--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/EMS_VariantDensityMapping.py	Fri May 09 17:46:56 2014 -0400
@@ -0,0 +1,127 @@
+#!/usr/bin/python
+
+import re
+import sys
+import optparse
+import csv
+from rpy import *
+
+def main():
+	parser = optparse.OptionParser()
+	parser.add_option('-s', '--snp_vcf', dest = 'snp_vcf', action = 'store', type = 'string', default = None, help = "VCF of SNPs")
+	parser.add_option('-c', '--hist_color', dest = 'hist_color', action = 'store', type = 'string', default = "darkgray", help = "Color for 1Mb histograms") 
+	parser.add_option('-y', '--ylim', dest = 'ylim', action = 'store', type = 'int', default= 100, help = "Upper limit of Y axis")
+	parser.add_option('-z', '--standardize', dest = 'standardize', default= 'false', help = "Standardize X-axis")
+	parser.add_option('-e', '--ems', dest = 'ems', default= 'false', help = "Whether EMS variants should be filtered for")
+	parser.add_option('-o', '--output', dest = 'plot_output', action = 'store', type = 'string', default = 'EMS_Variant_Density_Plot.pdf', help = "Output file name of plot")
+	(options, args) = parser.parse_args()
+
+
+	i, ii, iii, iv, v, x = parse_snp_vcf(snp_vcf = options.snp_vcf, ems=options.ems)
+
+	create_histograms(plot_output = options.plot_output, hist_color=options.hist_color, ylim=options.ylim, ems=options.ems, standardize=options.standardize, i = i, ii = ii, iii = iii, iv = iv, v = v, x = x)
+
+def create_histograms(plot_output = None, hist_color=None, ylim=None, ems=None, standardize=None , i = None, ii = None, iii = None, iv = None, v = None, x = None):
+	breaks = { 'I' : 16 , 'II' : 16,  'III' : 14, 'IV' : 18, 'V' : 21, 'X' : 18 }
+
+	try:
+		r.pdf(plot_output, 8, 8)
+		if len(i) > 0:
+		        plot_data(position_list = i, chr = "I", breaks = breaks["I"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize)
+        	if len(ii) > 0:
+			plot_data(position_list = ii, chr = "II", breaks = breaks["II"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize)
+		if len(iii) > 0:
+		        plot_data(position_list = iii, chr = "III", breaks = breaks["III"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize)
+        	if len(iv) > 0:
+			plot_data(position_list = iv, chr = "IV", breaks = breaks["IV"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize)
+		if len(v) > 0:
+		        plot_data(position_list = v, chr = "V", breaks = breaks["V"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize)
+		if len(x) > 0:
+	        	plot_data(position_list = x, chr = "X", breaks = breaks["X"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize)
+	        r.dev_off()
+    	except Exception as inst:
+        	print inst
+        	print "There was an error creating the plot pdf... Please try again"
+
+def parse_snp_vcf(snp_vcf = None, ems=None):
+	i_file = open(snp_vcf, 'rU')
+	reader = csv.reader(i_file, delimiter = '\t', quoting = csv.QUOTE_NONE)
+	skip_headers(reader = reader, i_file = i_file)
+
+	i_position_list = []
+	ii_position_list = []
+	iii_position_list = []
+	iv_position_list = []
+	v_position_list = []
+	x_position_list = []
+
+	for row in reader:
+		chromosome = row[0].upper()
+		chromosome = re.sub("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE)
+		chromosome = re.sub("chr", "", chromosome, flags = re.IGNORECASE)
+
+
+		position = row[1]
+		ref_allele = row[3]
+		alt_allele = row[4]
+
+		if  (ems=='true'):
+			if (ref_allele =="G" or ref_allele =="C") and (alt_allele =="A" or alt_allele =="T"):
+				if chromosome == "I":
+					i_position_list.append(position)
+				elif chromosome == "II":
+					ii_position_list.append(position)
+				elif chromosome == "III":
+					iii_position_list.append(position)
+				elif chromosome == "IV":
+					iv_position_list.append(position)
+				elif chromosome == "V":
+					v_position_list.append(position)
+				elif chromosome == "X":
+					x_position_list.append(position)
+		elif (ems=='false'):
+			if chromosome == "I":
+				i_position_list.append(position)
+			elif chromosome == "II":
+				ii_position_list.append(position)
+			elif chromosome == "III":
+				iii_position_list.append(position)
+			elif chromosome == "IV":
+				iv_position_list.append(position)
+			elif chromosome == "V":
+				v_position_list.append(position)
+			elif chromosome == "X":
+				x_position_list.append(position)
+
+	return i_position_list, ii_position_list, iii_position_list, iv_position_list, v_position_list, x_position_list
+
+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 plot_data(position_list = None, chr = None, breaks = None, hist_color=None, ylim = None, ems=None, standardize=None):
+	positions = ",".join(map(str, map(lambda x: float(x) / 1000000, position_list)))
+	positions = "c(" + positions + ")"
+	
+	if (standardize=='true'):
+		r("hist(" + positions + ", xlim=c(0,21), ylim=c(0, %d "%ylim +"),col='"+ hist_color + "', breaks = seq(0, as.integer( ' " + str(breaks) + " '), by=1), main = 'LG " + chr + "', ylab = 'Frequency Of SNPs', xlab = 'Location (Mb)')")
+		r("hist(" + positions + ", xlim=c(0,21), add=TRUE,  ylim=c(0, %d "%ylim +"), col=rgb(1, 0, 0, 1), breaks = seq(0, as.integer( ' " + str(breaks) + " '), by=.5), main = 'Chr " + chr + "', ylab = 'Number Of SNPs', xlab = 'Location (Mb)')")
+		r("axis(1, at=seq(0, 21, by=1), labels=FALSE, tcl=-0.5)")
+		r("axis(1, at=seq(0, 21, by=0.5), labels=FALSE, tcl=-0.25)")
+	elif (standardize=='false'):
+		r("hist(" + positions + ", xlim=c(0,as.integer( ' " + str(breaks) + " ')), ylim=c(0, %d "%ylim +"),col='"+ hist_color + "', breaks = seq(0, as.integer( ' " + str(breaks) + " '), by=1), main = 'LG " + chr + "', ylab = 'Frequency Of SNPs', xlab = 'Location (Mb)')")
+		r("hist(" + positions + ", xlim=c(0,as.integer( ' " + str(breaks) + " ')), add=TRUE,  ylim=c(0, %d "%ylim +"), col=rgb(1, 0, 0, 1), breaks = seq(0, as.integer( ' " + str(breaks) + " '), by=.5), main = 'Chr " + chr + "', ylab = 'Number Of SNPs', xlab = 'Location (Mb)')")
+		r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by=1), labels=FALSE, tcl=-0.5)")
+		r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by=0.5), labels=FALSE, tcl=-0.25)")
+
+
+
+if __name__ == "__main__":
+	main()