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
|
/*
* chimera.cpp
* Mothur
*
* Created by Sarah Westcott on 8/11/09.
* Copyright 2009 Schloss Lab Umass Amherst. All rights reserved.
*
*/
#include "mothurchimera.h"
//***************************************************************************************************************
//this is a vertical soft filter
string MothurChimera::createFilter(vector<Sequence*> seqs, float t) {
try {
filterString = "";
int threshold = int (t * seqs.size());
vector<int> gaps; gaps.resize(seqs[0]->getAligned().length(), 0);
vector<int> a; a.resize(seqs[0]->getAligned().length(), 0);
vector<int> t; t.resize(seqs[0]->getAligned().length(), 0);
vector<int> g; g.resize(seqs[0]->getAligned().length(), 0);
vector<int> c; c.resize(seqs[0]->getAligned().length(), 0);
filterString = (string(seqs[0]->getAligned().length(), '1'));
//for each sequence
for (int i = 0; i < seqs.size(); i++) {
if (m->getControl_pressed()) { return filterString; }
string seqAligned = seqs[i]->getAligned();
if (seqAligned.length() != filterString.length()) { m->mothurOut(seqs[i]->getName() + " is not the same length as the template sequences. Aborting!\n"); exit(1); }
for (int j = 0; j < seqAligned.length(); j++) {
//if this spot is a gap
if ((seqAligned[j] == '-') || (seqAligned[j] == '.')) { gaps[j]++; }
else if (toupper(seqAligned[j]) == 'A') { a[j]++; }
else if (toupper(seqAligned[j]) == 'T') { t[j]++; }
else if (toupper(seqAligned[j]) == 'G') { g[j]++; }
else if (toupper(seqAligned[j]) == 'C') { c[j]++; }
}
}
//zero out spot where all sequences have blanks
int numColRemoved = 0;
for(int i = 0;i < seqs[0]->getAligned().length(); i++){
if (m->getControl_pressed()) { return filterString; }
if(gaps[i] == seqs.size()) { filterString[i] = '0'; numColRemoved++; }
else if (((a[i] < threshold) && (t[i] < threshold) && (g[i] < threshold) && (c[i] < threshold))) { filterString[i] = '0'; numColRemoved++; }
}
if (threshold != 0) { m->mothurOut("Filter removed " + toString(numColRemoved) + " columns.\n"); }
return filterString;
}
catch(exception& e) {
m->errorOut(e, "MothurChimera", "createFilter");
exit(1);
}
}
//***************************************************************************************************************
map<int, int> MothurChimera::runFilter(Sequence* seq) {
try {
map<int, int> maskMap;
string seqAligned = seq->getAligned();
string newAligned = "";
int count = 0;
for (int j = 0; j < seqAligned.length(); j++) {
//if this spot is a gap
if (filterString[j] == '1') {
newAligned += seqAligned[j];
maskMap[count] = j;
count++;
}
}
seq->setAligned(newAligned);
return maskMap;
}
catch(exception& e) {
m->errorOut(e, "MothurChimera", "runFilter");
exit(1);
}
}
//***************************************************************************************************************
vector<Sequence*> MothurChimera::readSeqs(string file) {
try {
vector<Sequence*> container;
int count = 0;
length = 0;
unaligned = false;
m->mothurOut("Reading sequences from " + file + "..."); cout.flush();
ifstream in; Utils util; util.openInputFile(file, in);
//read in seqs and store in vector
while(!in.eof()){
if (m->getControl_pressed()) { return container; }
Sequence* current = new Sequence(in); gobble(in);
if (count == 0) { length = current->getAligned().length(); count++; } //gets first seqs length
else if (length != current->getAligned().length()) { unaligned = true; }
if (current->getName() != "") { container.push_back(current); }
}
in.close();
m->mothurOut("Done.\n");
filterString = (string(container[0]->getAligned().length(), '1'));
return container;
}
catch(exception& e) {
m->errorOut(e, "MothurChimera", "readSeqs");
exit(1);
}
}
//***************************************************************************************************************
void MothurChimera::setMask(string filename) {
try {
if (filename == "default") {
//default is from wigeon 236627 EU009184.1 Shigella dysenteriae str. FBD013
seqMask = ".....................................................................................................AAATTGAAGAGTTT-GA--T-CA-T-G-GCTC-AG-AT-TGAA-C-GC--TGG-C--G-GC-A-GG--C----C-T--AACACA-T-GC-A-AGT-CGA-A-CG----------G-TAA-CA-G----------------------------GAAG-A-AG----------------------------------------------------CTT-G----------------------------------------------------------------------------------CT-TCTTT----------------G-CT--G--AC--G--AG-T-GG-C-GG-A--C-------------GGG-TGAGT-A--AT-GT-C-T-G-GG---A-A--A-CT-G--C-C-TGA--TG-G------------------------------------------------------------------A-GG----GGG-AT-AA-CTA-------------------------C-T-G-----------------------GAA-A---CGG-TAG-CTAA-TA---CC-G--C-AT-A----------A--------------------C-------------------------------------GT-C-----------------------------------------------------------------------------------------------------------------------G-CA-A--------------------------------------------------------------------------------------------------------------------------------------G-A-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAA--G-A-G-GG-----G--GA-C-CT--------------------------------------------------------------------------------------------------------------------TCG-G----------------------------------------------------------------------------------------------------------------------G----CC-TC--T---T-G--------------C----C-A---T-CG-G---AT---G-T-----G-CCC-AGA--T-GGG--A------TT--A--G-CT-A----G---TAGG-T-G-GG-G-T----AAC-GG-C-T-C-ACCT--A-GG-C-G--A-CG-A------------TCC-C-T------AG-CT-G-G-TCT-G-AG----A--GG-AT--G-AC-C-AG-CCAC-A-CTGGA--A-C-TG-A-GA-C-AC-G-G-TCCAGA-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TG---GG-G-A-ATA-TTGCA-C-AA-T-GG--GC-GC-A----A-G-CC-T-GA-TG-CA-GCCA-TGCC-G-CG-T---G-T-A--T--GA-A-G--A--A-G-G-CC-----TT-CG---------G-G-T-T-G-T--A---AA-G-TAC--------TT-TC-A-G--C-GGG----GA-G--G---AA-GGGA---GTAA-AG----T--T--AA-T---A----C-----CT-T-TGC-TCA-TT-GA-CG-TT-A-C-CC-G-CA-G---------AA-----------GAAGC-ACC-GG-C-TAA---C--T-CCGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---GG-AG-GGT-GCA-A-G-CG-TTAA-T-CGG-AA-TT-A--C-T--GGGC-GTA----AA-GCGC-AC--G-CA-G-G-C-G------------G--T-TT-G-T-T-AA----G-T-C-A---G-ATG-TG-A-AA-TC--CC-CGG-G--------------------------------------------------------------------CT-C-AA-------------------------------------------------------------------------CC-T-G-GG-AA-C----T-G-C-A-T-C--------T--GA-T-A-C-T-G-GCA--A-G-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-T-G-A-G-T-C-----T-CG--TA-G-A------------G-GG-G-GG-T----AG--AATT-CCA-G-GT--GT-A-GCG-GTGAAA-TG-CGT-AGAG-A-TC-T-GGA--GG-A-AT-A-CC-GG--T--G--GC-GAA-G--G-C---G----G--C-C-CCCTG------G-AC-GA--------------------------------------------------------------AG-A-C-T--GA--CG-----CT-CA-GG--T-G-CGA--AA-G-C--------------G-TGGG-GAG-C-A-AACA--GG-ATTA-G-ATA-C-----CC-T-G-GTA-G-T----C-CA--C-G-CCG-T-AAA--C-GATG-TC--GA-CT---------T-GG--A--G-G-TT-G-TG-C--C--------------------------------------------------------------------------------------CTT-GA--------------------------------------------------------------------------------------------------------------------------------------------------G-G-C-GT--G-G-C-T-TC-C------GG--A----GC-TAA--CG-C-G-T--T--AA-GT--C----G-ACC-GCC-T-G-GG-GAG-TA---CGG-----C-C--G-C-A-A-GGT-T--AAA-ACTC-AAA---------TGAA-TTG-ACGGG-G-G-CCCG----C-A--C-A-A-GCG-GT-G--G--AG-CA-T--GT-GGT-TT-AATT-C-G-ATG-CAAC-G-CG-A-AG-A-A-CC-TT-A-CC-TGGTC-TT-G-AC-A-T-C--------------CAC-G-G-------------A-AG-T-T-T--TC--A-GA-G-A-T--G-A-G--A-A-T-G--T-G-----CC-------------------------------------T--TC-G------------------------------------------GG----A----A---CC-GTG---A--GA---------------------------------------------------C-A-G-G-T-GCTG-CA-TGG-CT--GTC-GTC-A-GC-TC---G-TG-TT-G--TGA-AA-TGT-T-GG-G-TT-AA-GT-CCCGC-AA--------C-GAG-CGC-A-ACC-C-T-TA--TC--C-TTTG--T-T-G-C-C---AG-C-G-----G-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GG---C----C-G------------G----G---A-A--CT---------------C-A-A-A-G-GA-G--AC-T-G-CCA--G-T------------------------------------G-A---TAA----------------------------------A-C-T-G--G-A-GG-A--AGG-T--GGGG-A-TGAC-GTC--AAGT-C---ATC-A-T-G-G-C-C-CTT----AC-G--AC-C-A-GG-GC-TA-CAC-ACGTG-C--TA--CAATG---G-CGCA-T-A--C-AAA-GA-GA--------------------------------------------------------------------------------------------------A-G-C-G-A--C-CTCG-C--G---------------------------------------A-GA-G-C-----------A--A-G-CG---G----------A--CCT-C------A-T-AAAGT-GC-G-T-C-G-TAG-TCC--------GGA-T-TGGAG-TC--T-GCAA-CT-C-------------------------------------------------------------------------------------------------G-ACTCC-A-T-G-AA-G-TC-GGAAT-CG-C-TA--G-TA-AT-C-G-T----GGA-TC-A-G--A------AT--GCC-AC-G-GT-G-AAT-ACGT-T-CCCGGGCCT-TGTA----CACACCG-CCC-GTC-----A---CA--CCA-TG-GG-A--G---TGG-G-TT-GC-AAA--A-GAA------G--T-AGG-TA-G-C-T-T-AA-C-C--------------------------------------------------------------TT----C-------------------------------------------------------------------------------------------------G--GG-A--GG-G--C---GC-TTA--CC--ACT-T----T-GTG-AT-TCA------------------------TG--ACT-GGGG-TG-AAG-TCGTAACAA-GGTAA-CCGT-AGGGGAA-CCTG-CGGT-TGGATCACCTCCTTA................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................";
}else if (filename == "") { //do nothing
seqMask = "";
}else{
ifstream infile;
Utils util; util.openInputFile(filename, infile);
if (!infile.eof()) {
Sequence temp(infile);
seqMask = temp.getAligned();
}else {
m->mothurOut("Problem with mask.\n");
seqMask = "";
}
infile.close();
}
}
catch(exception& e) {
m->errorOut(e, "MothurChimera", "setMask");
exit(1);
}
}
//***************************************************************************************************************
Sequence* MothurChimera::getSequence(string name) {
try{
Sequence* temp;
//look through templateSeqs til you find it
int spot = -1;
for (int i = 0; i < templateSeqs.size(); i++) {
if (name == templateSeqs[i]->getName()) {
spot = i;
break;
}
}
if(spot == -1) { m->mothurOut("Error: Could not find sequence.\n"); return nullptr; }
temp = new Sequence(templateSeqs[spot]->getName(), templateSeqs[spot]->getAligned());
return temp;
}
catch(exception& e) {
m->errorOut(e, "MothurChimera", "getSequence");
exit(1);
}
}
//***************************************************************************************************************
|
