--- /dev/null
+/*
+ * chimera.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 8/11/09.
+ * Copyright 2009 Schloss Lab Umass Amherst. All rights reserved.
+ *
+ */
+
+#include "chimera.h"
+#include "referencedb.h"
+
+//***************************************************************************************************************
+//this is a vertical soft filter
+string Chimera::createFilter(vector<Sequence*> seqs, float t) {
+ try {
+ filterString = "";
+ int threshold = int (t * seqs.size());
+//cout << "threshhold = " << threshold << endl;
+
+ 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->control_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->control_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++; }
+ //cout << "a = " << a[i] << " t = " << t[i] << " g = " << g[i] << " c = " << c[i] << endl;
+ }
+
+ if (threshold != 0.0) { m->mothurOut("Filter removed " + toString(numColRemoved) + " columns."); m->mothurOutEndLine(); }
+
+ return filterString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Chimera", "createFilter");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+map<int, int> Chimera::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, "Chimera", "runFilter");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+vector<Sequence*> Chimera::readSeqs(string file) {
+ try {
+
+ vector<Sequence*> container;
+ int count = 0;
+ length = 0;
+ unaligned = false;
+ ReferenceDB* rdb = ReferenceDB::getInstance();
+
+ if (file == "saved") {
+
+
+ m->mothurOutEndLine(); m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory."); m->mothurOutEndLine();
+
+ for (int i = 0; i < rdb->referenceSeqs.size(); i++) {
+ Sequence* temp = new Sequence(rdb->referenceSeqs[i].getName(), rdb->referenceSeqs[i].getAligned());
+
+ if (count == 0) { length = temp->getAligned().length(); count++; } //gets first seqs length
+ else if (length != temp->getAligned().length()) { unaligned = true; }
+
+ if (temp->getName() != "") { container.push_back(temp); }
+ }
+
+ templateFileName = rdb->getSavedReference();
+
+ }else {
+
+ m->mothurOut("Reading sequences from " + file + "..."); cout.flush();
+
+ #ifdef USE_MPI
+ int pid, processors;
+ vector<unsigned long long> positions;
+ int numSeqs;
+ int tag = 2001;
+ MPI_File inMPI;
+ MPI_Status status;
+
+ if (byGroup) {
+ char inFileName[1024];
+ strcpy(inFileName, file.c_str());
+
+ MPI_File_open(MPI_COMM_SELF, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+
+ positions = m->setFilePosFasta(file, numSeqs); //fills MPIPos, returns numSeqs
+
+ //read file
+ for(int i=0;i<numSeqs;i++){
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); return container; }
+
+ //read next sequence
+ int seqlength = positions[i+1] - positions[i];
+ char* buf4 = new char[seqlength];
+
+ MPI_File_read_at(inMPI, positions[i], buf4, seqlength, MPI_CHAR, &status);
+
+ string tempBuf = buf4;
+ if (tempBuf.length() > seqlength) { tempBuf = tempBuf.substr(0, seqlength); }
+ delete buf4;
+
+ istringstream iss (tempBuf,istringstream::in);
+
+ Sequence* current = new Sequence(iss);
+ if (current->getName() != "") {
+ if (count == 0) { length = current->getAligned().length(); count++; } //gets first seqs length
+ else if (length != current->getAligned().length()) { unaligned = true; }
+
+ container.push_back(current);
+ if (rdb->save) { rdb->referenceSeqs.push_back(*current); }
+ }
+ }
+
+ MPI_File_close(&inMPI);
+
+ }else {
+
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
+
+ //char* inFileName = new char[file.length()];
+ //memcpy(inFileName, file.c_str(), file.length());
+
+ char inFileName[1024];
+ strcpy(inFileName, file.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+ //delete inFileName;
+
+ if (pid == 0) {
+ positions = m->setFilePosFasta(file, numSeqs); //fills MPIPos, returns numSeqs
+
+ //send file positions to all processes
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+ MPI_Send(&positions[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ }
+ }else{
+ MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+ positions.resize(numSeqs+1);
+ MPI_Recv(&positions[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
+ }
+
+ //read file
+ for(int i=0;i<numSeqs;i++){
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); return container; }
+
+ //read next sequence
+ int seqlength = positions[i+1] - positions[i];
+ char* buf4 = new char[seqlength];
+
+ MPI_File_read_at(inMPI, positions[i], buf4, seqlength, MPI_CHAR, &status);
+
+ string tempBuf = buf4;
+ if (tempBuf.length() > seqlength) { tempBuf = tempBuf.substr(0, seqlength); }
+ delete buf4;
+
+ istringstream iss (tempBuf,istringstream::in);
+
+ Sequence* current = new Sequence(iss);
+ if (current->getName() != "") {
+ if (count == 0) { length = current->getAligned().length(); count++; } //gets first seqs length
+ else if (length != current->getAligned().length()) { unaligned = true; }
+
+ container.push_back(current);
+ if (rdb->save) { rdb->referenceSeqs.push_back(*current); }
+ }
+ }
+
+ MPI_File_close(&inMPI);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+ }
+ #else
+
+ ifstream in;
+ m->openInputFile(file, in);
+
+ //read in seqs and store in vector
+ while(!in.eof()){
+
+ if (m->control_pressed) { return container; }
+
+ Sequence* current = new Sequence(in); m->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);
+ if (rdb->save) { rdb->referenceSeqs.push_back(*current); }
+ }
+ }
+ in.close();
+ #endif
+
+ m->mothurOut("Done."); m->mothurOutEndLine();
+
+ filterString = (string(container[0]->getAligned().length(), '1'));
+ }
+
+ return container;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Chimera", "readSeqs");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+void Chimera::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{
+
+ #ifdef USE_MPI
+ MPI_File inMPI;
+ MPI_Offset size;
+ MPI_Status status;
+
+ //char* inFileName = new char[filename.length()];
+ //memcpy(inFileName, filename.c_str(), filename.length());
+
+ char inFileName[1024];
+ strcpy(inFileName, filename.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+ MPI_File_get_size(inMPI, &size);
+
+ //delete inFileName;
+
+ char* buffer = new char[size];
+ MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
+
+ string tempBuf = buffer;
+ if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size); }
+ istringstream iss (tempBuf,istringstream::in);
+
+ delete buffer;
+
+ if (!iss.eof()) {
+ Sequence temp(iss);
+ seqMask = temp.getAligned();
+ }else {
+ m->mothurOut("Problem with mask."); m->mothurOutEndLine();
+ seqMask = "";
+ }
+
+ MPI_File_close(&inMPI);
+ #else
+
+ ifstream infile;
+ m->openInputFile(filename, infile);
+
+ if (!infile.eof()) {
+ Sequence temp(infile);
+ seqMask = temp.getAligned();
+ }else {
+ m->mothurOut("Problem with mask."); m->mothurOutEndLine();
+ seqMask = "";
+ }
+ infile.close();
+ #endif
+
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Chimera", "setMask");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+Sequence* Chimera::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."); m->mothurOutEndLine(); return NULL; }
+
+ temp = new Sequence(templateSeqs[spot]->getName(), templateSeqs[spot]->getAligned());
+
+ return temp;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Chimera", "getSequence");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
+
+
+
projects / mothur.git / blobdiff