# HG changeset patch # User gregory-minevich # Date 1340654932 14400 # Node ID 9a760d9862685fc25bf6e395a524a94eccb5603f # Parent 1bee9742af9ba2c33556f06b993b3e70b5e2a52c Uploaded diff -r 1bee9742af9b -r 9a760d986268 EMS_VariantDensityMapping.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/EMS_VariantDensityMapping.py Mon Jun 25 16:08:52 2012 -0400 @@ -0,0 +1,126 @@ +#!/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("chr", "", chromosome, flags = re.IGNORECASE) + chromosome = re.sub("CHROMOSOME_", "", 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()