Mercurial > repos > gregory-minevich > snp_mapping_using_wgs

comparison SNP_Mapping.py @ 25:ad151f242a43 draft

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author gregory-minevich
date Mon, 08 Oct 2012 16:19:47 -0400
parents bdaadaee1cbb
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24:8cc52031c804 25:ad151f242a43
1 #!/usr/bin/python
2
3 import re
4 import sys
5 import optparse
6 import csv
7 import re
8 import pprint
9 from decimal import *
10 from rpy import *
11
12 def main():
13 csv.field_size_limit(1000000000)
14
15 parser = optparse.OptionParser()
16 parser.add_option('-v', '--sample_vcf', dest = 'sample_vcf', action = 'store', type = 'string', default = None, help = "Sample VCF from GATK Unified Genotyper")
17 parser.add_option('-l', '--loess_span', dest = 'loess_span', action = 'store', type = 'float', default = .01, help = "Loess span")
18 parser.add_option('-d', '--d_yaxis', dest = 'd_yaxis', action = 'store', type = 'float', default = .7, help = "y-axis upper limit for dot plot")
19 parser.add_option('-y', '--h_yaxis', dest = 'h_yaxis', action = 'store', type = 'int', default = 5, help = "y-axis upper limit for histogram plot")
20 parser.add_option('-c', '--points_color', dest = 'points_color', action = 'store', type = 'string', default = "gray27", help = "Color for data points")
21 parser.add_option('-k', '--loess_color', dest = 'loess_color', action = 'store', type = 'string', default = "red", help = "Color for loess regression line")
22 parser.add_option('-z', '--standardize', dest = 'standardize', default= 'true', help = "Standardize X-axis")
23 parser.add_option('-b', '--break_file', dest = 'break_file', action = 'store', type = 'string', default = 'C.elegans', help = "File defining the breaks per chromosome")
24 parser.add_option('-x', '--bin_size', dest = 'bin_size', action = 'store', type = 'int', default = 1000000, help = "Size of histogram bins, default is 1mb")
25 parser.add_option('-n', '--normalize_bins', dest = 'normalize_bins', default= 'true', help = "Normalize histograms")
26
27
28 parser.add_option('-o', '--output', dest = 'output', action = 'store', type = 'string', default = None, help = "Output file name")
29 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")
30
31 (options, args) = parser.parse_args()
32
33 vcf_info = parse_vcf(sample_vcf = options.sample_vcf)
34
35 output_vcf_info(output = options.output, vcf_info = vcf_info)
36
37 #output plot with all ratios
38 rounded_bin_size = int(round((float(options.bin_size) / 1000000), 1) * 1000000)
39
40 normalized_histogram_bins_per_mb = calculate_normalized_histogram_bins_per_xbase(vcf_info = vcf_info, xbase = rounded_bin_size, normalize_bins = options.normalize_bins)
41 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)
42
43 break_dict = parse_breaks(break_file = options.break_file)
44
45 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)
46
47
48 def skip_headers(reader = None, i_file = None):
49 # count headers
50 comment = 0
51 while reader.next()[0].startswith('#'):
52 comment = comment + 1
53
54 # skip headers
55 i_file.seek(0)
56 for i in range(0, comment):
57 reader.next()
58
59 def parse_breaks(break_file = None):
60 if break_file == 'C.elegans':
61 break_dict = { 'I' : 16 , 'II' : 16, 'III' : 14, 'IV' : 18, 'V' : 21, 'X' : 18 }
62 return break_dict
63 elif break_file == 'Arabidopsis':
64 break_dict = { '1' : 31 , '2' : 20, '3' : 24, '4' : 19, '5' : 27 }
65 return break_dict
66 else:
67 i_file = open(break_file, 'rU')
68 break_dict = {}
69 reader = csv.reader(i_file, delimiter = '\t')
70 for row in reader:
71 chromosome = row[0].upper()
72 chromosome = re.sub("chr", "", chromosome, flags = re.IGNORECASE)
73 chromosome = re.sub("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE)
74 break_count = row[1]
75 break_dict[chromosome] = int(break_count)
76 return break_dict
77
78
79 def location_comparer(location_1, location_2):
80 chr_loc_1 = location_1.split(':')[0]
81 pos_loc_1 = int(location_1.split(':')[1])
82
83 chr_loc_2 = location_2.split(':')[0]
84 pos_loc_2 = int(location_2.split(':')[1])
85
86 if chr_loc_1 == chr_loc_2:
87 if pos_loc_1 < pos_loc_2:
88 return -1
89 elif pos_loc_1 == pos_loc_1:
90 return 0
91 elif pos_loc_1 > pos_loc_2:
92 return 1
93 elif chr_loc_1 < chr_loc_2:
94 return -1
95 elif chr_loc_1 > chr_loc_2:
96 return 1
97
98 def output_vcf_info(output = None, vcf_info = None):
99 o_file = open(output, 'wb')
100 writer = csv.writer(o_file, delimiter = '\t')
101
102 writer.writerow(["#Chr\t", "Pos\t", "Alt Count\t", "Ref Count\t", "Read Depth\t", "Ratio\t"])
103
104 location_sorted_vcf_info_keys = sorted(vcf_info.keys(), cmp=location_comparer)
105
106 for location in location_sorted_vcf_info_keys:
107 alt_allele_count, ref_allele_count, read_depth, ratio = vcf_info[location]
108
109 location_info = location.split(':')
110 chromosome = location_info[0]
111 position = location_info[1]
112
113 writer.writerow([chromosome, position, alt_allele_count, ref_allele_count, read_depth, ratio])
114
115 o_file.close()
116
117 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):
118 positions = {}
119 current_chr = ""
120 prev_chr = ""
121
122 x_label = "Location (Mb)"
123 filtered_label = ''
124
125 location_sorted_vcf_info_keys = sorted(vcf_info.keys(), cmp=location_comparer)
126
127 break_unit = Decimal(rounded_bin_size) / Decimal(1000000)
128 max_breaks = max(breaks.values())
129
130 try:
131 r.pdf(location_plot_output, 8, 8)
132
133 for location in location_sorted_vcf_info_keys:
134 current_chr = location.split(':')[0]
135 position = location.split(':')[1]
136
137 alt_allele_count, ref_allele_count, read_depth, ratio = vcf_info[location]
138
139 if prev_chr != current_chr:
140 if prev_chr != "":
141 hist_dict_mb = get_hist_dict_by_chr(normalized_hist_per_xbase = normalized_hist_per_mb, chr = prev_chr)
142 hist_dict_5kb = get_hist_dict_by_chr(normalized_hist_per_xbase = normalized_hist_per_5kb, chr = prev_chr)
143
144 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)
145
146 prev_chr = current_chr
147 positions = {}
148
149 positions[position] = ratio
150
151 hist_dict_mb = get_hist_dict_by_chr(normalized_hist_per_xbase = normalized_hist_per_mb, chr = current_chr)
152 hist_dict_5kb = get_hist_dict_by_chr(normalized_hist_per_xbase = normalized_hist_per_5kb, chr = current_chr)
153
154 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)
155
156 r.dev_off()
157
158 except Exception as inst:
159 print inst
160 print "There was an error creating the location plot pdf... Please try again"
161
162 def get_hist_dict_by_chr(normalized_hist_per_xbase = None, chr = ''):
163 hist_dict = {}
164
165 for location in normalized_hist_per_xbase:
166 chromosome = location.split(':')[0]
167 if chromosome == chr:
168 position = int(location.split(':')[1])
169 hist_dict[position] = normalized_hist_per_xbase[location]
170
171 max_location = max(hist_dict.keys(), key=int)
172 for i in range(1, max_location):
173 if i not in hist_dict:
174 hist_dict[i] = 0
175
176 return hist_dict
177
178 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):
179 ratios = "c("
180 positions = "c("
181
182 for position in chr_dict:
183 ratio = chr_dict[position]
184 if divide_position:
185 position = float(position) / 1000000.0
186 positions = positions + str(position) + ", "
187 ratios = ratios + str(ratio) + ", "
188
189 if len(ratios) == 2:
190 ratios = ratios + ")"
191 else:
192 ratios = ratios[0:len(ratios) - 2] + ")"
193
194 if len(positions) == 2:
195 positions = positions + ")"
196 else:
197 positions = positions[0:len(positions) - 2] + ")"
198
199 r("x <- " + positions)
200 r("y <- " + ratios)
201
202 hist_mb_values = "c("
203 for position in sorted(hist_dict_mb):
204 hist_mb_values = hist_mb_values + str(hist_dict_mb[position]) + ", "
205
206 if len(hist_mb_values) == 2:
207 hist_mb_values = hist_mb_values + ")"
208 else:
209 hist_mb_values = hist_mb_values[0:len(hist_mb_values) - 2] + ")"
210
211 hist_5kb_values = "c("
212 for position in sorted(hist_dict_5kb):
213 hist_5kb_values = hist_5kb_values + str(hist_dict_5kb[position]) + ", "
214
215 if len(hist_5kb_values) == 2:
216 hist_5kb_values = hist_5kb_values + ")"
217 else:
218 hist_5kb_values = hist_5kb_values[0:len(hist_5kb_values) - 2] + ")"
219
220 r("xz <- " + hist_mb_values)
221 r("yz <- " + hist_5kb_values)
222
223
224 max_break_str = str(max_breaks)
225 break_unit_str = str(Decimal(break_unit))
226 half_break_unit_str = str(Decimal(break_unit) / Decimal(2))
227 break_penta_unit_str = str(Decimal(break_unit) * Decimal(5))
228
229 if (standardize=='true'):
230 r("plot(x, y, ,cex=0.60, xlim=c(0," + max_break_str + "), main='LG " + chr + "', xlab= '" + x_label + "', ylim = c(0, %f " %d_yaxis + "), ylab='Ratios of mapping strain alleles/total reads (at SNP positions)', pch=18, col='"+ points_color +"')")
231 r("lines(loess.smooth(x, y, span = %f "%loess_span + "), lwd=5, col='"+ loess_color +"')")
232 r("axis(1, at=seq(0, " + max_break_str + ", by=" + break_unit_str + "), labels=FALSE, tcl=-0.5)")
233 r("axis(1, at=seq(0, " + max_break_str + ", by=" + half_break_unit_str + "), labels=FALSE, tcl=-0.25)")
234 r("axis(2, at=seq(floor(min(y)), 1, by=0.1), labels=FALSE, tcl=-0.2)")
235 elif (standardize=='false'):
236 r("plot(x, y, cex=0.60, main='LG " + chr + "', xlab= '" + x_label + "', ylim = c(0, %f " %d_yaxis + "), ylab='Ratios of mapping strain alleles/total reads (at SNP positions)', pch=18, col='"+ points_color +"')")
237 r("lines(loess.smooth(x, y, span = %f "%loess_span + "), lwd=5, col='"+ loess_color +"')")
238 r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by= " + break_unit_str + "), labels=FALSE, tcl=-0.5)")
239 r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by= " + half_break_unit_str + "), labels=FALSE, tcl=-0.25)")
240 r("axis(2, at=seq(floor(min(y)), 1, by=0.1), labels=FALSE, tcl=-0.2)")
241
242 if draw_secondary_grid_lines:
243 r("abline(h = seq(floor(min(y)), 1, by=0.1), v = seq(floor(min(x)), length(x), by= 1), col='gray')")
244 else:
245 r("grid(lty = 1, col = 'gray')")
246
247 if (standardize=='true'):
248 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 + "')")
249 r("barplot(yz, space = 0, add=TRUE, width = " + half_break_unit_str + ", col=rgb(1, 0, 0, 1))")
250 r("axis(1, hadj = 1, at=seq(0, " + max_break_str + ", by= " + break_unit_str + "), labels=FALSE, tcl=-0.5)")
251 r("axis(1, at=seq(0, " + max_break_str + ", by= " + break_penta_unit_str + "), labels=TRUE, tcl=-0.5)")
252 r("axis(1, at=seq(0, " + max_break_str + ", by= " + half_break_unit_str + "), labels=FALSE, tcl=-0.25)")
253 elif (standardize=='false'):
254 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 + "')")
255 r("barplot(yz, space = 0, add=TRUE, width = 0.5, col=rgb(1, 0, 0, 1))")
256 r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by= " + break_unit_str + "), labels=FALSE, tcl=-0.5)")
257 r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by= " + break_penta_unit_str + "), labels=TRUE, tcl=-0.5)")
258 r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by= " + half_break_unit_str + "), labels=FALSE, tcl=-0.25)")
259
260
261
262 def calculate_normalized_histogram_bins_per_xbase(vcf_info = None, xbase = 1000000, normalize_bins = None):
263 normalized_histogram_bins_per_xbase = {}
264
265 ref_snp_count_per_xbase = get_ref_snp_count_per_xbase(vcf_info = vcf_info, xbase = xbase)
266 #print "ref_snp_count_per_xbase: " + str(ref_snp_count_per_xbase)
267 mean_zero_snp_count_per_chromosome = get_mean_zero_snp_count_per_chromosome(vcf_info = vcf_info, xbase = xbase)
268 #print "mean_zero_snp_count_per_chromosome: " + str(mean_zero_snp_count_per_chromosome)
269 zero_snp_count_per_xbase = get_zero_snp_count_per_xbase(vcf_info = vcf_info, xbase = xbase)
270 #print "zero_snp_count_per_xbase: " + str(zero_snp_count_per_xbase)
271
272 for location in ref_snp_count_per_xbase:
273 chromosome = location.split(':')[0]
274 mean_zero_snp_count = mean_zero_snp_count_per_chromosome[chromosome]
275 ref_snp_count = ref_snp_count_per_xbase[location]
276
277 zero_snp_count = 0
278 if location in zero_snp_count_per_xbase:
279 zero_snp_count = zero_snp_count_per_xbase[location]
280
281 if normalize_bins == 'true':
282 if zero_snp_count == 0 or ref_snp_count == 0:
283 normalized_histogram_bins_per_xbase[location] = 0
284 elif zero_snp_count == ref_snp_count:
285 normalized_histogram_bins_per_xbase[location] = 0
286 else:
287 normalized_histogram_bins_per_xbase[location] = (Decimal(zero_snp_count) / (Decimal(ref_snp_count)-Decimal(zero_snp_count))) * Decimal(mean_zero_snp_count)
288 else:
289 normalized_histogram_bins_per_xbase[location] = zero_snp_count
290
291 return normalized_histogram_bins_per_xbase
292
293
294 def get_ref_snp_count_per_xbase(vcf_info = None, xbase = 1000000):
295 ref_snps_per_xbase = {}
296
297 for location in vcf_info:
298 location_info = location.split(':')
299
300 chromosome = location_info[0].upper()
301 chromosome = re.sub("chr", "", chromosome, flags = re.IGNORECASE)
302 chromosome = re.sub("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE)
303
304 position = location_info[1]
305 xbase_position = (int(position) / xbase) + 1
306
307 location = chromosome + ":" + str(xbase_position)
308 if location in ref_snps_per_xbase:
309 ref_snps_per_xbase[location] = ref_snps_per_xbase[location] + 1
310 else:
311 ref_snps_per_xbase[location] = 1
312
313 return ref_snps_per_xbase
314
315
316
317 def get_mean_zero_snp_count_per_chromosome(vcf_info, xbase = 1000000):
318 sample_snp_count_per_xbase = {}
319
320 for location in vcf_info:
321 alt_allele_count, ref_allele_count, read_depth, ratio = vcf_info[location]
322
323 location_info = location.split(':')
324 chromosome = location_info[0]
325 position = location_info[1]
326 xbase_position = (int(position) / xbase) + 1
327 xbase_location = chromosome + ":" + str(xbase_position)
328
329 if int(alt_allele_count) == 0:
330 if xbase_location in sample_snp_count_per_xbase:
331 sample_snp_count_per_xbase[xbase_location] = sample_snp_count_per_xbase[xbase_location] + 1
332 else:
333 sample_snp_count_per_xbase[xbase_location] = 1
334
335 elif int(alt_allele_count) != 0 and xbase_location not in sample_snp_count_per_xbase:
336 sample_snp_count_per_xbase[xbase_location] = 0
337
338 mean_zero_snp_count_per_chromosome = {}
339 for location in sample_snp_count_per_xbase:
340 chromosome = location.split(':')[0]
341 sample_count = sample_snp_count_per_xbase[location]
342 if chromosome in mean_zero_snp_count_per_chromosome:
343 mean_zero_snp_count_per_chromosome[chromosome].append(sample_count)
344 else:
345 mean_zero_snp_count_per_chromosome[chromosome] = [sample_count]
346
347 for chromosome in mean_zero_snp_count_per_chromosome:
348 summa = sum(mean_zero_snp_count_per_chromosome[chromosome])
349 count = len(mean_zero_snp_count_per_chromosome[chromosome])
350
351 mean_zero_snp_count_per_chromosome[chromosome] = Decimal(summa) / Decimal(count)
352
353 return mean_zero_snp_count_per_chromosome
354
355
356 def get_zero_snp_count_per_xbase(vcf_info = None, xbase = 1000000):
357 zero_snp_count_per_xbase = {}
358
359 for location in vcf_info:
360 alt_allele_count, ref_allele_count, read_depth, ratio = vcf_info[location]
361
362 location_info = location.split(':')
363 chromosome = location_info[0]
364 position = location_info[1]
365 xbase_position = (int(position) / xbase) + 1
366 xbase_location = chromosome + ":" + str(xbase_position)
367
368 if int(alt_allele_count) == 0:
369 if xbase_location in zero_snp_count_per_xbase:
370 zero_snp_count_per_xbase[xbase_location] = zero_snp_count_per_xbase[xbase_location] + 1
371 else:
372 zero_snp_count_per_xbase[xbase_location] = 1
373
374 elif int(alt_allele_count) != 0 and xbase_location not in zero_snp_count_per_xbase:
375 zero_snp_count_per_xbase[xbase_location] = 0
376
377 return zero_snp_count_per_xbase
378
379
380 def parse_vcf(sample_vcf = None):
381 i_file = open(sample_vcf, 'rU')
382 reader = csv.reader(i_file, delimiter = '\t', quoting = csv.QUOTE_NONE)
383
384 skip_headers(reader = reader, i_file = i_file)
385 vcf_info = {}
386
387 for row in reader:
388 chromosome = row[0].upper()
389 chromosome = re.sub("chr", "", chromosome, flags = re.IGNORECASE)
390 chromosome = re.sub("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE)
391
392 if chromosome != 'MTDNA':
393 position = row[1]
394 #ref_allele = row[2]
395 #read_depth = row[3]
396 #read_bases = row[4]
397
398 vcf_format_info = row[8].split(":")
399 vcf_allele_freq_data = row[9]
400
401 read_depth_data_index = vcf_format_info.index("DP")
402 read_depth = vcf_allele_freq_data.split(":")[read_depth_data_index]
403
404 ref_and_alt_counts_data_index = vcf_format_info.index("AD")
405 ref_and_alt_counts = vcf_allele_freq_data.split(":")[ref_and_alt_counts_data_index]
406 ref_allele_count = ref_and_alt_counts.split(",")[0]
407 alt_allele_count = ref_and_alt_counts.split(",")[1]
408
409 location = chromosome + ":" + position
410
411 if (Decimal(read_depth)!=0):
412 getcontext().prec = 6
413 ratio = Decimal(alt_allele_count) / Decimal(read_depth)
414
415 vcf_info[location] = (alt_allele_count, ref_allele_count, read_depth, ratio)
416
417 #debug line
418 #print chromosome, position, read_depth, ref_allele_count, alt_allele_count, ratio, id
419
420 i_file.close()
421
422 return vcf_info
423
424 def parse_read_bases(read_bases = None, alt_allele = None):
425 read_bases = re.sub('\$', '', read_bases)
426 read_bases = re.sub('\^[^\s]', '', read_bases)
427
428 ref_allele_matches = re.findall("\.|\,", read_bases)
429 ref_allele_count = len(ref_allele_matches)
430
431 alt_allele_matches = re.findall(alt_allele, read_bases, flags = re.IGNORECASE)
432 alt_allele_count = len(alt_allele_matches)
433
434 #debug line
435 #print read_bases, alt_allele, alt_allele_count, ref_allele_count
436
437 return ref_allele_count, alt_allele_count
438
439 if __name__ == "__main__":
440 main()