# HG changeset patch # User gregory-minevich # Date 1399669157 14400 # Node ID f19399eea0c476268cc44232c68ed171f3864c93 # Parent 11da66cb721697bb44df7263d0bba32ce1a9b84c Deleted selected files diff -r 11da66cb7216 -r f19399eea0c4 SNP_Mapping.py --- a/SNP_Mapping.py Fri May 09 15:41:24 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,458 +0,0 @@ -#!/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 = .1, help = "Loess span") - parser.add_option('-d', '--d_yaxis', dest = 'd_yaxis', action = 'store', type = 'float', default = 1, help = "y-axis upper limit for dot plot") - parser.add_option('-y', '--h_yaxis', dest = 'h_yaxis', action = 'store', type = 'int', default = 0, 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) - - 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) - max_y_hist_mb = normalized_histogram_bins_per_mb[max(normalized_histogram_bins_per_mb, key = lambda x: normalized_histogram_bins_per_mb.get(x) )] - - 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) - max_y_hist_5kb = normalized_histogram_bins_per_5kb[max(normalized_histogram_bins_per_5kb, key = lambda x: normalized_histogram_bins_per_5kb.get(x) )] - - max_y_hist_overall = myround(max(max_y_hist_mb, max_y_hist_5kb) + int(round(round(max(max_y_hist_mb, max_y_hist_5kb)) * .1))) - - 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, max_y_hist_overall = max_y_hist_overall) - - -def myround(x, base=5): - return int(base * round(float(x)/base)) - -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 == 'Brachypodium': - break_dict = { '1' : 75 , '2' : 60, '3' : 60, '4' : 50, '5' : 30 } - 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("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE) - chromosome = re.sub("chr", "", 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, max_y_hist_overall = ""): - 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) - - if h_yaxis == 0: - 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=max_y_hist_overall, points_color=points_color, loess_color=loess_color, breaks = breaks[prev_chr], standardize=standardize, max_breaks = max_breaks, break_unit = break_unit) - else: - 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) - - if h_yaxis == 0: - 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=max_y_hist_overall, points_color=points_color, loess_color=loess_color, breaks = breaks[current_chr], standardize=standardize, max_breaks = max_breaks, break_unit = break_unit) - else: - 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) - - mean_zero_snp_count_per_chromosome = get_mean_zero_snp_count_per_chromosome(vcf_info = vcf_info, xbase = xbase) - - zero_snp_count_per_xbase = get_zero_snp_count_per_xbase(vcf_info = vcf_info, xbase = 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("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE) - chromosome = re.sub("chr", "", 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("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE) - chromosome = re.sub("chr", "", 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()