s]', '', read_bases)
+
+	ref_allele_matches = re.findall("\.|\,", read_bases)
+	ref_allele_count = len(ref_allele_matches)
+
+	alt_allele_matches = re.findall(alt_allele, read_bases, flags = re.IGNORECASE)
+	alt_allele_count = len(alt_allele_matches)
+
+	#debug line
+	#print read_bases, alt_allele, alt_allele_count, ref_allele_count
+
+	return ref_allele_count, alt_allele_count
+
+if __name__ == "__main__":
+	main()