forked from rishabgit/genomic-info-from-papers
-
Notifications
You must be signed in to change notification settings - Fork 1
/
Variant_to_genome.py
623 lines (492 loc) · 30 KB
/
Variant_to_genome.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
#!/usr/bin/env python
# from __future__ import division
# from __future__ import print_function
import os.path
import argparse
import re
import gffutils
from pyfaidx import Fasta
from wbpreader.translation import translate_dict
from wbpreader.translation import vars_from_GFF
from wbpreader.translation import sub_is
from wbpreader.translation import var_abspos
from wbpreader.translation import calculate_flanks
"""
Script for generating variants Ace from mutation
"""
# TODO
# Make it work for variants on reverese strand too - DONE
# Implement sub-routine clone_from_gene in translation.py to get data for the field Mapping_target
# Mapping_target "Y48B6A" <-clone name
# Mapping_target "F13G3" <-clone name
# Calculate Source_location
# Source_location 200 "CHROMOSOME_I" 4393280 4393280
# Source_location 200 "CHROMOSOME_I" 6461401 6461401
# Compare Source_location to current ones - if there is overlap they may need to merge
#
epi = ('\
\n\
Takes input variant and transcripts, and generates ace-format data\n\
The inupt file should contain 3 columns: \n\
1. Gene name eg WBGene00007063\n\
2. Transcript name eg 2L52.1b\n\
3. Variant code eg V600E K342* or W256amber\n\
Example: \n\
WBGene00007065 3R5.1b Q214L \n\
WBGene00007064 2RSSE.1a L10K \n\
WBGene00007064 2RSSE.1b A4ochre \n\
WBGene00007064 2RSSE.1b S7amber \n\
\n\
Note: The genome fasta, protein fasta and GFF needs to be from the same source, and pertain \n\
to the genome and annotation the variant originates from \n\
Note: If the GFF contains variants with VEP results, a smaller ACE file will be created for \n\
those new ones overlapping with existing ones\n\
Note: Wormbase GFFs have to be pre-processed using the script \n\
\n\
\n\
\n\
')
# Describe what the script does
parser = argparse.ArgumentParser(description='This script generates ace files from mutations', epilog= epi, formatter_class=argparse.RawTextHelpFormatter)
# Get inputs
parser.add_argument('-i', '--input', default=None, dest='inp', action='store', required=True, help="Variant eg K342* or W256amber")
parser.add_argument('-p', '--protein', default=None, dest='pro', action='store', required=True, help="Protein fasta file")
parser.add_argument('-gff', '--gff', default=None, dest='gff', action='store', required=True, help="GFF file with full path")
parser.add_argument('-g', '--genome', default=None, dest='genome', action='store', required=True, help="Genome fasta file")
args = parser.parse_args()
def is_valid_file(arg):
if not os.path.isfile(arg):
print("The file does not exist!", arg)
exit(1)
else:
pass
#print ("File exists", arg)
#return open(arg, 'r') # return an open file handle
# print ("Do", args, args.inp)
is_valid_file( args.inp)
is_valid_file( args.pro)
# is_valid_file( args.gff)
# is_valid_file( args.genome)
# read the input file
inp = open(args.inp, 'r')
# Get a translation table
prots=translate_dict('all')
#print (prots)
# Get all known variants from GFF
known_vars = vars_from_GFF(args.gff)
#print (known_vars)
#exit(0)
# create an object of new bed file and open in to write data.
output=args.inp+".ace"
out = open(output, 'w')
vars={}
# Save the variants and transcripts
for r in inp:
a = r.split()
#print (a[0],a[1],sep='\t')
v=a[0]+':'+a[1]
if v in vars:
vars[v][a[2]]={}
vars[v][a[2]]['PUB']=a[3]
else:
vars[v]={}
vars[v][a[2]]={}
vars[v][a[2]]['PUB']=a[3]
# Read in the gff coords + chromosome
fn = gffutils.example_filename(args.gff)
#print(open(fn).read())
db = gffutils.create_db(fn, ':memory:')
# Make a hash containing the clones all transcripts belong to
clone={}
for t in vars:
a=t.split(':')
a[0]='Gene:'+a[0]
clone[a[1]]='n'
clone=clone_from_ts(gff,db,clone)
#for v in vars[t]:
# clone=clone_from_ts
# vars[t][v]['CLONE']=clone
quit()
# Calculate the absolute genome position and chr
for t in vars:
a=t.split(':')
a[0]='Gene:'+a[0]
#print (a[0],a[1],sep='\t',end='\t')
for v in vars[t]:
vari=re.split('(\d+)',v)
varelstart=int(vari[1])*int(3)
varelend=int(varelstart)+int(3)
#print (vari,varelstart,varelend)
try:
gene = db[a[0]]
except:
print("WARNING: Gene", a[0] , "not found in GFF file, skipped")
break
#print (v, gene['Name'],gene.start, gene.end, varelstart, sep='\t')
# ABSPOS calculation for genes on the positive strand
(chro,abspos,geneori)=var_abspos(gene,a[1],varelstart,db)
vars[t][v]['ABSPOS']=abspos
vars[t][v]['CHR']=chro
vars[t][v]['ORI']=geneori
# Read in the genomic sequences
fas = Fasta(args.genome)
# Check if the extracted regions match and look up the flanking sequences
# Extrapolate the alt
for t in vars:
a=t.split(':')
#a[0]='Gene:'+a[0]
#print (a[0],a[1],sep='\t',end='\t')
for v in vars[t]:
vari=re.split('(\d+)',v)
(varseq,left,right)=calculate_flanks(vars[t][v],fas,prots,vari[0])
(ref,alt)=sub_is(varseq, vari[2])
vars[t][v]['REF']=varseq
vars[t][v]['LEFT']=left
vars[t][v]['RIGHT']=right
vars[t][v]['ALT']=alt
# Produce the ace file
print ("produce_ace",'\n')
i=99000000
for t in vars:
i=i+1
a=t.split(':')
for v in vars[t]:
vari=re.split('(\d+)',v)
# See if the variant has been found before
varid="WBVar" + str(i)
ts=a[1]+'.1'
ts2=a[1]+'.2'
# Make stop codons general
vmod=v.replace('amber','*')
vmod=vmod.replace('opal','*')
vmod=vmod.replace('ochre','*')
# Variant is known since before, so we only add minimal data
if ts in known_vars:
if v in known_vars[ts]:
#print("Known vars", a[0], a[1],v , known_vars[a[1]][v])
(varid,chr,start,end)=known_vars[ts][v].split(':')
print ("KNOWN", varid,chr,start,end)
elif vmod in known_vars[ts]:
#print("Known vars", a[0], a[1],v , known_vars[a[1]][v])
(varid,chr,start,end)=known_vars[ts][vmod].split(':')
print ("KNOWN", varid,chr,start,end)
else:
print("KNOWN TS", a[0], ts,v, known_vars[ts])
pass
elif ts2 in known_vars:
if v in known_vars[ts2]:
#print("Known vars", a[0], a[1],v , known_vars[a[1]][v])
(varid,chr,start,end)=known_vars[ts2][v].split(':')
print ("KNOWN", varid,chr,start,end)
elif vmod in known_vars[ts2]:
#print("Known vars", a[0], a[1],v , known_vars[a[1]][v])
(varid,chr,start,end)=known_vars[ts2][vmod].split(':')
print ("KNOWN", varid,chr,start,end)
else:
print("KNOWN TS", a[0], ts2,v, known_vars[ts2])
pass
# This is a new variant, so we add as much information as we can
else:
print("NOT KNOWN vars", ts,v)
pass
print ("Variation : \"", varid , "\"", sep='')
print ("Evidence\t ", "Paper_evidence \"", vars[t][v]['PUB'], "\"", sep='')
print("Transcript\t \"",a[1],".1\" Missense ", vari[1], " \"", vari[0] , " to ", vari[2],"\"",sep='')
#Transcript "Y51H7C.11.1" Missense 151 "G to E"
print ("Substitution ", "\"",vars[t][v]['REF'] , "\" \"", vars[t][v]['ALT'] , "\" Paper_evidence \"", vars[t][v]['PUB'] ,"\"",sep='') # Sequence_details Type_of_mutation
if vars[t][v]['ORI']=='+':
try:
print("Source_location 200 \"CHROMOSOME_", vars[t][v]['CHR'] , "\" " , vars[t][v]['ABSPOS'] , " ", vars[t][v]['ABSPOS']+2 , sep='')
except:
pass
elif vars[t][v]['ORI']=='-':
try:
print("Source_location 200 \"CHROMOSOME_", vars[t][v]['CHR'] , "\" " , vars[t][v]['ABSPOS'] , " ", vars[t][v]['ABSPOS']+2 , sep='')
except:
pass
else:
print("WARNING: this should not happen")
try:
print("HGVSg\t \"CHROMOSOME_",vars[t][v]['CHR'] ,':g.',vars[t][v]['ABSPOS'],ref,'>',alt, "\"", sep='')
#HGVSg "CHROMOSOME_V:g.20824795C>T"
#HGVSg "CHROMOSOME_V:g.20821901C>T"
except:
pass
try:
print ("Sequence_details Flanking_sequences \"", vars[t][v]['LEFT'] , "\" \"" , vars[t][v]['RIGHT'] ,"\"",sep='')
except:
pass
print("Sequence_details SeqStatus Sequenced")
print("Variation_type Allele")
print("Variation_type Predicted_SNP")
print("Sequence_details Mapping_target \"###\"")
print("Species \"Caenorhabditis elegans\"")
print("Origin\t Status Live")
print("Method\t \"Substitution_allele\"")
print("Reference\t \"", vars[t][v]['PUB'], "\"" ,sep='')
print("Affects Gene \"", a[0], "\"", sep='')
print("Delete Not_sequenced or Pending_curation and replace with Sequenced")
print()
'''
Variation : "WBVar00000002" -O "2013-08-13_09:50:15_pad"
Evidence -O "2010-02-05_10:07:16_mt3" Paper_evidence -O "2010-02-05_10:07:16_mt3" "WBPaper00035215" -O "2010-02-05_10:07:16_mt3"
Name -O "2010-02-05_10:07:16_mt3" Public_name -O "2010-02-05_10:07:16_mt3" "ac1" -O "2010-02-05_10:07:16_mt3"
Sequence_details -O "2010-02-05_10:07:16_mt3" Flanking_sequences -O "2010-02-05_10:07:16_mt3" "aattcgaaaaagtcgagttcacagccggtg" -O "2010-02-05_10:07:16_mt3" "agcccacagagatgacccaattttcgcgg
a" -O "2010-02-05_10:07:16_mt3"
Sequence_details -O "2010-02-05_10:07:16_mt3" Mapping_target -O "2012-12-14_16:52:32_mt3" "Y51H7C" -O "2012-12-14_16:52:32_mt3"
Sequence_details -O "2010-02-05_10:07:16_mt3" Type_of_mutation -O "2010-02-05_10:07:16_mt3" Substitution -O "2010-02-05_10:07:16_mt3" "g" -O "2010-02-05_10:07:16_mt3" "a" -O "2010-02-05_10:07:16_mt3" Paper_evidence -O "2010-02-05_10:07:16_mt3" "WBPaper00035215" -O "2010-02-05_10:07:16_mt3"
Sequence_details -O "2010-02-05_10:07:16_mt3" SeqStatus -O "2010-02-05_10:07:16_mt3" Sequenced -O "2010-02-05_10:07:16_mt3"
Variation_type -O "2010-02-05_10:07:16_mt3" Allele -O "2010-02-05_10:07:16_mt3"
Origin -O "2009-11-19_10:37:46_CGC_strain_update" Species -O "2010-02-05_10:07:16_mt3" "Caenorhabditis elegans" -O "2010-02-05_10:07:16_mt3"
Origin -O "2009-11-19_10:37:46_CGC_strain_update" Strain -O "2018-03-09_15:35:45_CGC_strain_update" "WBStrain00000321" -O "2018-03-09_15:35:45_CGC_strain_update"
Origin -O "2009-11-19_10:37:46_CGC_strain_update" Laboratory -O "2010-02-05_10:07:16_mt3" "AY" -O "2010-02-05_10:07:16_mt3"
Origin -O "2009-11-19_10:37:46_CGC_strain_update" Status -O "2010-09-14_09:18:54_mt3" Live -O "2010-09-14_09:18:54_mt3"
Affects -O "2009-11-19_10:45:16_CGC_strain_update" Gene -O "2009-11-19_10:45:16_CGC_strain_update" "WBGene00021789" -O "2009-11-19_10:45:16_CGC_strain_update"
Reference -O "2010-05-04_10:16:36_mt3" "WBPaper00035215" -O "2010-05-04_10:16:36_mt3"
Reference -O "2010-05-04_10:16:36_mt3" "WBPaper00047105" -O "2015-10-21_16:22:47_caltech_Paper"
Method -O "2010-02-05_10:07:16_mt3" "Substitution_allele" -O "2010-02-05_10:07:16_mt3"
Variation : "WBVar00000007" -O "2013-08-13_09:45:32_pad"
Evidence -O "2004-03-19_17:26:22_ck1" Author_evidence -O "2004-03-19_17:26:22_ck1" "Curtis L" -O "2004-03-19_17:26:22_ck1"
Name -O "2005-02-11_17:13:21_mt3" Public_name -O "2006-08-08_10:18:36_Public_name_patch" "ad446" -O "2006-08-08_10:18:36_Public_name_patch"
Sequence_details -O "2004-03-19_17:26:22_ck1" Flanking_sequences -O "2004-03-19_17:26:22_ck1" "agactgggcaaaaatctttgacgatctcgaaaatgtggtggtgaa" -O "2004-03-24_12:40:04_ck1" "aaaatacaaaataa
tgaagtaggcacgtgtatgtaggcag" -O "2004-03-24_12:40:04_ck1"
Sequence_details -O "2004-03-19_17:26:22_ck1" Mapping_target -O "2012-12-14_16:52:32_mt3" "C05D2"C05D2" -O "2012-12-14_16:52:32_mt3"
Variation : "WBVar00000009" -O "2013-08-13_09:50:15_pad"
Evidence -O "2004-09-17_15:15:15_rem" Paper_evidence -O "2004-09-17_15:15:15_rem" "WBPaper00006439" -O "2004-09-17_15:15:15_rem"
Name -O "2005-02-11_17:13:21_mt3" Public_name -O "2006-08-08_10:18:36_Public_name_patch" "ad451" -O "2006-08-08_10:18:36_Public_name_patch"
Sequence_details -O "2004-09-17_15:15:15_rem" Flanking_sequences -O "2004-09-17_15:15:15_rem" "aatgactacaaactacgatggtctcctgag" -O "2004-09-17_15:15:15_rem" "agtacggtaatattactacgttgcaaatt
c" -O "2004-09-17_15:15:15_rem"
Sequence_details -O "2004-09-17_15:15:15_rem" Mapping_target -O "2012-12-14_16:52:32_mt3" "Y48B6A" -O "2012-12-14_16:52:32_mt3"
Sequence_details -O "2004-09-17_15:15:15_rem" Type_of_mutation -O "2004-09-17_15:15:15_rem" Substitution -O "2004-09-17_15:15:15_rem" "g" -O "2008-05-02_10:12:16_mt3" "a" -O "2004-09-17_
15:15:15_rem"
Sequence_details -O "2004-09-17_15:15:15_rem" SeqStatus -O "2006-02-23_16:08:40_mt3" Sequenced -O "2006-02-23_16:08:40_mt3"
Variation_type -O "2005-02-09_11:38:48_mt3" Allele -O "2005-02-09_11:38:48_mt3"
Origin -O "2005-01-31_16:47:30_ar2" Species -O "2003-07-21_12:08:26_ck1" "Caenorhabditis elegans" -O "2003-07-21_12:08:26_ck1"
Origin -O "2005-01-31_16:47:30_ar2" Laboratory -O "2004-05-17_13:53:37_ck1" "DA" -O "2004-05-17_13:53:37_ck1"
Origin -O "2005-01-31_16:47:30_ar2" Status -O "2005-05-25_17:33:42_mt3" Live -O "2005-05-25_17:33:42_mt3"
Affects -O "2004-04-07_11:23:34_wormpub" Gene -O "2004-04-07_11:23:34_wormpub" "WBGene00001133" -O "2004-04-07_11:23:34_wormpub"
Reference -O "2010-04-01_13:56:13_mt3" "WBPaper00017350" -O "2010-04-01_13:56:13_mt3"
Reference -O "2010-04-01_13:56:13_mt3" "WBPaper00015559" -O "2010-04-01_13:56:13_mt3"
Method -O "2003-01-06_10:01:54_ck1" "Substitution_allele" -O "2004-09-17_15:15:15_rem"
Variation : "WBVar02153522" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021"
Evidence -O "2021-07-10_01:45:23_curation_Variation" Person_evidence -O "2021-07-10_01:45:23_curation_Variation" "WBPerson1928" -O "2021-07-10_01:45:23_curation_Variation"
Name -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" Public_name -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "ix259" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021"
Sequence_details -O "2021-07-10_01:45:23_curation_Variation" Flanking_sequences -O "2021-07-10_01:45:23_curation_Variation" "cattcttgttcggctttttcgagacgttct" -O "2021-07-10_01:45:23_curation_Variation" "tgaaaaataatttttttttggaaattttct" -O "2021-07-10_01:45:23_curation_Variation"
Sequence_details -O "2021-07-10_01:45:23_curation_Variation" Mapping_target -O "2021-07-10_01:45:23_curation_Variation" "F15D3" -O "2021-07-10_01:45:23_curation_Variation"
Sequence_details -O "2021-07-10_01:45:23_curation_Variation" Type_of_mutation -O "2021-07-10_01:45:23_curation_Variation" Substitution -O "2021-07-10_01:45:23_curation_Variation" "c" -O "2021-07-10_01:45:23_curation_Variation" "t" -O "2021-07-10_01:45:23_curation_Variation"
Sequence_details -O "2021-07-10_01:45:23_curation_Variation" SeqStatus -O "2021-07-10_01:45:23_curation_Variation" Sequenced -O "2021-07-10_01:45:23_curation_Variation"
Affects -O "2021-07-10_01:45:07_curation_Gene" Gene -O "2021-07-10_01:45:07_curation_Gene" "WBGene00001131" -O "2021-07-10_01:45:07_curation_Gene"
Possibly_affects -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "WBGene00001131" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" Paper_evidence -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "WBPaper00060694" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021"
Possibly_affects -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "WBGene00001131" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" Remark -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "CGC_name dys-1" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021"
Isolation -O "2021-07-10_01:45:23_curation_Variation" Mutagen -O "2021-07-10_01:45:23_curation_Variation" "EMS" -O "2021-07-10_01:45:23_curation_Variation"
Isolation -O "2021-07-10_01:45:23_curation_Variation" Forward_genetics -O "2021-07-10_01:45:23_curation_Variation" "standard phenotypic screen" -O "2021-07-10_01:45:23_curation_Variation"
Reference -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "WBPaper00060694" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021"
Remark -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "[2021-07-07T15:47:18.438Z WBPerson51134] New Variation: Reference WBPaper00060694\; Gene WBGene00001131 (dys-1)" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" Curator_confirmed -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "WBPerson51134" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021"
Remark -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "alt_det = g to a mut_det = ag to aa" -O "2021-07-10_01:45:23_curation_Variation" Paper_evidence -O "2021-07-10_01:45:23_curation_Variation" "WBPaper00060694" -O "2021-07-10_01:45:23_curation_Variation"
Remark -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "alt_det = g to a mut_det = ag to aa" -O "2021-07-10_01:45:23_curation_Variation" Person_evidence -O "2021-07-10_01:45:23_curation_Variation" "WBPerson1928" -O "2021-07-10_01:45:23_curation_Variation"
Remark -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "alt_det = g to a mut_det = ag to aa" -O "2021-07-10_01:45:23_curation_Variation" Curator_confirmed -O "2021-07-10_01:45:23_curation_Variation" "WBPerson51134" -O "2021-07-10_01:45:23_curation_Variation"
Remark -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "Variation information submitted by WBPerson1928 on 2021-04-23_02:24:25 via the Allele submission form." -O "2021-07-10_01:45:23_curation_Variation" Curator_confirmed -O "2021-07-10_01:45:23_curation_Variation" "WBPerson51134" -O "2021-07-10_01:45:23_curation_Variation"
Method -O "2021-07-10_01:45:23_curation_Variation" "Substitution_allele" -O "2021-07-10_01:45:23_curation_Variation"
Variation : "WBVar02153521" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021"
Evidence -O "2021-07-10_01:45:23_curation_Variation" Person_evidence -O "2021-07-10_01:45:23_curation_Variation" "WBPerson1928" -O "2021-07-10_01:45:23_curation_Variation"
Name -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" Public_name -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "ix261" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021"
Sequence_details -O "2021-07-10_01:45:23_curation_Variation" Flanking_sequences -O "2021-07-10_01:45:23_curation_Variation" "CACAAACCATAAGTAGTCAAATTGAATACT" -O "2021-07-10_01:45:23_curation_Variation" "CTAGCCGATCTCCTGCCAGTGAATCGGCAC" -O "2021-07-10_01:45:23_curation_Variation"
Sequence_details -O "2021-07-10_01:45:23_curation_Variation" Mapping_target -O "2021-07-10_01:45:23_curation_Variation" "R06C1" -O "2021-07-10_01:45:23_curation_Variation"
Sequence_details -O "2021-07-10_01:45:23_curation_Variation" Type_of_mutation -O "2021-07-10_01:45:23_curation_Variation" Substitution -O "2021-07-10_01:45:23_curation_Variation" "C" -O "2021-07-10_01:45:23_curation_Variation" "T" -O "2021-07-10_01:45:23_curation_Variation"
Sequence_details -O "2021-07-10_01:45:23_curation_Variation" SeqStatus -O "2021-07-10_01:45:23_curation_Variation" Sequenced -O "2021-07-10_01:45:23_curation_Variation"
Origin -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" Species -O "2021-07-10_01:45:23_curation_Variation" "Caenorhabditis elegans" -O "2021-07-10_01:45:23_curation_Variation"
Origin -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" Strain -O "2021-07-10_01:45:23_curation_Variation" "WBStrain00048692" -O "2021-07-10_01:45:23_curation_Variation"
Origin -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" Production_method -O "2021-07-10_01:45:23_curation_Variation" CRISPR_Cas9 -O "2021-07-10_01:45:23_curation_Variation"
Origin -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" Status -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" Live -O "2021-07-10_01:44:05_NewNS_data_ace_10072021"
Affects -O "2021-07-10_01:45:07_curation_Gene" Gene -O "2021-07-10_01:45:07_curation_Gene" "WBGene00001836" -O "2021-07-10_01:45:07_curation_Gene"
Possibly_affects -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "WBGene00001836" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" Paper_evidence -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "WBPaper00060694" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021"
Possibly_affects -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "WBGene00001836" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" Remark -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "CGC_name hda-3" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021"
Reference -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "WBPaper00060694" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021"
Remark -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "[2021-07-07T13:24:49.168Z WBPerson51134] New Variation: Reference WBPaper00060694\; allele of WBGene00001836 (hda-3)" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" Curator_confirmed -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "WBPerson51134" -O "2021-07-10_01:44:05_NewNS_data_ace_10072021"
Remark -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "OF1355 strain also has a synonymous mutation (g to a) at R(269)." -O "2021-07-10_01:45:23_curation_Variation" Paper_evidence -O "2021-07-10_01:45:23_curation_Variation" "WBPaper00060694" -O "2021-07-10_01:45:23_curation_Variation"
Remark -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "OF1355 strain also has a synonymous mutation (g to a) at R(269)." -O "2021-07-10_01:45:23_curation_Variation" Person_evidence -O "2021-07-10_01:45:23_curation_Variation" "WBPerson1928" -O "2021-07-10_01:45:23_curation_Variation"
Remark -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "OF1355 strain also has a synonymous mutation (g to a) at R(269)." -O "2021-07-10_01:45:23_curation_Variation" Curator_confirmed -O "2021-07-10_01:45:23_curation_Variation" "WBPerson51134" -O "2021-07-10_01:45:23_curation_Variation"
Remark -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "alt_det = g to a mut_det = G(271)E" -O "2021-07-10_01:45:23_curation_Variation" Paper_evidence -O "2021-07-10_01:45:23_curation_Variation" "WBPaper00060694" -O "2021-07-10_01:45:23_curation_Variation"
Remark -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "alt_det = g to a mut_det = G(271)E" -O "2021-07-10_01:45:23_curation_Variation" Person_evidence -O "2021-07-10_01:45:23_curation_Variation" "WBPerson1928" -O "2021-07-10_01:45:23_curation_Variation"
Remark -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "alt_det = g to a mut_det = G(271)E" -O "2021-07-10_01:45:23_curation_Variation" Curator_confirmed -O "2021-07-10_01:45:23_curation_Variation" "WBPerson51134" -O "2021-07-10_01:45:23_curation_Variation"
Remark -O "2021-07-10_01:44:05_NewNS_data_ace_10072021" "Variation information submitted by WBPerson1928 on 2021-04-22_19:21:33 via the Allele submission form." -O "2021-07-10_01:45:23_curation_Variation" Curator_confirmed -O "2021-07-10_01:45:23_curation_Variation" "WBPerson51134" -O "2021-07-10_01:45:23_curation_Variation"
Method -O "2021-07-10_01:45:23_curation_Variation" "Engineered_allele" -O "2021-07-10_01:45:23_curation_Variation"
Variation : "WBVar02153513" -O "2021-06-23_17:11:25_pad"
Name -O "2021-07-12_00:35:14_Variation_public_name_ace" Public_name -O "2021-07-12_00:35:14_Variation_public_name_ace" "xf61" -O "2021-07-12_00:35:14_Variation_public_name_ace"
Sequence_details -O "2021-06-23_17:11:25_pad" SeqStatus -O "2021-06-23_17:11:25_pad" Pending_curation -O "2021-06-23_17:11:25_pad"
Variation_type -O "2021-06-23_17:11:25_pad" Engineered_allele -O "2021-06-23_17:11:25_pad"
Origin -O "2021-06-23_17:11:25_pad" Species -O "2021-06-23_17:11:25_pad" "Caenorhabditis elegans" -O "2021-06-23_17:11:25_pad"
Origin -O "2021-06-23_17:11:25_pad" Strain -O "2021-06-23_17:11:25_pad" "WBStrain00048727" -O "2021-06-23_17:11:25_pad"
Origin -O "2021-06-23_17:11:25_pad" Strain -O "2021-06-23_17:11:25_pad" "WBStrain00048721" -O "2021-06-23_17:11:25_pad"
Origin -O "2021-06-23_17:11:25_pad" Laboratory -O "2021-06-23_17:11:25_pad" "RFK" -O "2021-06-23_17:11:25_pad"
Origin -O "2021-06-23_17:11:25_pad" Production_method -O "2021-06-23_17:11:25_pad" CRISPR_Cas9 -O "2021-06-23_17:11:25_pad"
Origin -O "2021-06-23_17:11:25_pad" Status -O "2021-06-23_17:11:25_pad" Live -O "2021-06-23_17:11:25_pad"
Method -O "2021-06-23_17:11:25_pad" "Engineered_allele" -O "2021-06-23_17:11:25_pad"
'''
out.close()
quit()
'''
#### FILTER OUT #####
# Shared called total
# Filter out sites which
chr = r.chrom
pos = r.pos
id = str(r.id)
varID=':'.join([id.split(":")[0],id.split(":")[1]])
#altb = r.ref
#altb = r.alts
score = r.qual
filter = r.filter
info = r.info
format = r.format
samples = r.samples
end = r.stop # r.info["END"]
strand='.'
svtype='NA'
if 'SVTYPE' in r.info.keys():
svtype = r.info.get('SVTYPE', "")
#for key in r.info.keys():
# data = r.info.get(key, "")
# print (key,data)
# svtype=r.info['SVTYPE']
# FORMAT
#['PR', 'SR', 'RC', 'BC', 'CN', 'MCC']
# Split out Manta calls
if re.match(r'Manta', varID):
pass
#print("Manta",chr, pos, end, varID, score, strand, sep='\t')
#print (list((r.header.filters)))
#print(list((r.header.formats)))
elif re.match(r'Canvas', varID):
# Extract relevant information
cn='NA'
mcc='NA'
filter='NA'
rc='NA'
if 'CN' in r.samples[0].keys():
cn=r.samples[0]['CN']
if 'MCC' in r.samples[0].keys():
mcc=r.samples[0]['MCC']
if 'RC' in r.samples[0].keys():
rc=r.samples[0]['RC']
for key in r.filter.keys():
filter=key
print (chr,pos,end,varID,score,strand,filter,svtype,rc,cn,mcc,sep='\t', file=out)
else:
print("Unknown",chr, pos, end, varID, score, strand, sep='\t')
out.close()
'''
"""
# open up file
with open(args.vcf, 'rb') as csvfile:
reader = csv.reader(csvfile, delimiter ='\t')
for row in reader:
tsvout =""
# pass header
if row[0].startswith("#"):
pass
# CANVAS
# only count canvas if Gain or Loss
elif "Canvas" in row[2] and "REF" not in row[2]:
# add to tsv file
varID= row[2].split(":")
end = row[7].split('END=')[-1]
# if fist line do not add line break
if len(tsvout) < 1:
# sample chr start end QUAL Filter tool change
tsvout += sample + "\t"+ row[0] + "\t"+ row[1]+ "\t"+ end +"\t"+ row[5]+"\t"+ row[6] +\
"\t"+ varID[0]+ "\t"+ varID[1]
else:
tsvout += "\n"+ sample + "\t"+ row[0] + "\t"+ row[1]+ "\t"+ end +"\t"+ row[5]+"\t"+ row[6] + \
"\t" + varID[0]+ "\t"+ varID[1]
# add to tallies
if "PASS" in row:
canvasT += 1
if "LOSS" in row[2]:
canvasLoss += 1
elif "GAIN" in row[2]:
canvasGain += 1
print(tsvout)
# MANTA
# tally up Manta outputs
elif "Manta" in row[2]:
# find SV type
varID = row[2].split(":")
QUAL = "."
vcffilter = "."
end = "."
# identify translocations
if "MantaBND" in row[2]:
# No Ends in BND cases as they are translocations - add N/A to end field for the TSV
end = "."
QUAL = "."
vcffilter = row[6]
# add to tallys
if "PASS" in row:
MantaT += 1
MantaBND += 1
# identify Dels - can be problematic
elif "MantaDEL" in row[2]:
# some Dels columns out of sync with no ref or QUAL field so need to find end value from appropated field
if len(row) ==11:
end = row[7].split(';')[0]
QUAL = row[5]
vcffilter = row[6]
elif len(row) < 11:
#check which column end and Filter criteria are in
if "END=" in row[5]:
end = row[5].split(';')[0]
QUAL = "."
vcffilter = row[4]
elif "END=" in row[6]:
end = row[6].split(';')[0]
QUAL = "."
vcffilter = row[4]
else:
pass
else:
pass
end = "".join(i for i in end if i.isdigit())
# add to tallys
if "PASS" in row:
MantaT += 1
MantaDEL += 1
# Finds invs
elif "MantaINV" in row[2]:
end = row[7].split(';')[0]
end = "".join(i for i in end if i.isdigit())
QUAL = row[5]
vcffilter = row[6]
# add to tallys
if "PASS" in row:
MantaT += 1
MantaINV += 1
# find DUPs
elif "MantaDUP" in row[2]:
end = row[7].split(';')[0]
end = "".join(i for i in end if i.isdigit())
QUAL = row[5]
vcffilter = row[6]
# add to tallys
if "PASS" in row:
MantaT += 1
MantaDUP += 1
# write to tsv. If first record do not add the \n
if len(tsvout) < 1:
# sample chr start end QUAL Filter tool change
tsvout += sample + "\t" + row[0] + "\t" + row[1] + "\t" + end + "\t" + QUAL + "\t" + vcffilter + \
"\tManta\t" + varID[0]
else:
tsvout += "\n" + sample + "\t" + row[0] + "\t" + row[1] + "\t" + end + "\t" + QUAL + "\t" + vcffilter + \
"\tManta\t" + varID[0]
print(tsvout)
else:
pass
tally_out = open(output, 'w')
tally_out.write("Sample\tcanvas_Total\tcanvas_Gain\tcanvas_Loss\tManta_Total\tManta_BND\tManta_DEL\tManta_INV\tMantaDUP\n")
tally_out.write(str(sample) + "\t" + str(canvasT)+ "\t" + str(canvasGain) + "\t" + str(canvasLoss)+ "\t" +
str(MantaT) + "\t" + str(MantaBND)+ "\t" + str(MantaDEL)+ "\t" +str(MantaINV) +"\t" + str(MantaDUP) + "\n")
tally_out.close()
"""
out.close()
exit(0)