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
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
|
/*
* screenseqscommand.cpp
* Mothur
*
* Created by Pat Schloss on 6/3/09.
* Copyright 2009 Patrick D. Schloss. All rights reserved.
*
*/
#include "screenseqscommand.h"
#include "counttable.h"
#include "summary.hpp"
#include "removeseqscommand.h"
#include "alignreport.hpp"
#include "contigsreport.hpp"
//**********************************************************************************************************************
vector<string> ScreenSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
CommandParameter pcontigsreport("contigsreport", "InputTypes", "", "", "report", "none", "none","contigsreport",false,false,true); parameters.push_back(pcontigsreport);
CommandParameter palignreport("alignreport", "InputTypes", "", "", "report", "none", "none","alignreport",false,false); parameters.push_back(palignreport);
CommandParameter psummary("summary", "InputTypes", "", "", "report", "none", "none","summary",false,false); parameters.push_back(psummary);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup);
CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","qfile",false,false); parameters.push_back(pqfile);
CommandParameter ptax("taxonomy", "InputTypes", "", "", "none", "none", "none","taxonomy",false,false); parameters.push_back(ptax);
CommandParameter pstart("start", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pstart);
CommandParameter pend("end", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pend);
CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxambig);
CommandParameter pmaxhomop("maxhomop", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxhomop);
CommandParameter pminlength("minlength", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pminlength);
CommandParameter pmaxlength("maxlength", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxlength);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter pcriteria("criteria", "Number", "", "90", "", "", "","",false,false); parameters.push_back(pcriteria);
CommandParameter poptimize("optimize", "Multiple", "none-start-end-maxambig-maxhomop-minlength-maxlength", "none", "", "", "","",true,false); parameters.push_back(poptimize);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
//report parameters
CommandParameter pminoverlap("minoverlap", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pminoverlap);
CommandParameter postart("ostart", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(postart);
CommandParameter poend("oend", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(poend);
CommandParameter pmismatches("mismatches", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmismatches);
CommandParameter pmaxn("maxn", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxn);
CommandParameter pminscore("minscore", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pminscore);
CommandParameter pmaxinsert("maxinsert", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxinsert);
CommandParameter pminsim("minsim", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pminsim);
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["alignreport"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
outputTypes["count"] = tempOutNames;
outputTypes["contigsreport"] = tempOutNames;
outputTypes["summary"] = tempOutNames;
abort = false; calledHelp = false;
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string ScreenSeqsCommand::getHelpString(){
try {
string helpString = "";
helpString += "The screen.seqs command reads a fasta file and screens sequences.\n";
helpString += "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, count, qfile, alignreport, contigsreport, summary, taxonomy, optimize, criteria and processors. The fasta parameter is required.\n";
helpString += "The contigsreport parameter allows you to use the contigsreport file to determine if a sequence is good. Screening parameters include: minoverlap, ostart, oend and mismatches. \n";
helpString += "The alignreport parameter allows you to use the alignreport file to determine if a sequence is good. Screening parameters include: minsim, minscore and maxinsert. \n";
helpString += "The summary parameter allows you to use the summary file from summary.seqs to save time processing.\n";
helpString += "The taxonomy parameter allows you to remove bad seqs from taxonomy files.\n";
helpString += "The start parameter is used to set a position the \"good\" sequences must start by. The default is -1, meaning ignore.\n";
helpString += "The end parameter is used to set a position the \"good\" sequences must end after. The default is -1, meaning ignore.\n";
helpString += "The maxambig parameter allows you to set the maximum number of ambiguous bases allowed. The default is -1, meaning ignore.\n";
helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
helpString += "The minlength parameter allows you to set and minimum sequence length. Default=10.\n";
helpString += "The maxn parameter allows you to set and maximum number of N's allowed in a sequence. \n";
helpString += "The minoverlap parameter allows you to set and minimum overlap. The default is -1, meaning ignore. \n";
helpString += "The ostart parameter is used to set an overlap position the \"good\" sequences must start by. The default is -1, meaning ignore. \n";
helpString += "The oend parameter is used to set an overlap position the \"good\" sequences must end after. The default is -1, meaning ignore.\n";
helpString += "The mismatches parameter allows you to set and maximum mismatches in the contigs.report. \n";
helpString += "The minsim parameter allows you to set the minimum similarity to template sequences during alignment. Found in column \'SimBtwnQuery&Template\' in align.report file.\n";
helpString += "The minscore parameter allows you to set the minimum search score during alignment. Found in column \'SearchScore\' in align.report file.\n";
helpString += "The maxinsert parameter allows you to set the maximum number of insertions during alignment. Found in column \'LongestInsert\' in align.report file.\n";
helpString += "The processors parameter allows you to specify the number of processors to use while running the command. The default is all available.\n";
helpString += "The optimize and criteria parameters allow you set the start, end, maxabig, maxhomop, minlength and maxlength parameters relative to your set of sequences.\n";
helpString += "For example optimize=start-end, criteria=90, would set the start and end values to the position 90% of your sequences started and ended.\n";
helpString += "The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n";
helpString += "The screen.seqs command should be in the following format: \n";
helpString += "screen.seqs(fasta=yourFastaFile, count=yourCountFile, start=yourStart, end=yourEnd)\n";
helpString += "Example screen.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table, start=1968, end=11550, maxhomop=8)\n";
getCommonQuestions();
return helpString;
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string ScreenSeqsCommand::getCommonQuestions(){
try {
vector<string> questions, issues, qanswers, ianswers, howtos, hanswers;
string issue = "Screen.seqs is removing most / all of my sequences. What do I do?"; issues.push_back(issue);
string ianswer = "\tThe most common cause of mothur removing all of your reads is a misunderstanding of the start and end parameter options. The start parameter is used to set a position the \"good\" sequences must START BY. Any read with a start position before the value given to start will be removed. The end parameter is used to set a position the \"good\" sequences must END AFTER. Any read that ends before the value given to end will be removed. Alternatively, reads may be removed if there is poor or no overlap in your dataset.\n"; ianswers.push_back(ianswer);
string howto = "How do I set the start and end parameters?"; howtos.push_back(howto);
string hanswer = "\tRun summary.seqs(fasta=yourFastaFile) to summarize your datasets start and end positions. \n\n\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs\nMinimum:\t1250\t10693\t250\t0\t3\t1\n2.5%-tile:\t1968\t11550\t252\t0\t3\t3222\n25%-tile:\t1968\t11550\t252\t0\t4\t32219\nMedian:\t\t1968\t11550\t252\t0\t4\t64437\n75%-tile:\t1968\t11550\t253\t0\t5\t96655\n97.5%-tile:\t1968\t11550\t253\t0\t6\t125651\nMaximum:\t1982\t13400\t270\t0\t12\t128872\nMean:\t\t1967.99\t11550\t252.462\t0\t4.36693\n# of unique seqs:\t16426\ntotal # of seqs:\t128872\n\nThe start parameter is used to set a position the \"good\" sequences must start by. In general, you want to select the start value found at 97.5%. Meaning 97.5% of your reads start by this position. In the example above we want to set start=1968. The end parameter is used to set a position the \"good\" sequences must end after. In general you set this to the end position at 2.5%. Meaning 97.5% of your reads end after this position. In the example above we want to set end=11550.\n"; hanswers.push_back(hanswer);
string commonQuestions = util.getFormattedHelp(questions, qanswers, issues, ianswers, howtos, hanswers);
return commonQuestions;
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "getCommonQuestions");
exit(1);
}
}
//**********************************************************************************************************************
string ScreenSeqsCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fasta") { pattern = "[filename],good,[extension]"; }
else if (type == "taxonomy") { pattern = "[filename],good,[extension]"; }
else if (type == "name") { pattern = "[filename],good,[extension]"; }
else if (type == "group") { pattern = "[filename],good,[extension]"; }
else if (type == "count") { pattern = "[filename],good,[extension]"; }
else if (type == "accnos") { pattern = "[filename],bad.accnos"; }
else if (type == "qfile") { pattern = "[filename],good,[extension]"; }
else if (type == "alignreport") { pattern = "[filename],good.[extension]"; }
else if (type == "contigsreport") { pattern = "[filename],good.[extension]"; }
else if (type == "summary") { pattern = "[filename],good.summary"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "getOutputPattern");
exit(1);
}
}
//***************************************************************************************************************
ScreenSeqsCommand::ScreenSeqsCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
fileType = "name file";
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta");
if (fastafile == "not found") {
fastafile = current->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter.\n"); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required.\n"); abort = true; }
}
else if (fastafile == "not open") { abort = true; }
else { current->setFastaFile(fastafile); }
groupfile = validParameter.validFile(parameters, "group");
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
else { current->setGroupFile(groupfile); }
qualfile = validParameter.validFile(parameters, "qfile");
if (qualfile == "not open") { abort = true; }
else if (qualfile == "not found") { qualfile = ""; }
else { current->setQualFile(qualfile); }
namefile = validParameter.validFile(parameters, "name");
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { current->setNameFile(namefile); }
countfile = validParameter.validFile(parameters, "count");
if (countfile == "not open") { countfile = ""; abort = true; }
else if (countfile == "not found") { countfile = ""; }
else { current->setCountFile(countfile); fileType = "count file"; }
contigsreport = validParameter.validFile(parameters, "contigsreport");
if (contigsreport == "not open") { contigsreport = ""; abort = true; }
else if (contigsreport == "not found") { contigsreport = ""; }
summaryfile = validParameter.validFile(parameters, "summary");
if (summaryfile == "not open") { summaryfile = ""; abort = true; }
else if (summaryfile == "not found") { summaryfile = ""; }
else { current->setSummaryFile(summaryfile); }
if ((namefile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: name or count.\n"); abort = true;
}
if ((groupfile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: group or count.\n"); abort=true;
}
alignreport = validParameter.validFile(parameters, "alignreport");
if (alignreport == "not open") { abort = true; }
else if (alignreport == "not found") { alignreport = ""; }
taxonomy = validParameter.validFile(parameters, "taxonomy");
if (taxonomy == "not open") { abort = true; }
else if (taxonomy == "not found") { taxonomy = ""; }
if (outputdir == ""){ outputdir += util.hasPath(fastafile); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
temp = validParameter.valid(parameters, "start"); if (temp == "not found") { temp = "-1"; }
util.mothurConvert(temp, startPos);
temp = validParameter.valid(parameters, "end"); if (temp == "not found") { temp = "-1"; }
util.mothurConvert(temp, endPos);
temp = validParameter.valid(parameters, "maxambig"); if (temp == "not found") { temp = "-1"; }
util.mothurConvert(temp, maxAmbig);
temp = validParameter.valid(parameters, "maxhomop"); if (temp == "not found") { temp = "-1"; }
util.mothurConvert(temp, maxHomoP);
temp = validParameter.valid(parameters, "minlength"); if (temp == "not found") { temp = "10"; }
util.mothurConvert(temp, minLength);
temp = validParameter.valid(parameters, "maxlength"); if (temp == "not found") { temp = "-1"; }
util.mothurConvert(temp, maxLength);
temp = validParameter.valid(parameters, "processors"); if (temp == "not found"){ temp = current->getProcessors(); }
processors = current->setProcessors(temp);
temp = validParameter.valid(parameters, "minoverlap"); if (temp == "not found") { temp = "-1"; }
util.mothurConvert(temp, minOverlap);
temp = validParameter.valid(parameters, "ostart"); if (temp == "not found") { temp = "-1"; }
util.mothurConvert(temp, oStart);
temp = validParameter.valid(parameters, "oend"); if (temp == "not found") { temp = "-1"; }
util.mothurConvert(temp, oEnd);
temp = validParameter.valid(parameters, "mismatches"); if (temp == "not found") { temp = "-1"; }
util.mothurConvert(temp, mismatches);
temp = validParameter.valid(parameters, "maxn"); if (temp == "not found") { temp = "-1"; }
util.mothurConvert(temp, maxN);
temp = validParameter.valid(parameters, "minscore"); if (temp == "not found") { temp = "-1"; }
util.mothurConvert(temp, minScore);
temp = validParameter.valid(parameters, "maxinsert"); if (temp == "not found") { temp = "-1"; }
util.mothurConvert(temp, maxInsert);
temp = validParameter.valid(parameters, "minsim"); if (temp == "not found") { temp = "-1"; }
util.mothurConvert(temp, minSim);
temp = validParameter.valid(parameters, "optimize"); //optimizing trumps the optimized values original value
if (temp == "not found"){ temp = "none"; }
util.splitAtDash(temp, optimize);
if ((contigsreport != "") && ((summaryfile != "") || ( alignreport != ""))) {
m->mothurOut("[ERROR]: You may only provide one of the following: contigsreport, alignreport or summary, aborting.\n"); abort=true;
}
if ((alignreport != "") && ((summaryfile != "") || ( contigsreport != ""))) {
m->mothurOut("[ERROR]: You may only provide one of the following: contigsreport, alignreport or summary, aborting.\n"); abort=true;
}
if ((summaryfile != "") && ((alignreport != "") || ( contigsreport != ""))) {
m->mothurOut("[ERROR]: You may only provide one of the following: contigsreport, alignreport or summary, aborting.\n"); abort=true;
}
//check to make sure you have the files you need for certain screening
if ((contigsreport == "") && ((minOverlap != -1) || (oStart != -1) || (oEnd != -1) || (mismatches != -1))) {
m->mothurOut("[ERROR]: minoverlap, ostart, oend and mismatches can only be used with a contigs.report file, aborting.\n"); abort=true;
}
if ((alignreport == "") && (!util.isEqual(minScore, -1) || (maxInsert != -1) || !util.isEqual(minSim, -1))) {
m->mothurOut("[ERROR]: minscore, maxinsert and minsim can only be used with a align.report file, aborting.\n"); abort=true;
}
//check for invalid optimize options
set<string> validOptimizers;
validOptimizers.insert("none"); validOptimizers.insert("start"); validOptimizers.insert("end"); validOptimizers.insert("maxambig"); validOptimizers.insert("maxhomop"); validOptimizers.insert("minlength"); validOptimizers.insert("maxlength"); validOptimizers.insert("maxn");
if (contigsreport != "") { validOptimizers.insert("minoverlap"); validOptimizers.insert("ostart"); validOptimizers.insert("oend"); validOptimizers.insert("mismatches"); }
if (alignreport != "") { validOptimizers.insert("minscore"); validOptimizers.insert("maxinsert"); validOptimizers.insert("minsim"); }
for (int i = 0; i < optimize.size(); i++) {
if (validOptimizers.count(optimize[i]) == 0) {
m->mothurOut(optimize[i] + " is not a valid optimizer with your input files. Valid options are ");
string valid = "";
for (set<string>::iterator it = validOptimizers.begin(); it != validOptimizers.end(); it++) { valid += (*it) + ", "; }
if (valid.length() != 0) { valid = valid.substr(0, valid.length()-2); }
m->mothurOut(valid + ".\n");
optimize.erase(optimize.begin()+i);
i--;
}
}
if (optimize.size() == 1) { if (optimize[0] == "none") { optimize.clear(); } }
temp = validParameter.valid(parameters, "criteria"); if (temp == "not found"){ temp = "90"; }
util.mothurConvert(temp, criteria);
}
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
exit(1);
}
}
//***************************************************************************************************************
int ScreenSeqsCommand::execute(){
try{
if (abort) { if (calledHelp) { return 0; } return 2; }
map<string, string> badSeqNames;
long start = time(nullptr);
long long numFastaSeqs = 0;
//use the namefile to optimize correctly
if (namefile != "") { nameMap = util.readNames(namefile); }
else if (countfile != "") {
CountTable ct;
ct.readTable(countfile, true, false);
nameMap = ct.getNameMap();
}
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(fastafile));
badAccnosFile = getOutputFileName("accnos",variables);
if ((contigsreport == "") && (summaryfile == "") && (alignreport == "")) { numFastaSeqs = screenFasta(badSeqNames); }
else { numFastaSeqs = screenReports(badSeqNames); }
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
//don't write or keep if blank
bool wroteAccnos = false;
if (util.isBlank(badAccnosFile)) { m->mothurOut("[NOTE]: no sequences were bad, removing " + badAccnosFile + "\n\n"); util.mothurRemove(badAccnosFile); }
else { outputNames.push_back(badAccnosFile); outputTypes["accnos"].push_back(badAccnosFile); wroteAccnos = true; }
if (wroteAccnos) {
//use remove.seqs to create new name, group and count file
if ((countfile != "") || (namefile != "") || (groupfile != "") || (qualfile != "") || (taxonomy != "")) {
string strippedAccnos = printAccnos(badSeqNames);
string inputString = "accnos=" + strippedAccnos;
if (countfile != "") { inputString += ", count=" + countfile; }
else{
if (namefile != "") { inputString += ", name=" + namefile; }
if (groupfile != "") { inputString += ", group=" + groupfile; }
}
if(qualfile != "") { inputString += ", qfile=" + qualfile; }
if(taxonomy != "") { inputString += ", taxonomy=" + taxonomy; }
m->mothurOut("/******************************************/\n");
m->mothurOut("Running command: remove.seqs(" + inputString + ")\n");
current->setMothurCalling(true);
Command* removeCommand = new RemoveSeqsCommand(inputString);
removeCommand->execute();
map<string, vector<string> > filenames = removeCommand->getOutputFiles();
delete removeCommand;
current->setMothurCalling(false);
m->mothurOut("/******************************************/\n");
util.mothurRemove(strippedAccnos);
if (groupfile != "") {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(groupfile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(groupfile));
variables["[extension]"] = util.getExtension(groupfile);
string outGroup = getOutputFileName("group", variables);
util.renameFile(filenames["group"][0], outGroup);
outputNames.push_back(outGroup); outputTypes["group"].push_back(outGroup);
}
if (namefile != "") {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(namefile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(namefile));
variables["[extension]"] = util.getExtension(namefile);
string outName = getOutputFileName("name", variables);
util.renameFile(filenames["name"][0], outName);
outputNames.push_back(outName); outputTypes["name"].push_back(outName);
}
if (countfile != "") {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(countfile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(countfile));
variables["[extension]"] = util.getExtension(countfile);
string outCount = getOutputFileName("count", variables);
util.renameFile(filenames["count"][0], outCount);
outputNames.push_back(outCount); outputTypes["count"].push_back(outCount);
}
if (qualfile != "") {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(qualfile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(qualfile));
variables["[extension]"] = util.getExtension(qualfile);
string outQual = getOutputFileName("qfile", variables);
util.renameFile(filenames["qfile"][0], outQual);
outputNames.push_back(outQual); outputTypes["qfile"].push_back(outQual);
}
if (taxonomy != "") {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(taxonomy); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(taxonomy));
variables["[extension]"] = util.getExtension(taxonomy);
string outTax = getOutputFileName("taxonomy", variables);
util.renameFile(filenames["taxonomy"][0], outTax);
outputNames.push_back(outTax); outputTypes["taxonomy"].push_back(outTax);
}
}
}
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
m->mothurOut("\nOutput File Names:\n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); }
m->mothurOut("\n\n");
//set fasta file as new current fastafile
string currentName = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setFastaFile(currentName); }
}
itTypes = outputTypes.find("name");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setNameFile(currentName); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setGroupFile(currentName); }
}
itTypes = outputTypes.find("qfile");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setQualFile(currentName); }
}
itTypes = outputTypes.find("taxonomy");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setTaxonomyFile(currentName); }
}
itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setCountFile(currentName); }
}
itTypes = outputTypes.find("accnos");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setAccnosFile(currentName); }
}
m->mothurOut("It took " + toString(time(nullptr) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.\n");
return 0;
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "execute");
exit(1);
}
}
//***************************************************************************************************************/
string ScreenSeqsCommand::printAccnos(map<string, string>& badSeqNames){
try{
string filename = badAccnosFile + ".temp";
ofstream out; util.openOutputFile(filename, out);
for (map<string, string>::iterator it = badSeqNames.begin(); it != badSeqNames.end(); it++) { out << it->first << endl; }
out.close();
return filename;
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "printAccnos");
exit(1);
}
}
//***************************************************************************************************************/
int ScreenSeqsCommand::runFastaScreening(map<string, string>& badSeqNames){
try{
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(fastafile));
variables["[extension]"] = util.getExtension(fastafile);
string goodSeqFile = getOutputFileName("fasta", variables);
outputNames.push_back(goodSeqFile); outputTypes["fasta"].push_back(goodSeqFile);
int numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames);
if (m->getControl_pressed()) { util.mothurRemove(goodSeqFile); return numFastaSeqs; }
return numFastaSeqs;
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "runFastaScreening");
exit(1);
}
}
//***************************************************************************************************************/
int ScreenSeqsCommand::screenReports(map<string, string>& badSeqNames){
try{
int numFastaSeqs = 0;
//did not provide a summary file, but set a parameter that requires summarizing the fasta file
//or did provide a summary file, but set maxn parameter so we must summarize the fasta file
if (((summaryfile == "") && ((util.inUsersGroups("maxambig", optimize)) ||(util.inUsersGroups("maxhomop", optimize)) ||(util.inUsersGroups("maxlength", optimize)) || (util.inUsersGroups("minlength", optimize)) || (util.inUsersGroups("start", optimize)) || (util.inUsersGroups("end", optimize)))) || ((summaryfile != "") && util.inUsersGroups("maxn", optimize))) {
getSummary();
}
if ((summaryfile != "") && ((util.inUsersGroups("maxambig", optimize)) ||(util.inUsersGroups("maxhomop", optimize)) ||(util.inUsersGroups("maxlength", optimize)) || (util.inUsersGroups("minlength", optimize)) || (util.inUsersGroups("start", optimize)) || (util.inUsersGroups("end", optimize)))) { //summarize based on summaryfile
getSummaryReport();
}else if ((contigsreport != "") && ((util.inUsersGroups("minoverlap", optimize)) || (util.inUsersGroups("ostart", optimize)) || (util.inUsersGroups("oend", optimize)) || (util.inUsersGroups("mismatches", optimize)))) { //optimize settings based on contigs file
optimizeContigs();
}else if ((alignreport != "") && ((util.inUsersGroups("minsim", optimize)) || (util.inUsersGroups("minscore", optimize)) || (util.inUsersGroups("maxinsert", optimize)))) { //optimize settings based on contigs file
optimizeAlign();
}
//provided summary file, and did not set maxn so no need to summarize fasta
if (summaryfile != "") { numFastaSeqs = screenSummary(badSeqNames); }
//add in any seqs that fail due to contigs report results
else if (contigsreport != "") { numFastaSeqs = screenContigs(badSeqNames); }
//add in any seqs that fail due to align report
else if (alignreport != "") { numFastaSeqs = screenAlignReport(badSeqNames); }
return numFastaSeqs;
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "screenReports");
exit(1);
}
}
//***************************************************************************************************************
int ScreenSeqsCommand::screenAlignReport(map<string, string>& badSeqNames){
try {
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(alignreport));
variables["[extension]"] = util.getExtension(alignreport);
string outSummary = getOutputFileName("alignreport",variables);
outputNames.push_back(outSummary); outputTypes["alignreport"].push_back(outSummary);
ofstream out; util.openOutputFile(outSummary, out);
ifstream in; util.openInputFile(alignreport, in);
AlignReport report;
report.readHeaders(in); gobble(in);
report.printHeaders(out);
int count = 0;
while (!in.eof()) {
if (m->getControl_pressed()) { in.close(); out.close(); return 0; }
report.read(in); gobble(in);
string trashCode = ""; bool goodSeq = true; // innocent until proven guilty
//check longest insert
int LongestInsert = report.getLongestInsert();
if(maxInsert != -1 && maxInsert < LongestInsert) { goodSeq = false; trashCode += "insert|"; }
//check searchscore
float SearchScore = report.getSearchScore();
if(!util.isEqual(minScore, -1) && minScore > SearchScore) { goodSeq = false; trashCode += "score|"; }
//check similarity to template
float SimBtwnQueryTemplate = report.getSimBtwnQueryAndTemplate();
if(!util.isEqual(minSim, -1) && minSim > SimBtwnQueryTemplate) { goodSeq = false; trashCode += "sim|"; }
//print or assign to badSeqs
if(goodSeq){ report.print(out); }
else{ badSeqNames[report.getQueryName()] = trashCode; }
count++;
}
in.close(); out.close();
int oldBadSeqsCount = badSeqNames.size();
int numFastaSeqs = runFastaScreening(badSeqNames);
if (oldBadSeqsCount != badSeqNames.size()) { //more seqs were removed by maxns
util.renameFile(outSummary, outSummary+".temp");
ofstream out2; util.openOutputFile(outSummary, out2);
ifstream in2; util.openInputFile(outSummary+".temp", in2);
report.readHeaders(in2); gobble(in2);
report.printHeaders(out2);
while (!in2.eof()) {
if (m->getControl_pressed()) { in2.close(); out2.close(); return 0; }
report.read(in2); gobble(in2);
//are you good?
if (badSeqNames.count(report.getQueryName()) == 0) { report.print(out2); }
}
in2.close(); out2.close();
util.mothurRemove(outSummary+".temp");
}
if (numFastaSeqs != count) { m->mothurOut("[ERROR]: found " + toString(numFastaSeqs) + " sequences in your fasta file, and " + toString(count) + " sequences in your align report file, quitting.\n"); m->setControl_pressed(true); }
return count;
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
exit(1);
}
}
//***************************************************************************************************************/
int ScreenSeqsCommand::screenContigs(map<string, string>& badSeqNames){
try{
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(contigsreport));
variables["[extension]"] = util.getExtension(contigsreport);
string outSummary = getOutputFileName("contigsreport",variables);
outputNames.push_back(outSummary); outputTypes["contigsreport"].push_back(outSummary);
ofstream out; util.openOutputFile(outSummary, out);
ifstream in;util.openInputFile(contigsreport, in);
ContigsReport report;
report.readHeaders(in); gobble(in);
report.printHeaders(out);
int count = 0;
while (!in.eof()) {
if (m->getControl_pressed()) { in.close(); out.close(); return 0; }
report.read(in); gobble(in);
bool goodSeq = true; // innocent until proven guilty
string trashCode = "";
if(oStart != -1 && oStart < report.getOverlapStart()) { goodSeq = false; trashCode += "ostart|"; }
if(oEnd != -1 && oEnd > report.getOverlapEnd()) { goodSeq = false; trashCode += "oend|"; }
if(maxN != -1 && maxN < report.getNumNs()) { goodSeq = false; trashCode += "n|"; }
if(minOverlap != -1 && minOverlap > report.getOverlapLength()) { goodSeq = false; trashCode += "olength|"; }
if(mismatches != -1 && mismatches < report.getMisMatches()) { goodSeq = false; trashCode += "mismatches|"; }
if(goodSeq) { report.print(out); }
else { badSeqNames[report.getName()] = trashCode; }
count++;
}
in.close(); out.close();
int oldBadSeqsCount = badSeqNames.size();
int numFastaSeqs = runFastaScreening(badSeqNames);
if (oldBadSeqsCount != badSeqNames.size()) { //more seqs were removed by maxns
util.renameFile(outSummary, outSummary+".temp");
ofstream out2; util.openOutputFile(outSummary, out2);
ifstream in2; util.openInputFile(outSummary+".temp", in2);
report.readHeaders(in2); gobble(in2);
report.printHeaders(out2);
while (!in2.eof()) {
if (m->getControl_pressed()) { in2.close(); out2.close(); return 0; }
report.read(in2); gobble(in2);
if (badSeqNames.count(report.getName()) == 0) { report.print(out2); }
}
in2.close(); out2.close();
util.mothurRemove(outSummary+".temp");
}
if (numFastaSeqs != count) { m->mothurOut("[ERROR]: found " + toString(numFastaSeqs) + " sequences in your fasta file, and " + toString(count) + " sequences in your contigs report file, quitting.\n"); m->setControl_pressed(true); }
return count;
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "screenContigs");
exit(1);
}
}
//***************************************************************************************************************/
int ScreenSeqsCommand::screenSummary(map<string, string>& badSeqNames){
try{
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(summaryfile));
string outSummary = getOutputFileName("summary",variables);
outputNames.push_back(outSummary); outputTypes["summary"].push_back(outSummary);
string name;
int start, end, length, ambigs, polymer, numReps;
ofstream out; util.openOutputFile(outSummary, out);
ifstream in; util.openInputFile(summaryfile, in);
out << (util.getline(in)) << endl; //skip headers
int count = 0;
while (!in.eof()) {
if (m->getControl_pressed()) { in.close(); out.close(); return 0; }
//seqname start end nbases ambigs polymer numSeqs
in >> name >> start >> end >> length >> ambigs >> polymer >> numReps; gobble(in);
bool goodSeq = true; // innocent until proven guilty
string trashCode = "";
if(startPos != -1 && startPos < start) { goodSeq = false; trashCode += "start|"; }
if(endPos != -1 && endPos > end) { goodSeq = false; trashCode += "end|"; }
if(maxAmbig != -1 && maxAmbig < ambigs) { goodSeq = false; trashCode += "ambig|"; }
if(maxHomoP != -1 && maxHomoP < polymer) { goodSeq = false; trashCode += "homop|"; }
if(minLength > length) { goodSeq = false; trashCode += "<length|"; }
if(maxLength != -1 && maxLength < length) { goodSeq = false; trashCode += ">length|"; }
if(goodSeq){
out << name << '\t' << start << '\t' << end << '\t' << length << '\t' << ambigs << '\t' << polymer << '\t' << numReps << endl;
}
else{ badSeqNames[name] = trashCode; }
count++;
}
in.close();
out.close();
int oldBadSeqsCount = badSeqNames.size();
int numFastaSeqs = runFastaScreening(badSeqNames);
if (oldBadSeqsCount != badSeqNames.size()) { //more seqs were removed by maxns
util.renameFile(outSummary, outSummary+".temp");
ofstream out2;
util.openOutputFile(outSummary, out2);
//read summary file
ifstream in2;
util.openInputFile(outSummary+".temp", in2);
out2 << (util.getline(in2)) << endl; //skip headers
while (!in2.eof()) {
if (m->getControl_pressed()) { in2.close(); out2.close(); return 0; }
//seqname start end nbases ambigs polymer numSeqs
in2 >> name >> start >> end >> length >> ambigs >> polymer >> numReps; gobble(in2);
if (badSeqNames.count(name) == 0) { //are you good?
out2 << name << '\t' << start << '\t' << end << '\t' << length << '\t' << ambigs << '\t' << polymer << '\t' << numReps << endl;
}
}
in2.close();
out2.close();
util.mothurRemove(outSummary+".temp");
}
if (numFastaSeqs != count) { m->mothurOut("[ERROR]: found " + toString(numFastaSeqs) + " sequences in your fasta file, and " + toString(count) + " sequences in your summary file, quitting.\n"); m->setControl_pressed(true); }
return count;
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "screenSummary");
exit(1);
}
}
//***************************************************************************************************************/
int ScreenSeqsCommand::screenFasta(map<string, string>& badSeqNames){
try{
if (optimize.size() != 0) { getSummary(); }
if (m->getControl_pressed()) { return 0; }
int numFastaSeqs = runFastaScreening(badSeqNames);
return numFastaSeqs;
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "screenFasta");
exit(1);
}
}
//***************************************************************************************************************
int ScreenSeqsCommand::getSummaryReport(){
try {
Summary sum(processors);
sum.summarizeFastaSummary(summaryfile);
double criteriaPercentile = criteria;
double mincriteriaPercentile = (100 - criteria);
for (int i = 0; i < optimize.size(); i++) {
if (optimize[i] == "start") { startPos = sum.getStart(criteriaPercentile); m->mothurOut("Optimizing start to " + toString(startPos) + ".\n"); }
else if (optimize[i] == "end") { endPos = sum.getEnd(mincriteriaPercentile); m->mothurOut("Optimizing end to " + toString(endPos) + ".\n"); }
else if (optimize[i] == "maxambig") { maxAmbig = sum.getAmbig(criteriaPercentile); m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + ".\n"); }
else if (optimize[i] == "maxhomop") { maxHomoP = sum.getAmbig(criteriaPercentile); m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + ".\n"); }
else if (optimize[i] == "minlength") { minLength = sum.getLength(mincriteriaPercentile); m->mothurOut("Optimizing minlength to " + toString(minLength) + ".\n"); if (minLength < 0) { m->setControl_pressed(true); } }
else if (optimize[i] == "maxlength") { maxLength = sum.getLength(criteriaPercentile); m->mothurOut("Optimizing maxlength to " + toString(maxLength) + ".\n"); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "getSummaryReport");
exit(1);
}
}
//***************************************************************************************************************
int ScreenSeqsCommand::optimizeContigs(){
try{
Summary sum(processors);
sum.summarizeContigsSummary(contigsreport);
double criteriaPercentile = criteria;
double mincriteriaPercentile = (100 - criteria);
for (int i = 0; i < optimize.size(); i++) {
if (optimize[i] == "ostart") { oStart = sum.getOStart(criteriaPercentile); m->mothurOut("Optimizing ostart to " + toString(oStart) + ".\n"); }
else if (optimize[i] == "oend") { oEnd = sum.getOEnd(mincriteriaPercentile); m->mothurOut("Optimizing oend to " + toString(oEnd) + ".\n"); }
else if (optimize[i] == "mismatches") { mismatches = sum.getMisMatches(criteriaPercentile); m->mothurOut("Optimizing mismatches to " + toString(mismatches) + ".\n"); }
else if (optimize[i] == "maxn") { maxN = sum.getNumNs(criteriaPercentile); m->mothurOut("Optimizing maxn to " + toString(maxN) + ".\n"); }
else if (optimize[i] == "minoverlap") { minOverlap = sum.getOLength(mincriteriaPercentile); m->mothurOut("Optimizing minoverlap to " + toString(minOverlap) + ".\n"); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "optimizeContigs");
exit(1);
}
}
//***************************************************************************************************************
int ScreenSeqsCommand::optimizeAlign(){
try {
Summary sum(processors);
sum.summarizeAlignSummary(alignreport);
double mincriteriaPercentile = (100 - criteria);
for (int i = 0; i < optimize.size(); i++) {
if (optimize[i] == "minsim") { minSim = sum.getSims(mincriteriaPercentile); m->mothurOut("Optimizing minsim to " + toString(minSim) + ".\n"); }
else if (optimize[i] == "minscore") { minScore = sum.getScores(mincriteriaPercentile); m->mothurOut("Optimizing minscore to " + toString(minScore) + ".\n"); }
else if (optimize[i] == "maxinsert") { maxInsert = sum.getNumInserts(mincriteriaPercentile); m->mothurOut("Optimizing maxinsert to " + toString(maxInsert) + ".\n"); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "optimizeAlign");
exit(1);
}
}
//***************************************************************************************************************
int ScreenSeqsCommand::getSummary(){
try {
Summary sum(processors);
sum.summarizeFasta(fastafile, "");
//numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs
double criteriaPercentile = criteria;
double mincriteriaPercentile = (100 - criteria);
for (int i = 0; i < optimize.size(); i++) {
if (optimize[i] == "start") { startPos = sum.getStart(criteriaPercentile); m->mothurOut("Optimizing start to " + toString(startPos) + ".\n"); }
else if (optimize[i] == "end") { endPos = sum.getEnd(mincriteriaPercentile); m->mothurOut("Optimizing end to " + toString(endPos) + ".\n"); }
else if (optimize[i] == "maxambig") { maxAmbig = sum.getAmbig(criteriaPercentile); m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + ".\n"); }
else if (optimize[i] == "maxhomop") { maxHomoP = sum.getAmbig(criteriaPercentile); m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + ".\n"); }
else if (optimize[i] == "minlength") { minLength = sum.getLength(mincriteriaPercentile); m->mothurOut("Optimizing minlength to " + toString(minLength) + ".\n"); if (minLength < 0) { m->setControl_pressed(true); } }
else if (optimize[i] == "maxlength") { maxLength = sum.getLength(criteriaPercentile); m->mothurOut("Optimizing maxlength to " + toString(maxLength) + ".\n"); }
else if (optimize[i] == "maxn") { maxN = sum.getNumNs(criteriaPercentile); m->mothurOut("Optimizing maxn to " + toString(maxN) + ".\n"); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "getSummary");
exit(1);
}
}
//**********************************************************************************************************************
void driverScreen(sumScreenData* params){
try {
ifstream inFASTA;
params->util.openInputFile(params->filename, inFASTA);
inFASTA.seekg(params->start);
//print header if you are process 0
if (params->start == 0) { params->util.zapGremlins(inFASTA); gobble(inFASTA); }
bool done = false;
params->count = 0;
while (!done) {
if (params->m->getControl_pressed()) { break; }
Sequence currSeq(inFASTA); gobble(inFASTA);
if (currSeq.getName() != "") {
bool goodSeq = true; // innocent until proven guilty
string trashCode = "";
//have the report files found you bad
map<string, string>::iterator it = params->badSeqNames.find(currSeq.getName());
if (it != params->badSeqNames.end()) { goodSeq = 0; trashCode = it->second; }
if (params->summaryfile == "") { //summaryfile includes these so no need to check again
if(params->startPos != -1 && params->startPos < currSeq.getStartPos()) { goodSeq = false; trashCode += "start|"; }
if(params->endPos != -1 && params->endPos > currSeq.getEndPos()) { goodSeq = false; trashCode += "end|"; }
if(params->maxAmbig != -1 && params->maxAmbig < currSeq.getAmbigBases()) { goodSeq = false; trashCode += "ambig|"; }
if(params->maxHomoP != -1 && params->maxHomoP < currSeq.getLongHomoPolymer()) { goodSeq = false; trashCode += "homop|"; }
if(params->minLength > currSeq.getNumBases()) { goodSeq = false; trashCode += "<length|";}
if(params->maxLength != -1 && params->maxLength < currSeq.getNumBases()) { goodSeq = false; trashCode += ">length|";}
if (params->m->getDebug()) { params->m->mothurOut("[DEBUG]: " + currSeq.getName() + "\t" + toString(currSeq.getStartPos()) + "\t" + toString(currSeq.getEndPos()) + "\t" + toString(currSeq.getNumBases()) + "\n"); }
}
if (params->contigsreport == "") { //contigs report includes this so no need to check again
if(params->maxN != -1 && params->maxN < currSeq.getNumNs()) { goodSeq = false; trashCode += "n|"; }
}
if(goodSeq){
currSeq.printSequence(params->outputWriter);
}else{
string badAccnos = currSeq.getName() + '\t' + trashCode.substr(0, trashCode.length()-1) + '\n';
params->accnosWriter->write(badAccnos);
params->badSeqNames[currSeq.getName()] = trashCode;
}
params->count++;
}
#if defined NON_WINDOWS
unsigned long long pos = inFASTA.tellg();
if ((pos == -1) || (pos >= params->end)) { break; }
#else
if (params->end == params->count) { break; }
#endif
//report progress
if((params->count) % 1000 == 0){ params->m->mothurOutJustToScreen(toString(params->count)+"\n"); }
}
//report progress
if((params->count) % 1000 != 0){ params->m->mothurOutJustToScreen(toString(params->count)+"\n"); }
inFASTA.close();
}
catch(exception& e) {
params->m->errorOut(e, "ScreenSeqsCommand", "driverScreen");
exit(1);
}
}
/**************************************************************************************************/
int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, map<string, string>& badSeqNames) {
try {
vector<linePair> lines;
vector<double> positions;
#if defined NON_WINDOWS
positions = util.divideFile(fastafile, processors);
for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
#else
long long numFastaSeqs = 0;
positions = util.setFilePosFasta(fastafile, numFastaSeqs);
if (numFastaSeqs < processors) { processors = numFastaSeqs; }
//figure out how many sequences you have to process
int numSeqsPerProcessor = numFastaSeqs / processors;
for (int i = 0; i < processors; i++) {
int startIndex = i * numSeqsPerProcessor;
if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; }
lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
}
#endif
//create array of worker threads
vector<std::thread*> workerThreads;
vector<sumScreenData*> data;
long long num = 0;
time_t start, end;
time(&start);
auto synchronizedOutputFile = std::make_shared<SynchronizedOutputFile>(goodFileName);
auto synchronizedAccnosFile = std::make_shared<SynchronizedOutputFile>(badAccnos);
//Lauch worker threads
for (int i = 0; i < processors-1; i++) {
OutputWriter* outputThreadWriter = new OutputWriter(synchronizedOutputFile);
OutputWriter* accnosThreadWriter = new OutputWriter(synchronizedAccnosFile);
sumScreenData* dataBundle = new sumScreenData(startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, maxN, badSeqNames, filename, summaryfile, contigsreport, lines[i+1].start, lines[i+1].end,outputThreadWriter, accnosThreadWriter);
data.push_back(dataBundle);
workerThreads.push_back(new std::thread(driverScreen, dataBundle));
}
OutputWriter* outputThreadWriter = new OutputWriter(synchronizedOutputFile);
OutputWriter* accnosThreadWriter = new OutputWriter(synchronizedAccnosFile);
sumScreenData* dataBundle = new sumScreenData(startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, maxN, badSeqNames, filename, summaryfile, contigsreport, lines[0].start, lines[0].end,outputThreadWriter, accnosThreadWriter);
driverScreen(dataBundle);
num = dataBundle->count;
for (map<string, string>::iterator it = dataBundle->badSeqNames.begin(); it != dataBundle->badSeqNames.end(); it++) { badSeqNames[it->first] = it->second; }
for (int i = 0; i < processors-1; i++) {
workerThreads[i]->join();
num += data[i]->count;
for (map<string, string>::iterator it = data[i]->badSeqNames.begin(); it != data[i]->badSeqNames.end(); it++) { badSeqNames[it->first] = it->second; }
delete data[i]->outputWriter;
delete data[i]->accnosWriter;
delete data[i];
delete workerThreads[i];
}
long long numRemoved = badSeqNames.size();
time(&end);
m->mothurOut("\nIt took " + toString(difftime(end, start)) + " secs to screen " + toString(num) + " sequences, removed " + toString(numRemoved) + ".\n\n");
delete outputThreadWriter; delete accnosThreadWriter;
delete dataBundle;
return num;
}
catch(exception& e) {
m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
exit(1);
}
}
//***************************************************************************************************************
|
