Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.py @ 81:b6f9a640e098 draft

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author davidvanzessen
date Fri, 19 Feb 2021 15:10:54 +0000
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80:a4617f1d1d89 81:b6f9a640e098
1 import argparse
2 import logging
3 import sys
4 import os
5 import re
6
7 from collections import defaultdict
8
9 def main():
10 parser = argparse.ArgumentParser()
11 parser.add_argument("--input", help="The '7_V-REGION-mutation-and-AA-change-table' and '10_V-REGION-mutation-hotspots' merged together, with an added 'best_match' annotation")
12 parser.add_argument("--genes", help="The genes available in the 'best_match' column")
13 parser.add_argument("--empty_region_filter", help="Where does the sequence start?", choices=['leader', 'FR1', 'CDR1', 'FR2'])
14 parser.add_argument("--output", help="Output file")
15
16 args = parser.parse_args()
17
18 infile = args.input
19 genes = str(args.genes).split(",")
20 empty_region_filter = args.empty_region_filter
21 outfile = args.output
22
23 genedic = dict()
24
25 mutationdic = dict()
26 mutationMatcher = re.compile("^(.)(\d+).(.),?[ ]?(.)?(\d+)?.?(.)?(.?.?.?.?.?)?")
27 mutationMatcher = re.compile("^([actg])(\d+).([actg]),?[ ]?([A-Z])?(\d+)?.?([A-Z])?(.*)?")
28 mutationMatcher = re.compile("^([actg])(\d+).([actg]),?[ ]?([A-Z])?(\d+)?[>]?([A-Z;])?(.*)?")
29 mutationMatcher = re.compile("^([nactg])(\d+).([nactg]),?[ ]?([A-Z])?(\d+)?[>]?([A-Z;])?(.*)?")
30 NAMatchResult = (None, None, None, None, None, None, '')
31 geneMatchers = {gene: re.compile("^" + gene + ".*") for gene in genes}
32 linecount = 0
33
34 IDIndex = 0
35 best_matchIndex = 0
36 fr1Index = 0
37 cdr1Index = 0
38 fr2Index = 0
39 cdr2Index = 0
40 fr3Index = 0
41 first = True
42 IDlist = []
43 mutationList = []
44 mutationListByID = {}
45 cdr1LengthDic = {}
46 cdr2LengthDic = {}
47
48 fr1LengthDict = {}
49 fr2LengthDict = {}
50 fr3LengthDict = {}
51
52 cdr1LengthIndex = 0
53 cdr2LengthIndex = 0
54
55 fr1SeqIndex = 0
56 fr2SeqIndex = 0
57 fr3SeqIndex = 0
58
59 tandem_sum_by_class = defaultdict(int)
60 expected_tandem_sum_by_class = defaultdict(float)
61
62 with open(infile, 'ru') as i:
63 for line in i:
64 if first:
65 linesplt = line.split("\t")
66 IDIndex = linesplt.index("Sequence.ID")
67 best_matchIndex = linesplt.index("best_match")
68 fr1Index = linesplt.index("FR1.IMGT")
69 cdr1Index = linesplt.index("CDR1.IMGT")
70 fr2Index = linesplt.index("FR2.IMGT")
71 cdr2Index = linesplt.index("CDR2.IMGT")
72 fr3Index = linesplt.index("FR3.IMGT")
73 cdr1LengthIndex = linesplt.index("CDR1.IMGT.length")
74 cdr2LengthIndex = linesplt.index("CDR2.IMGT.length")
75 fr1SeqIndex = linesplt.index("FR1.IMGT.seq")
76 fr2SeqIndex = linesplt.index("FR2.IMGT.seq")
77 fr3SeqIndex = linesplt.index("FR3.IMGT.seq")
78 first = False
79 continue
80 linecount += 1
81 linesplt = line.split("\t")
82 ID = linesplt[IDIndex]
83 genedic[ID] = linesplt[best_matchIndex]
84
85 mutationdic[ID + "_FR1"] = []
86 if len(linesplt[fr1Index]) > 5 and empty_region_filter == "leader":
87 mutationdic[ID + "_FR1"] = [mutationMatcher.match(x).groups() for x in linesplt[fr1Index].split("|") if x]
88
89 mutationdic[ID + "_CDR1"] = []
90 if len(linesplt[cdr1Index]) > 5 and empty_region_filter in ["leader", "FR1"]:
91 mutationdic[ID + "_CDR1"] = [mutationMatcher.match(x).groups() for x in linesplt[cdr1Index].split("|") if x]
92
93 mutationdic[ID + "_FR2"] = []
94 if len(linesplt[fr2Index]) > 5 and empty_region_filter in ["leader", "FR1", "CDR1"]:
95 mutationdic[ID + "_FR2"] = [mutationMatcher.match(x).groups() for x in linesplt[fr2Index].split("|") if x]
96
97 mutationdic[ID + "_CDR2"] = []
98 if len(linesplt[cdr2Index]) > 5:
99 mutationdic[ID + "_CDR2"] = [mutationMatcher.match(x).groups() for x in linesplt[cdr2Index].split("|") if x]
100
101 mutationdic[ID + "_FR2-CDR2"] = mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"]
102
103 mutationdic[ID + "_FR3"] = []
104 if len(linesplt[fr3Index]) > 5:
105 mutationdic[ID + "_FR3"] = [mutationMatcher.match(x).groups() for x in linesplt[fr3Index].split("|") if x]
106
107 mutationList += mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"]
108 mutationListByID[ID] = mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"]
109
110 try:
111 cdr1Length = int(linesplt[cdr1LengthIndex])
112 except:
113 cdr1Length = 0
114
115 try:
116 cdr2Length = int(linesplt[cdr2LengthIndex])
117 except:
118 cdr2Length = 0
119
120 #print linesplt[fr2SeqIndex]
121 fr1Length = len(linesplt[fr1SeqIndex]) if empty_region_filter == "leader" else 0
122 fr2Length = len(linesplt[fr2SeqIndex]) if empty_region_filter in ["leader", "FR1", "CDR1"] else 0
123 fr3Length = len(linesplt[fr3SeqIndex])
124
125 cdr1LengthDic[ID] = cdr1Length
126 cdr2LengthDic[ID] = cdr2Length
127
128 fr1LengthDict[ID] = fr1Length
129 fr2LengthDict[ID] = fr2Length
130 fr3LengthDict[ID] = fr3Length
131
132 IDlist += [ID]
133 print "len(mutationdic) =", len(mutationdic)
134
135 with open(os.path.join(os.path.dirname(os.path.abspath(infile)), "mutationdict.txt"), 'w') as out_handle:
136 for ID, lst in mutationdic.iteritems():
137 for mut in lst:
138 out_handle.write("{0}\t{1}\n".format(ID, "\t".join([str(x) for x in mut])))
139
140 #tandem mutation stuff
141 tandem_frequency = defaultdict(int)
142 mutation_frequency = defaultdict(int)
143
144 mutations_by_id_dic = {}
145 first = True
146 mutation_by_id_file = os.path.join(os.path.dirname(outfile), "mutation_by_id.txt")
147 with open(mutation_by_id_file, 'r') as mutation_by_id:
148 for l in mutation_by_id:
149 if first:
150 first = False
151 continue
152 splt = l.split("\t")
153 mutations_by_id_dic[splt[0]] = int(splt[1])
154
155 tandem_file = os.path.join(os.path.dirname(outfile), "tandems_by_id.txt")
156 with open(tandem_file, 'w') as o:
157 highest_tandem_length = 0
158
159 o.write("Sequence.ID\tnumber_of_mutations\tnumber_of_tandems\tregion_length\texpected_tandems\tlongest_tandem\ttandems\n")
160 for ID in IDlist:
161 mutations = mutationListByID[ID]
162 if len(mutations) == 0:
163 continue
164 last_mut = max(mutations, key=lambda x: int(x[1]))
165
166 last_mut_pos = int(last_mut[1])
167
168 mut_positions = [False] * (last_mut_pos + 1)
169
170 for mutation in mutations:
171 frm, where, to, frmAA, whereAA, toAA, thing = mutation
172 where = int(where)
173 mut_positions[where] = True
174
175 tandem_muts = []
176 tandem_start = -1
177 tandem_length = 0
178 for i in range(len(mut_positions)):
179 if mut_positions[i]:
180 if tandem_start == -1:
181 tandem_start = i
182 tandem_length += 1
183 #print "".join(["1" if x else "0" for x in mut_positions[:i+1]])
184 else:
185 if tandem_length > 1:
186 tandem_muts.append((tandem_start, tandem_length))
187 #print "{0}{1} {2}:{3}".format(" " * (i - tandem_length), "^" * tandem_length, tandem_start, tandem_length)
188 tandem_start = -1
189 tandem_length = 0
190 if tandem_length > 1: # if the sequence ends with a tandem mutation
191 tandem_muts.append((tandem_start, tandem_length))
192
193 if len(tandem_muts) > 0:
194 if highest_tandem_length < len(tandem_muts):
195 highest_tandem_length = len(tandem_muts)
196
197 region_length = fr1LengthDict[ID] + cdr1LengthDic[ID] + fr2LengthDict[ID] + cdr2LengthDic[ID] + fr3LengthDict[ID]
198 longest_tandem = max(tandem_muts, key=lambda x: x[1]) if len(tandem_muts) else (0, 0)
199 num_mutations = mutations_by_id_dic[ID] # len(mutations)
200 f_num_mutations = float(num_mutations)
201 num_tandem_muts = len(tandem_muts)
202 expected_tandem_muts = f_num_mutations * (f_num_mutations - 1.0) / float(region_length)
203 o.write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\n".format(ID,
204 str(num_mutations),
205 str(num_tandem_muts),
206 str(region_length),
207 str(round(expected_tandem_muts, 2)),
208 str(longest_tandem[1]),
209 str(tandem_muts)))
210 gene = genedic[ID]
211 if gene.find("unmatched") == -1:
212 tandem_sum_by_class[gene] += num_tandem_muts
213 expected_tandem_sum_by_class[gene] += expected_tandem_muts
214
215 tandem_sum_by_class["all"] += num_tandem_muts
216 expected_tandem_sum_by_class["all"] += expected_tandem_muts
217
218 gene = gene[:3]
219 if gene in ["IGA", "IGG"]:
220 tandem_sum_by_class[gene] += num_tandem_muts
221 expected_tandem_sum_by_class[gene] += expected_tandem_muts
222 else:
223 tandem_sum_by_class["unmatched"] += num_tandem_muts
224 expected_tandem_sum_by_class["unmatched"] += expected_tandem_muts
225
226
227 for tandem_mut in tandem_muts:
228 tandem_frequency[str(tandem_mut[1])] += 1
229 #print "\t".join([ID, str(len(tandem_muts)), str(longest_tandem[1]) , str(tandem_muts)])
230
231 tandem_freq_file = os.path.join(os.path.dirname(outfile), "tandem_frequency.txt")
232 with open(tandem_freq_file, 'w') as o:
233 for frq in sorted([int(x) for x in tandem_frequency.keys()]):
234 o.write("{0}\t{1}\n".format(frq, tandem_frequency[str(frq)]))
235
236 tandem_row = []
237 genes_extra = list(genes)
238 genes_extra.append("all")
239 for x, y, in zip([tandem_sum_by_class[x] for x in genes_extra], [expected_tandem_sum_by_class[x] for x in genes_extra]):
240 if y != 0:
241 tandem_row += [x, round(y, 2), round(x / y, 2)]
242 else:
243 tandem_row += [x, round(y, 2), 0]
244
245 tandem_freq_file = os.path.join(os.path.dirname(outfile), "shm_overview_tandem_row.txt")
246 with open(tandem_freq_file, 'w') as o:
247 o.write("Tandems/Expected (ratio),{0}\n".format(",".join([str(x) for x in tandem_row])))
248
249 #print mutationList, linecount
250
251 AALength = (int(max(mutationList, key=lambda i: int(i[4]) if i[4] and i[5] != ";" else 0)[4]) + 1) # [4] is the position of the AA mutation, None if silent
252 if AALength < 60:
253 AALength = 64
254
255 AA_mutation = [0] * AALength
256 AA_mutation_dic = {"IGA": AA_mutation[:], "IGG": AA_mutation[:], "IGM": AA_mutation[:], "IGE": AA_mutation[:], "unm": AA_mutation[:], "all": AA_mutation[:]}
257 AA_mutation_empty = AA_mutation[:]
258
259 print "AALength:", AALength
260 aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/aa_id_mutations.txt"
261 with open(aa_mutations_by_id_file, 'w') as o:
262 o.write("ID\tbest_match\t" + "\t".join([str(x) for x in range(1,AALength)]) + "\n")
263 for ID in mutationListByID.keys():
264 AA_mutation_for_ID = AA_mutation_empty[:]
265 for mutation in mutationListByID[ID]:
266 if mutation[4] and mutation[5] != ";":
267 AA_mutation_position = int(mutation[4])
268 try:
269 AA_mutation[AA_mutation_position] += 1
270 AA_mutation_for_ID[AA_mutation_position] += 1
271 except Exception as e:
272 print e
273 print mutation
274 sys.exit()
275 clss = genedic[ID][:3]
276 AA_mutation_dic[clss][AA_mutation_position] += 1
277 o.write(ID + "\t" + genedic[ID] + "\t" + "\t".join([str(x) for x in AA_mutation_for_ID[1:]]) + "\n")
278
279
280
281 #absent AA stuff
282 absentAACDR1Dic = defaultdict(list)
283 absentAACDR1Dic[5] = range(29,36)
284 absentAACDR1Dic[6] = range(29,35)
285 absentAACDR1Dic[7] = range(30,35)
286 absentAACDR1Dic[8] = range(30,34)
287 absentAACDR1Dic[9] = range(31,34)
288 absentAACDR1Dic[10] = range(31,33)
289 absentAACDR1Dic[11] = [32]
290
291 absentAACDR2Dic = defaultdict(list)
292 absentAACDR2Dic[0] = range(55,65)
293 absentAACDR2Dic[1] = range(56,65)
294 absentAACDR2Dic[2] = range(56,64)
295 absentAACDR2Dic[3] = range(57,64)
296 absentAACDR2Dic[4] = range(57,63)
297 absentAACDR2Dic[5] = range(58,63)
298 absentAACDR2Dic[6] = range(58,62)
299 absentAACDR2Dic[7] = range(59,62)
300 absentAACDR2Dic[8] = range(59,61)
301 absentAACDR2Dic[9] = [60]
302
303 absentAA = [len(IDlist)] * (AALength-1)
304 for k, cdr1Length in cdr1LengthDic.iteritems():
305 for c in absentAACDR1Dic[cdr1Length]:
306 absentAA[c] -= 1
307
308 for k, cdr2Length in cdr2LengthDic.iteritems():
309 for c in absentAACDR2Dic[cdr2Length]:
310 absentAA[c] -= 1
311
312
313 aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/absent_aa_id.txt"
314 with open(aa_mutations_by_id_file, 'w') as o:
315 o.write("ID\tcdr1length\tcdr2length\tbest_match\t" + "\t".join([str(x) for x in range(1,AALength)]) + "\n")
316 for ID in IDlist:
317 absentAAbyID = [1] * (AALength-1)
318 cdr1Length = cdr1LengthDic[ID]
319 for c in absentAACDR1Dic[cdr1Length]:
320 absentAAbyID[c] -= 1
321
322 cdr2Length = cdr2LengthDic[ID]
323 for c in absentAACDR2Dic[cdr2Length]:
324 absentAAbyID[c] -= 1
325 o.write(ID + "\t" + str(cdr1Length) + "\t" + str(cdr2Length) + "\t" + genedic[ID] + "\t" + "\t".join([str(x) for x in absentAAbyID]) + "\n")
326
327 if linecount == 0:
328 print "No data, exiting"
329 with open(outfile, 'w') as o:
330 o.write("RGYW (%)," + ("0,0,0\n" * len(genes)))
331 o.write("WRCY (%)," + ("0,0,0\n" * len(genes)))
332 o.write("WA (%)," + ("0,0,0\n" * len(genes)))
333 o.write("TW (%)," + ("0,0,0\n" * len(genes)))
334 import sys
335
336 sys.exit()
337
338 hotspotMatcher = re.compile("[actg]+,(\d+)-(\d+)\((.*)\)")
339 RGYWCount = {}
340 WRCYCount = {}
341 WACount = {}
342 TWCount = {}
343
344 #IDIndex = 0
345 ataIndex = 0
346 tatIndex = 0
347 aggctatIndex = 0
348 atagcctIndex = 0
349 first = True
350 with open(infile, 'ru') as i:
351 for line in i:
352 if first:
353 linesplt = line.split("\t")
354 ataIndex = linesplt.index("X.a.t.a")
355 tatIndex = linesplt.index("t.a.t.")
356 aggctatIndex = linesplt.index("X.a.g.g.c.t..a.t.")
357 atagcctIndex = linesplt.index("X.a.t..a.g.c.c.t.")
358 first = False
359 continue
360 linesplt = line.split("\t")
361 gene = linesplt[best_matchIndex]
362 ID = linesplt[IDIndex]
363 RGYW = [(int(x), int(y), z) for (x, y, z) in
364 [hotspotMatcher.match(x).groups() for x in linesplt[aggctatIndex].split("|") if x]]
365 WRCY = [(int(x), int(y), z) for (x, y, z) in
366 [hotspotMatcher.match(x).groups() for x in linesplt[atagcctIndex].split("|") if x]]
367 WA = [(int(x), int(y), z) for (x, y, z) in
368 [hotspotMatcher.match(x).groups() for x in linesplt[ataIndex].split("|") if x]]
369 TW = [(int(x), int(y), z) for (x, y, z) in
370 [hotspotMatcher.match(x).groups() for x in linesplt[tatIndex].split("|") if x]]
371 RGYWCount[ID], WRCYCount[ID], WACount[ID], TWCount[ID] = 0, 0, 0, 0
372
373 with open(os.path.join(os.path.dirname(os.path.abspath(infile)), "RGYW.txt"), 'a') as out_handle:
374 for hotspot in RGYW:
375 out_handle.write("{0}\t{1}\n".format(ID, "\t".join([str(x) for x in hotspot])))
376
377 mutationList = mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"]
378 for mutation in mutationList:
379 frm, where, to, AAfrm, AAwhere, AAto, junk = mutation
380 mutation_in_RGYW = any(((start <= int(where) <= end) for (start, end, region) in RGYW))
381 mutation_in_WRCY = any(((start <= int(where) <= end) for (start, end, region) in WRCY))
382 mutation_in_WA = any(((start <= int(where) <= end) for (start, end, region) in WA))
383 mutation_in_TW = any(((start <= int(where) <= end) for (start, end, region) in TW))
384
385 in_how_many_motifs = sum([mutation_in_RGYW, mutation_in_WRCY, mutation_in_WA, mutation_in_TW])
386
387 if in_how_many_motifs > 0:
388 RGYWCount[ID] += (1.0 * int(mutation_in_RGYW)) / in_how_many_motifs
389 WRCYCount[ID] += (1.0 * int(mutation_in_WRCY)) / in_how_many_motifs
390 WACount[ID] += (1.0 * int(mutation_in_WA)) / in_how_many_motifs
391 TWCount[ID] += (1.0 * int(mutation_in_TW)) / in_how_many_motifs
392
393 mutations_in_motifs_file = os.path.join(os.path.dirname(os.path.abspath(infile)), "mutation_in_motifs.txt")
394 if not os.path.exists(mutation_by_id_file):
395 with open(mutations_in_motifs_file, 'w') as out_handle:
396 out_handle.write("{0}\n".format("\t".join([
397 "Sequence.ID",
398 "mutation_position",
399 "region",
400 "from_nt",
401 "to_nt",
402 "mutation_position_AA",
403 "from_AA",
404 "to_AA",
405 "motif",
406 "motif_start_nt",
407 "motif_end_nt",
408 "rest"
409 ])))
410
411 with open(mutations_in_motifs_file, 'a') as out_handle:
412 motif_dic = {"RGYW": RGYW, "WRCY": WRCY, "WA": WA, "TW": TW}
413 for mutation in mutationList:
414 frm, where, to, AAfrm, AAwhere, AAto, junk = mutation
415 for motif in motif_dic.keys():
416
417 for start, end, region in motif_dic[motif]:
418 if start <= int(where) <= end:
419 out_handle.write("{0}\n".format(
420 "\t".join([
421 ID,
422 where,
423 region,
424 frm,
425 to,
426 str(AAwhere),
427 str(AAfrm),
428 str(AAto),
429 motif,
430 str(start),
431 str(end),
432 str(junk)
433 ])
434 ))
435
436
437
438 def mean(lst):
439 return (float(sum(lst)) / len(lst)) if len(lst) > 0 else 0.0
440
441
442 def median(lst):
443 lst = sorted(lst)
444 l = len(lst)
445 if l == 0:
446 return 0
447 if l == 1:
448 return lst[0]
449
450 l = int(l / 2)
451
452 if len(lst) % 2 == 0:
453 return float(lst[l] + lst[(l - 1)]) / 2.0
454 else:
455 return lst[l]
456
457 funcs = {"mean": mean, "median": median, "sum": sum}
458
459 directory = outfile[:outfile.rfind("/") + 1]
460 value = 0
461 valuedic = dict()
462
463 for fname in funcs.keys():
464 for gene in genes:
465 with open(directory + gene + "_" + fname + "_value.txt", 'r') as v:
466 valuedic[gene + "_" + fname] = float(v.readlines()[0].rstrip())
467 with open(directory + "all_" + fname + "_value.txt", 'r') as v:
468 valuedic["total_" + fname] = float(v.readlines()[0].rstrip())
469
470
471 def get_xyz(lst, gene, f, fname):
472 x = round(round(f(lst), 1))
473 y = valuedic[gene + "_" + fname]
474 z = str(round(x / float(y) * 100, 1)) if y != 0 else "0"
475 return (str(x), str(y), z)
476
477 dic = {"RGYW": RGYWCount, "WRCY": WRCYCount, "WA": WACount, "TW": TWCount}
478 arr = ["RGYW", "WRCY", "WA", "TW"]
479
480 for fname in funcs.keys():
481 func = funcs[fname]
482 foutfile = outfile[:outfile.rindex("/")] + "/hotspot_analysis_" + fname + ".txt"
483 with open(foutfile, 'w') as o:
484 for typ in arr:
485 o.write(typ + " (%)")
486 curr = dic[typ]
487 for gene in genes:
488 geneMatcher = geneMatchers[gene]
489 if valuedic[gene + "_" + fname] is 0:
490 o.write(",0,0,0")
491 else:
492 x, y, z = get_xyz([curr[x] for x in [y for y, z in genedic.iteritems() if geneMatcher.match(z)]], gene, func, fname)
493 o.write("," + x + "," + y + "," + z)
494 x, y, z = get_xyz([y for x, y in curr.iteritems() if not genedic[x].startswith("unmatched")], "total", func, fname)
495 #x, y, z = get_xyz([y for x, y in curr.iteritems()], "total", func, fname)
496 o.write("," + x + "," + y + "," + z + "\n")
497
498
499 # for testing
500 seq_motif_file = outfile[:outfile.rindex("/")] + "/motif_per_seq.txt"
501 with open(seq_motif_file, 'w') as o:
502 o.write("ID\tRGYW\tWRCY\tWA\tTW\n")
503 for ID in IDlist:
504 #o.write(ID + "\t" + str(round(RGYWCount[ID], 2)) + "\t" + str(round(WRCYCount[ID], 2)) + "\t" + str(round(WACount[ID], 2)) + "\t" + str(round(TWCount[ID], 2)) + "\n")
505 o.write(ID + "\t" + str(RGYWCount[ID]) + "\t" + str(WRCYCount[ID]) + "\t" + str(WACount[ID]) + "\t" + str(TWCount[ID]) + "\n")
506
507 if __name__ == "__main__":
508 main()