-
Notifications
You must be signed in to change notification settings - Fork 1
/
gene_finder.py
585 lines (498 loc) · 24.8 KB
/
gene_finder.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
import sys, os, re, glob
import subprocess
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import generic_dna
from Bio.Alphabet import IUPAC
def Translator(infile, datahandler2):
datahandler_list2 = []
datahandler_nucl_list2 = []
for seq_record in SeqIO.parse(infile, 'fasta'): ###PMH: removed iupac designation
for i in range(3): #(i=0 - i=1 - i=2)
s = seq_record.seq[i:] #starts the sequence at the open reading frame "i" (0, 1, or 2)
while len(s)%3 != 0: # add N to the end of the region if not devisable by 3
s += 'N'
translated_record = SeqRecord(seq=s.translate(table=1), id=seq_record.id, description=seq_record.description+' frame='+str(i))
datahandler_list2.append(translated_record)
s = seq_record.seq[:-i].reverse_complement() #reverse complements the sequence
while len(s)%3 != 0: # add N to the end of the region if not devisable by 3
s += 'N'
translated_record = SeqRecord(seq=s.translate(table=1), id=seq_record.id+"_reverse_complement", description="frame="+str(i))
datahandler_list2.append(translated_record)
SeqIO.write(datahandler_list2, datahandler2, 'fasta')
print('-'*20)
print('// Translated sequence to amino acids')
print('-'*20)
def OrfFinder(datahandler2, min_prot_len, datahandler3, orfs, max_prot_len, max_d2m): #orfs is a blank, it is not duplicating up/down regions
u=0
unique_orfs=[]
for seq_record in SeqIO.parse(datahandler2, 'fasta', IUPAC.protein):
genomic_region_start = int(seq_record.description.split('region:')[1].split('_')[0])
genomic_region_stop = int(seq_record.description.split('region:')[1].split('_')[1].split(' ')[0])
frame = int(seq_record.description.split('frame=')[1].split('\n')[0])
if str(seq_record.description.split(' ')[0].split('_')[-1]) == str("complement"):
rc = True
else:
rc = False
MetStop(seq_record.seq, seq_record.id, genomic_region_start, genomic_region_stop, min_prot_len, datahandler3, orfs, max_prot_len, max_d2m, frame, rc,u,seq_record)
u+=1
SeqIO.write(orfs, datahandler3, 'fasta')
'''
for o in orfs:
if '_us' in o.id:
check_name=o.id.split('_us')[0]
check_location=o.id.split('|')[1]+'|'
elif '_upstream' in o.id:
check_name=o.id.split('_upstream')[0]
check_location=o.id.split('|')[1]+'|'
else:
check_name=o.id.split('_ds')[0]
check_location=o.id.split('|')[1]+'|'
if 'reverse_complement' in o.id:
unique_orf_record=o
unique_orf_record.id=check_name+'_r_'+check_location
unique_orfs.append(unique_orf_record)
else:
unique_orf_record=o
unique_orf_record.id=check_name+check_location
unique_orfs.append(unique_orf_record)
SeqIO.write(unique_orfs, datahandler3.split('.fasta')[0]+'_unique_names.fasta', 'fasta')
'''
#print [all_orfs]
#with open (datahandler3+'_test.fasta','w') as file:
# file.writelines(str(all_orfs))
# file.close()
#print int(1/0)
#print u
print('// Wrote %s protein sequences with a mimp IR motif in their promoter and an ORF >%i and <%i aa to %s' % (len(orfs), min_prot_len, max_prot_len, datahandler3))
print('-'*20)
def MetStop(sequence, ident, genomic_region_start, genomic_region_stop, min_prot_len, datahandler3, orfs, max_prot_len, max_d2m, frame, rc,u, seq_record): #frame removec
met_location = [i for i, a in enumerate(sequence) if a == 'M']
#print [met_location]
region_length = int(genomic_region_stop)-int(genomic_region_start) #for calculating start/stop locations for orfs in reverse complement of up/down region
#print len(orfs)
add_to_orfs=True
x=0
while x<len(met_location):
if met_location[x] >= 0:# and stop_location>=0:
stop_location = sequence.find('*', met_location[x])
#print stop_location, "stop"
if stop_location>0:
prot = sequence[met_location[x]:stop_location+1] #+1 = add STOP
if rc == False:
if frame == 0:
dist_to_start = (met_location[x]*3)
dist_to_stop = (stop_location*3)
if frame == 1:
dist_to_start = ((met_location[x]*3)+1)
dist_to_stop = ((stop_location*3)+1)
if frame == 2:
dist_to_start = ((met_location[x]*3)+2)
dist_to_stop = ((stop_location*3)+2)
if len(prot) > min_prot_len:
startpos = genomic_region_start+dist_to_start
endpos = genomic_region_start+dist_to_stop
orf_record = SeqRecord(seq=prot.strip('*'), id=str(ident).replace('downstream', 'ds').replace('upstream', 'us') +"|"+str(startpos)+'-'+str(endpos)+'|d2m:'+str(dist_to_start)+'|len:'+str(len(prot)-1)+"|rc="+str(rc), description='')
if len(prot) < int(max_prot_len):
if '_us' in orf_record.id:
check_name=orf_record.id.split('_us')[0]
check_location='|'+str(startpos)+'-'+str(endpos)+'|'
elif '_upstream' in orf_record.id:
check_name=orf_record.id.split('_upstream')[0]
check_location='|'+str(startpos)+'-'+str(endpos)+'|'
else:
check_name=orf_record.id.split('_ds')[0]
check_location='|'+str(startpos)+'-'+str(endpos)+'|'
t=0
#while t<len(orfs):
#if '1191186-1191414' in str(orfs[t].id) and '1191186-1191414' in check_location:
# print [orfs[t].id]
# print [check_name],[check_location]
# print check_name
# print ident.split('_downstream')[0], '\n\n'
#if check_name in orfs[t].id and check_location in orfs[t].id:
# if '1191186-1191414' in str(orfs[t].id):
# print "huh"
# t=len(orfs)+3
#t+=1
for o in orfs:
if check_name in o.id and check_location in o.id:
#if '1191186-1191414' in str(o.id):
# print "huh"
add_to_orfs=False
if add_to_orfs:
#if t!=len(orfs)+3:
orf_record.id='id'+str(u)+'_'+str(x)+'_'+orf_record.id
orfs.append(orf_record)
#if '1191186-1191414' in str(orf_record):
# print 'test ', u, seq_record.id, seq_record.description, '\n', orf_record.id
# print orfs[-1].id
#print 'fail'
# print check_name
# print check_location
else:
if frame == 0:
dist_to_start = (region_length-met_location[x]*3)
dist_to_stop = (region_length-stop_location*3)
if frame == 1:
dist_to_start = ((region_length-met_location[x]*3)-1)
dist_to_stop = ((region_length-stop_location*3)-1)
if frame == 2:
dist_to_start = ((region_length-met_location[x]*3)-2)
dist_to_stop = ((region_length-stop_location*3)-2)
if len(prot) > min_prot_len:
startpos = genomic_region_start+dist_to_start
endpos = genomic_region_start+dist_to_stop
orf_record = SeqRecord(seq=prot.strip('*'), id=str(ident).replace('downstream', 'ds').replace('upstream', 'us') +"|"+str(startpos)+'-'+str(endpos)+'|d2m:'+str(dist_to_start)+'|len:'+str(len(prot)-1)+"|rc="+str(rc), description='')
if len(prot) < int(max_prot_len):
if '_us' in orf_record.id:
check_name=orf_record.id.split('_us')[0]
check_location='|'+str(startpos)+'-'+str(endpos)+'|'
elif '_upstream' in orf_record.id:
check_name=orf_record.id.split('_upstream')[0]
check_location='|'+str(startpos)+'-'+str(endpos)+'|'
else:
check_name=orf_record.id.split('_ds')[0]
check_location='|'+str(startpos)+'-'+str(endpos)+'|'
for o in orfs:
if check_name in o.id and check_location in o.id:
#if '1191186-1191414' in str(o.id):
# print "huh"
add_to_orfs=False
if add_to_orfs:
#if t!=len(orfs)+3:
orf_record.id='temp_id'+str(u)+'_'+orf_record.id
orfs.append(orf_record)
#if 'reverse_complement' in orf_record.id:
# unique_orf_record=orf_record
# unique_orf_record.id=check_name+'_r_'+check_location
# unique_orfs.append(unique_orf_record)
#else:
# unique_orf_record=orf_record
# unique_orf_record.id=check_name+check_location
# unique_orfs.append(unique_orf_record)
#if '1191186-1191414' in str(orf_record):
# print 'test ', u, seq_record.id, seq_record.description, '\n', orf_record.id
#print 'fail'
# print check_name
# print check_location
x+=1
#return orfs
#####important
def OrfWriter(datahandler3, signalpfile, min_prot_len, proteinoutfile, SignalPpath, SignalP_threshold,outdirectory):
RunSignalP(datahandler3, signalpfile, 'euk', SignalPpath, SignalP_threshold,outdirectory)
SPorfs = []
files = os.listdir(outdirectory)
orfs = SeqIO.parse(datahandler3, 'fasta', IUPAC.protein)
with open( datahandler3, 'r') as file:
data=file.readlines()
file.close()
test =True
test2 =True
test3 =True
x=0
check =[]
for file in files:
if '.summary_out' in file:
with open(outdirectory+file, 'r') as sp:
temp_file=sp.readlines()
sp.close()
for line in temp_file:
if 'Name=' in line:
sp_name = line.split('Name=')[1].split('\tSP=')[0]
x=0
for orf in data:
if '>' in orf:
orf_id=orf.split('>')[1].split(' ')[0]
if sp_name in orf_id:
sp_present = line.split('\tSP=\'')[1].split('\'')[0] # SP: YES OR NO
orf_id += '|SP=' + sp_present
orf_id += ';D='+line.split(' D=0')[1].split(' ')[0] # SP D-value
if 'Y' in sp_present:
y=x+1 #add all seqence parts together
orf_seq=''
while y<len(data) and "|" not in data[y]:
orf_seq+=data[y].split("\n")[0]
y+=1
cleavage_site_pos1 = line.split('Cleavage site between pos. ')[1].split(' and ')[0]
cleavage_site_pos2 = line.split('Cleavage site between pos. ')[1].split(' and ')[1].split(': ')[0]
if 'X' not in (orf_seq[:int(cleavage_site_pos2)-1]): #prevent 'NNN' translated to 'X' in signalpeptides to end up in the list
temp_id=''
for i in orf_id:
if i==',':
temp_id+=''
else:
temp_id+=i
orf_id=temp_id
signalpeptideseq = str(orf_seq[:int(cleavage_site_pos2)-1])
seq = str(signalpeptideseq.lower()+orf_seq[int(cleavage_site_pos2)-1:].upper())
orfie=orf.replace('\n','')+' signalpeptideseq='+signalpeptideseq+'\n'+seq+"\n\n"
if orfie not in SPorfs:
SPorfs.append(orfie)
x+=1
sp.close()
list(set(SPorfs))
print(' Total # of sequences matching the criteria: %i' % len(SPorfs))
#print [SPorfs[0:3]]
with open(proteinoutfile, 'w') as file:
file.writelines(SPorfs)
file.close()
def RunSignalP(datahandler3, signalpfile, organism, SignalPpath, SignalP_threshold,outdirectory):
print('// Parsing data into batches...')
with open(datahandler3, 'r') as file:
data =file.readlines()
file.close()
if len(data) >20000:
x=1
storage=[]
temp=[]
y=0
for seq in data:
if len(temp)>=9998 and ">" in seq:
storage.append(temp)
y+=1
temp=[]
temp.append(str(seq))
if len(storage) >10000:
end()
storage.append(temp)
y+=1
z=1
for s in storage:
with open(outdirectory+"split_data_"+str(z)+".fasta","w") as file:
file.writelines(s)
file.close()
z+=1
print("Number of batches made: "+str(y))
print('// Running SignalP 4.1 on batches...')
while y>0:
cline = SignalPpath+' -t %s -f summary -u %s %s > %s' % (organism, SignalP_threshold, outdirectory+"/split_data_"+str(y)+".fasta", signalpfile+str(y)+'.summary_out')
os.system(cline)
y-=1
# cline="rm -f "+ outdirectory+"split_data_*.fasta" #Removes previous iteration data
subprocess.check_output(['bash','-c', cline])
else:
print('// Running SignalP 4.1 on batches...')
cline = SignalPpath+' -t %s -f summary -u %s %s > %s' % (organism, SignalP_threshold, datahandler3, signalpfile+'.summary_out')
os.system(cline)
#####
def ExtractOrfToFasta(proteinsfasta, uberinfile, puteff_dnaseqs, genome, puteff_logfile, combined_puteff_fasta, combined_puteff_logfile, filecounter, combined_puteff_logfile2):
#EXTRACT GENOMIC SEQUENSE:
open(puteff_dnaseqs, 'wb').close() #clear genomic DNA sequence fastafile
dnaoutfile = open(puteff_dnaseqs, 'a')
open(puteff_logfile, 'wb').close()
logheader="genome\tputeff_supercontig\tgenomic_start_pos\tgenomic_end_pos\tdist2mimp\torientation\tprotlength\tD_value\tmimp_IR_seq\tmimp_IR_pos\tsignalpeptideseq\tproteinseq\tgenomicsequence\n"
logheader2="genome\tnr_of_complete_mimps\tnr_of_incomplete_mimps\tnr_of_put_eff_MetStop\n"
puteff_logfile_writer = open(puteff_logfile, 'a')
puteff_logfile_writer.write(logheader) #for each genome, write a log with a header.
combined_putefffile = open(combined_puteff_fasta, 'a')
combined_puteff_logfile_writer = open(combined_puteff_logfile, 'a')
combined_puteff_logfile2_writer = open(combined_puteff_logfile2, 'a')
if filecounter < 1: # During running of the first genome file, the log header should be added at the top in the case of a combined log file.
combined_puteff_logfile_writer.write(logheader)
combined_puteff_logfile2_writer.write(logheader2)
#proteinsfastafile = SeqIO.parse(proteinsfasta, 'fasta')
with open(proteinsfasta, 'r') as file:
proteinsfastafile=file.readlines()
file.close()
n=0
#all_contigs = list(SeqIO.parse(uberinfile, "fasta", IUPAC.unambiguous_dna))
with open(uberinfile, 'r') as file:
all_contigs=file.readlines()
file.close()
#test=True
from_previous_program=False
for seq_record in proteinsfastafile:
if '>' in seq_record:
#print(seq_record)
puteff_supercontig=''
if '_ds_' in seq_record:
temp_record_id=seq_record.split('_ds_')[0]
temp_record_id=temp_record_id.split('_')[2:]
for x in temp_record_id:
puteff_supercontig+=x+'_'
else:
temp_record_id=seq_record.split('_us_')[0]
temp_record_id=temp_record_id.split('_')[2:]
for x in temp_record_id:
puteff_supercontig+=x+'_'
puteff_supercontig=puteff_supercontig[:-1]
genomic_start_pos = int(seq_record.split('|')[1].split('-')[0])
genomic_end_pos = int(seq_record.split('|')[1].split('-')[1].split('|')[0])
dist2mimp = seq_record.split('d2m:')[1].split('|')[0]
protlength = seq_record.split('|len:')[1].split('|')[0]
signalpeptideseq = seq_record.split('signalpeptideseq=')[1].replace('\n','')
rc = seq_record.split('=')[1].split(' ')[0] #ORF from reverse complement of upstream/downstream or not
proteinseq = proteinsfastafile[n+1]
x=0
for sc in all_contigs:
#print('*screams internally*')
sc_id=''
r_start=0
r_end=0
if '>' in sc:
if 'downstream' in sc:
sc_id=sc.split('_downstream_')[0].split('>')[1]
#if test==True:
# print(sc_id, puteff_supercontig)
# test=False
else:
sc_id=sc.split('_upstream')[0].split('>')[1]
if 'region' in sc:
from_previous_program=True
r_start =int(sc.split('region:')[1].split('_')[0])
r_end =int(sc.split('region:')[1].split('_')[1].replace('\n',''))
if from_previous_program==False and sc_id == puteff_supercontig:
genomicsequence = all_contigs[x+1][genomic_start_pos-1:genomic_end_pos-1]#, len(sc.seq[genomic_start_pos-1:genomic_end_pos-1])
print(' '+str(puteff_supercontig)+'\tposition '+str(genomic_start_pos)+'-'+str(genomic_end_pos)+'\t'+signalpeptideseq)
putEff_fastaentry = ">"+str(n).zfill(4)+'.'+signalpeptideseq+"_"+genome+"_d2m"+str(dist2mimp)+"_len"+str(protlength)+"\n"+str(genomicsequence)+"\n"
dnaoutfile.write(putEff_fastaentry)
#orientation #D_value, mimp_IR_seq, mimp_IR_pos
puteff_attributes = [genome, puteff_supercontig, genomic_start_pos, genomic_end_pos, dist2mimp, protlength, signalpeptideseq, proteinseq, genomicsequence]
putEff_logentry = ('\t'.join(map(str,puteff_attributes)))+'\n'
puteff_logfile_writer.write(putEff_logentry)
combined_putefffile.write(putEff_fastaentry)
combined_puteff_logfile_writer.write(putEff_logentry)
elif from_previous_program==True and sc_id == puteff_supercontig:
if rc == "True": #if ORF is from reverse complement (rc) of up/downstream region
genomicsequence = Seq(all_contigs[x+1][(genomic_end_pos-r_start):(genomic_start_pos-r_start)], generic_dna)# for sequences from rc: end positions < start positions
if genomicsequence!='':
genomicsequence = genomicsequence.reverse_complement()
print(' '+str(puteff_supercontig)+'\tposition '+str(genomic_start_pos)+'-'+str(genomic_end_pos)+'\t'+signalpeptideseq)
putEff_fastaentry = ">"+str(n).zfill(4)+'.'+signalpeptideseq+"_"+sc_id+"_d2m"+str(dist2mimp)+"_len"+str(protlength)+"\n"+str(genomicsequence)+"\n"
dnaoutfile.write(putEff_fastaentry)
#orientation #D_value, mimp_IR_seq, mimp_IR_pos
puteff_attributes = [genome, puteff_supercontig, genomic_start_pos, genomic_end_pos, dist2mimp, protlength, signalpeptideseq, proteinseq, genomicsequence]
putEff_logentry = ('\t'.join(map(str,puteff_attributes)))+'\n'
puteff_logfile_writer.write(putEff_logentry)
#combined_putefffile will collect all the output from the mimpsearch; this means there will be many redundant put effectors.
combined_putefffile.write(putEff_fastaentry)
combined_puteff_logfile_writer.write(putEff_logentry)
break
elif rc == "False" and r_start<=genomic_start_pos and r_end>=genomic_end_pos:
genomicsequence = all_contigs[x+1][(genomic_start_pos-r_start):(genomic_end_pos-r_start)]#, len(sc.seq[genomic_start_pos-1:genomic_end_pos-1])
if genomicsequence!='':
print(' '+str(puteff_supercontig)+'\tposition '+str(genomic_start_pos)+'-'+str(genomic_end_pos)+'\t'+signalpeptideseq)
putEff_fastaentry = ">"+str(n).zfill(4)+'.'+signalpeptideseq+"_"+sc_id+"_d2m"+str(dist2mimp)+"_len"+str(protlength)+"\n"+str(genomicsequence)+"\n"
dnaoutfile.write(putEff_fastaentry)
#orientation #D_value, mimp_IR_seq, mimp_IR_pos
puteff_attributes = [genome, puteff_supercontig, genomic_start_pos, genomic_end_pos, dist2mimp, protlength, signalpeptideseq, proteinseq, genomicsequence]
putEff_logentry = ('\t'.join(map(str,puteff_attributes)))+'\n'
puteff_logfile_writer.write(putEff_logentry)
#combined_putefffile will collect all the output from the mimpsearch; this means there will be many redundant put effectors.
combined_putefffile.write(putEff_fastaentry)
combined_puteff_logfile_writer.write(putEff_logentry)
break
#else:
# print('error')
# print(seq_record)
# print(puteff_supercontig)
# print(sc, sc_id)
# print(r_start,r_end,genomic_start_pos,genomic_end_pos)
x+=1
n+=1
putEff_logentry2 = genome+'\t'+str(n)+'\n'
combined_puteff_logfile2_writer.write(putEff_logentry2)
dnaoutfile.close() #collects inside genome out folder all DNA sequences of the putative effectors
puteff_logfile_writer.close() #writes a log for all puteff found in the current genome (inside genome out folder)
combined_putefffile.close() #collects inside the out folder all DNA sequences of the putative effectors of all genomes that are being processed by the script.
combined_puteff_logfile_writer.close() #writes a general log file with more details of the putative effectors identified
combined_puteff_logfile2_writer.close()
print('-'*20)
print("// Finished with genome of %s; wrote %i genomic DNA sequences of putEff ORFs to %s" % (genome, n/2, puteff_dnaseqs))
def MainDef(genomefastafile, directory, folder, combined_puteff_fasta, combined_puteff_logfile, filecounter, combined_puteff_logfile2, combined_puteff_dir,min_prot_len,max_prot_len,max_d2m,SignalPpath,SignalP_threshold,force):
print(directory, " ", folder)
infilename, infileextension = os.path.splitext(genomefastafile)
infile = directory+folder+'/'+genomefastafile
outdirectory = combined_puteff_dir+infilename.split("_downstream_")[0]+'_mimpfinder_out/'
if not os.path.exists(outdirectory):
os.makedirs(outdirectory)
datahandler2 = outdirectory+infilename.split("_downstream_")[0]+'_1_gene_finder_translateddownstreamregions.fasta'
datahandler3 = outdirectory+infilename.split("_downstream_")[0]+'_2_gene_finder_putativeORFs.fasta'
signalpfile = outdirectory+infilename.split("_downstream_")[0]+'_3_gene_finder_SignalP'
proteinoutfile = outdirectory+infilename.split("_downstream_")[0]+'_4_gene_finder_proteinseq_out.fasta'
puteff_dnaseqs = outdirectory+infilename.split("_downstream_")[0]+'_5_gene_finder_puteff_genomicseq_out.fasta'
puteff_logfile = outdirectory+infilename.split("_downstream_")[0]+'_6_gene_finder_puteff_logfile.txt'
#motiefje = 'TT[TA]TTGC..CCCACTG..'
#motiefje_rc = '..CAGTGGG..GCAA[TA]AA'
#motiefje = 'TT[TAC]TTGC[ACG][CTA]C[CT][CT]ACTG..' ## (Mara Bergemann, 2008)
#motiefje_rc = '..CAGT[GA][GA]G[GAT][TGC]GCAA[TAG]AA'
orfs = []
#nrofcompletemimps, nrofincompletemimps = MimpFinder(infile, sc_prefix, forward_mimps, reverse_mimps, datahandler, distance, mimpsequencesfile, infilename) #ir_dict[i] = [m.start()+1, m.end(), seq_record.seq[m.start():m.end()], seq_record.seq[m.end():m.end()+distance]]
if force!=True and (os.path.isfile(datahandler2)==True or os.path.isfile(datahandler3)==True or os.path.isfile(signalpfile)==True or os.path.isfile(proteinoutfile)==True or os.path.isfile(puteff_dnaseqs)==True or os.path.isfile(puteff_logfile)==True):
pass
else:
print(("translator infile is: "+infile))
Translator(infile, datahandler2)
OrfFinder(datahandler2, min_prot_len, datahandler3, orfs, max_prot_len, max_d2m)
OrfWriter(datahandler3, signalpfile, min_prot_len, proteinoutfile, SignalPpath, SignalP_threshold,outdirectory)
ExtractOrfToFasta(proteinoutfile, infile, puteff_dnaseqs, infilename, puteff_logfile, combined_puteff_fasta, combined_puteff_logfile, filecounter, combined_puteff_logfile2)
#return mimpsequencesfile
class gene_finderApp():
def __init__(self):
self.verbose = False
def start(self, force, directory_folder, output_dir, SignalPpath ='signalP', min_prot_len=50, max_d2m=2500, max_prot_len=134, SignalP_threshold=.45, working=''):
#####################
if working!='':
if working[-1]!='/':
working+='/'
if '../' in working:
dir = os.path.dirname(__file__)
working = os.path.join(dir, working)
os.chdir(working)
else:
working=os.path.dirname(__file__)
if '../' in directory_folder or directory_folder[0]!='/':
dir = os.path.dirname(working)
directory_folder = os.path.join(dir, directory_folder)
directory_folder = os.path.abspath(os.path.realpath(directory_folder))
if '../' in output_dir or output_dir[0]!='/':
dir = os.path.dirname(working)
output_dir = os.path.join(dir, output_dir)
output_dir = os.path.abspath(os.path.realpath(output_dir))
if '../' in SignalPpath or SignalPpath[0]!='/':
dir = os.path.dirname(working)
SignalPpath = os.path.join(dir, SignalPpath)
SignalPpath = os.path.abspath(os.path.realpath(SignalPpath))
if directory_folder[-1]=="/":
directory_folder=directory_folder[:-1]
if output_dir[-1]=="/":
output_dir=output_dir[:-1]
folder = directory_folder.split('/')[-1]
directory = directory_folder.split(folder)[0]
file_extensions = (".fa", ".fasta", ".fas", "fna") # Specify the suffix of the genome files (.fa, .fasta, etc)
combined_puteff_dir = output_dir+'/'
# combined_puteff_dir = output_dir+'/01.gene_finder/'+folder+'_MetStopOut/' ##old version
if not os.path.exists(combined_puteff_dir):
os.makedirs(combined_puteff_dir)
combined_puteff_fasta = combined_puteff_dir+'all_putative_genes.fasta'
#open(combined_puteff_fasta, 'w').close()
combined_puteff_logfile = combined_puteff_dir+'all_putative_genes_log.txt'
#open(combined_puteff_logfile, 'w').close()
combined_puteff_logfile2 = combined_puteff_dir+'all_putative_genes_log2.txt'
#open(combined_puteff_logfile2, 'w').close()
if force!=True:
x=2
while os.path.isfile(combined_puteff_fasta)==True and os.path.isfile(combined_puteff_logfile)==True and os.path.isfile(combined_puteff_logfile2)==True:
combined_puteff_fasta = combined_puteff_dir+'all_putative_genes_run_'+str(x)+ '.fasta'
combined_puteff_logfile = combined_puteff_dir+'all_putative_genes_log_run_'+str(x)+ '.txt'
combined_puteff_logfile2 = combined_puteff_dir+'all_putative_genes_log2_run_'+str(x)+ '.txt'
x+=1
else:
open(combined_puteff_fasta, 'w').close()
open(combined_puteff_logfile, 'w').close()
open(combined_puteff_logfile2, 'w').close()
######################
filecounter=0
for genomefastafile in os.listdir(directory_folder):
#print("Examining "+ str(genomefastafile))
if genomefastafile.endswith(file_extensions):
print("\n// executing mimpfinder_MetStop script for "+genomefastafile)
MainDef(genomefastafile, directory, folder, combined_puteff_fasta, combined_puteff_logfile, filecounter, combined_puteff_logfile2, combined_puteff_dir, min_prot_len, max_prot_len, max_d2m, SignalPpath, SignalP_threshold,force)
filecounter+=1
print('-'*20)
print('// THE END')
print("No more files with extension '%s' were found in directory '%s'" % (file_extensions, (directory+folder)))
print("Executed the script for %i files." % (filecounter))
print('-'*20)