2 * screenseqscommand.cpp
5 * Created by Pat Schloss on 6/3/09.
6 * Copyright 2009 Patrick D. Schloss. All rights reserved.
10 #include "screenseqscommand.h"
11 #include "sequence.hpp"
13 //***************************************************************************************************************
15 ScreenSeqsCommand::ScreenSeqsCommand(string option) {
19 //allow user to run help
20 if(option == "help") { help(); abort = true; }
23 //valid paramters for this command
24 string AlignArray[] = {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength",
25 "name", "group", "alignreport","processors","outputdir","inputdir"};
26 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
28 OptionParser parser(option);
29 map<string,string> parameters = parser.getParameters();
31 ValidParameters validParameter;
32 map<string,string>::iterator it;
34 //check to make sure all parameters are valid for command
35 for (it = parameters.begin(); it != parameters.end(); it++) {
36 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
39 //if the user changes the input directory command factory will send this info to us in the output parameter
40 string inputDir = validParameter.validFile(parameters, "inputdir", false);
41 if (inputDir == "not found"){ inputDir = ""; }
44 it = parameters.find("fasta");
45 //user has given a template file
46 if(it != parameters.end()){
47 path = hasPath(it->second);
48 //if the user has not given a path then, add inputdir. else leave path alone.
49 if (path == "") { parameters["fasta"] = inputDir + it->second; }
52 it = parameters.find("group");
53 //user has given a template file
54 if(it != parameters.end()){
55 path = hasPath(it->second);
56 //if the user has not given a path then, add inputdir. else leave path alone.
57 if (path == "") { parameters["group"] = inputDir + it->second; }
60 it = parameters.find("name");
61 //user has given a template file
62 if(it != parameters.end()){
63 path = hasPath(it->second);
64 //if the user has not given a path then, add inputdir. else leave path alone.
65 if (path == "") { parameters["name"] = inputDir + it->second; }
68 it = parameters.find("alignreport");
69 //user has given a template file
70 if(it != parameters.end()){
71 path = hasPath(it->second);
72 //if the user has not given a path then, add inputdir. else leave path alone.
73 if (path == "") { parameters["alignreport"] = inputDir + it->second; }
77 //check for required parameters
78 fastafile = validParameter.validFile(parameters, "fasta", true);
79 if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the screen.seqs command."); m->mothurOutEndLine(); abort = true; }
80 else if (fastafile == "not open") { abort = true; }
82 groupfile = validParameter.validFile(parameters, "group", true);
83 if (groupfile == "not open") { abort = true; }
84 else if (groupfile == "not found") { groupfile = ""; }
86 namefile = validParameter.validFile(parameters, "name", true);
87 if (namefile == "not open") { abort = true; }
88 else if (namefile == "not found") { namefile = ""; }
90 alignreport = validParameter.validFile(parameters, "alignreport", true);
91 if (alignreport == "not open") { abort = true; }
92 else if (alignreport == "not found") { alignreport = ""; }
94 //if the user changes the output directory command factory will send this info to us in the output parameter
95 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
97 outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
100 //check for optional parameter and set defaults
101 // ...at some point should added some additional type checking...
103 temp = validParameter.validFile(parameters, "start", false); if (temp == "not found") { temp = "-1"; }
104 convert(temp, startPos);
106 temp = validParameter.validFile(parameters, "end", false); if (temp == "not found") { temp = "-1"; }
107 convert(temp, endPos);
109 temp = validParameter.validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; }
110 convert(temp, maxAmbig);
112 temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found") { temp = "-1"; }
113 convert(temp, maxHomoP);
115 temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "-1"; }
116 convert(temp, minLength);
118 temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "-1"; }
119 convert(temp, maxLength);
121 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
122 convert(temp, processors);
127 catch(exception& e) {
128 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
132 //**********************************************************************************************************************
134 void ScreenSeqsCommand::help(){
136 m->mothurOut("The screen.seqs command reads a fastafile and creates .....\n");
137 m->mothurOut("The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group and processors.\n");
138 m->mothurOut("The fasta parameter is required.\n");
139 m->mothurOut("The start parameter .... The default is -1.\n");
140 m->mothurOut("The end parameter .... The default is -1.\n");
141 m->mothurOut("The maxambig parameter .... The default is -1.\n");
142 m->mothurOut("The maxhomop parameter .... The default is -1.\n");
143 m->mothurOut("The minlength parameter .... The default is -1.\n");
144 m->mothurOut("The maxlength parameter .... The default is -1.\n");
145 m->mothurOut("The processors parameter allows you to specify the number of processors to use while running the command. The default is 1.\n");
146 m->mothurOut("The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n");
147 m->mothurOut("The screen.seqs command should be in the following format: \n");
148 m->mothurOut("screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig, \n");
149 m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n");
150 m->mothurOut("Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
151 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
154 catch(exception& e) {
155 m->errorOut(e, "ScreenSeqsCommand", "help");
160 //***************************************************************************************************************
162 ScreenSeqsCommand::~ScreenSeqsCommand(){ /* do nothing */ }
164 //***************************************************************************************************************
166 int ScreenSeqsCommand::execute(){
169 if (abort == true) { return 0; }
171 string goodSeqFile = outputDir + getRootName(getSimpleName(fastafile)) + "good" + getExtension(fastafile);
172 string badSeqFile = outputDir + getRootName(getSimpleName(fastafile)) + "bad" + getExtension(fastafile);
173 string badAccnosFile = outputDir + getRootName(getSimpleName(fastafile)) + "bad.accnos";
175 int numFastaSeqs = 0;
176 set<string> badSeqNames;
177 int start = time(NULL);
180 int pid, end, numSeqsPerProcessor;
185 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
186 MPI_Comm_size(MPI_COMM_WORLD, &processors);
191 MPI_File outMPIBadAccnos;
193 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
194 int inMode=MPI_MODE_RDONLY;
196 char outGoodFilename[1024];
197 strcpy(outGoodFilename, goodSeqFile.c_str());
199 char outBadFilename[1024];
200 strcpy(outBadFilename, badSeqFile.c_str());
202 char outBadAccnosFilename[1024];
203 strcpy(outBadAccnosFilename, badAccnosFile.c_str());
205 char inFileName[1024];
206 strcpy(inFileName, fastafile.c_str());
208 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
209 MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood);
210 MPI_File_open(MPI_COMM_WORLD, outBadFilename, outMode, MPI_INFO_NULL, &outMPIBad);
211 MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos);
213 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBad); MPI_File_close(&outMPIBadAccnos); return 0; }
215 if (pid == 0) { //you are the root process
217 MPIPos = setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
219 //send file positions to all processes
220 MPI_Bcast(&numFastaSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs
221 MPI_Bcast(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
223 //figure out how many sequences you have to align
224 numSeqsPerProcessor = numFastaSeqs / processors;
225 int startIndex = pid * numSeqsPerProcessor;
226 if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
229 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBad, outMPIBadAccnos, MPIPos, badSeqNames);
231 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); MPI_File_close(&outMPIBad); return 0; }
233 for (int i = 1; i < processors; i++) {
237 MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
238 /*for (int j = 0; j < badSize; j++) {
240 MPI_Recv(&length, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status); //recv the length of the name
241 char* buf2 = new char[length]; //make space to recieve it
242 MPI_Recv(buf2, length, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); //get name
244 string tempBuf = buf2;
245 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
248 badSeqNames.insert(tempBuf);
251 }else{ //you are a child process
252 MPI_Bcast(&numFastaSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
253 MPIPos.resize(numFastaSeqs+1);
254 MPI_Bcast(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
256 //figure out how many sequences you have to align
257 numSeqsPerProcessor = numFastaSeqs / processors;
258 int startIndex = pid * numSeqsPerProcessor;
259 if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
262 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBad, outMPIBadAccnos, MPIPos, badSeqNames);
264 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBad); MPI_File_close(&outMPIBadAccnos); return 0; }
267 int badSize = badSeqNames.size();
268 MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
271 set<string>::iterator it;
272 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
274 int length = name.length();
275 char* buf2 = new char[length];
276 memcpy(buf2, name.c_str(), length);
278 MPI_Send(&length, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
279 MPI_Send(buf2, length, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
284 MPI_File_close(&inMPI);
285 MPI_File_close(&outMPIGood);
286 MPI_File_close(&outMPIBad);
287 MPI_File_close(&outMPIBadAccnos);
291 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
294 openInputFile(fastafile, inFASTA);
295 numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
298 lines.push_back(new linePair(0, numFastaSeqs));
300 driver(lines[0], goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
302 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
305 vector<int> positions;
306 processIDS.resize(0);
309 openInputFile(fastafile, inFASTA);
312 while(!inFASTA.eof()){
313 input = getline(inFASTA);
314 if (input.length() != 0) {
315 if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
320 numFastaSeqs = positions.size();
322 int numSeqsPerProcessor = numFastaSeqs / processors;
324 for (int i = 0; i < processors; i++) {
325 long int startPos = positions[ i * numSeqsPerProcessor ];
326 if(i == processors - 1){
327 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
329 lines.push_back(new linePair(startPos, numSeqsPerProcessor));
332 createProcesses(goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
334 rename((goodSeqFile + toString(processIDS[0]) + ".temp").c_str(), goodSeqFile.c_str());
335 rename((badSeqFile + toString(processIDS[0]) + ".temp").c_str(), badSeqFile.c_str());
336 rename((badAccnosFile + toString(processIDS[0]) + ".temp").c_str(), badAccnosFile.c_str());
338 //append alignment and report files
339 for(int i=1;i<processors;i++){
340 appendFiles((goodSeqFile + toString(processIDS[i]) + ".temp"), goodSeqFile);
341 remove((goodSeqFile + toString(processIDS[i]) + ".temp").c_str());
343 appendFiles((badSeqFile + toString(processIDS[i]) + ".temp"), badSeqFile);
344 remove((badSeqFile + toString(processIDS[i]) + ".temp").c_str());
346 appendFiles((badAccnosFile + toString(processIDS[i]) + ".temp"), badAccnosFile);
347 remove((badAccnosFile + toString(processIDS[i]) + ".temp").c_str());
350 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
352 //read badSeqs in because root process doesnt know what other "bad" seqs the children found
354 int ableToOpen = openInputFile(badAccnosFile, inBad, "no error");
356 if (ableToOpen == 0) {
359 while (!inBad.eof()) {
360 inBad >> tempName; gobble(inBad);
361 badSeqNames.insert(tempName);
368 openInputFile(fastafile, inFASTA);
369 numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
372 lines.push_back(new linePair(0, numFastaSeqs));
374 driver(lines[0], goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
376 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
383 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
385 if (pid == 0) { //only one process should fix files
387 //read accnos file with all names in it, process 0 just has its names
388 MPI_File inMPIAccnos;
391 char inFileName[1024];
392 strcpy(inFileName, badAccnosFile.c_str());
394 MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos); //comm, filename, mode, info, filepointer
395 MPI_File_get_size(inMPIAccnos, &size);
397 char* buffer = new char[size];
398 MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status);
400 string tempBuf = buffer;
401 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size); }
402 istringstream iss (tempBuf,istringstream::in);
405 MPI_File_close(&inMPIAccnos);
410 iss >> tempName; gobble(iss);
411 badSeqNames.insert(tempName);
415 if(namefile != "" && groupfile != "") {
416 screenNameGroupFile(badSeqNames);
417 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
418 }else if(namefile != "") {
419 screenNameGroupFile(badSeqNames);
420 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
421 }else if(groupfile != "") { screenGroupFile(badSeqNames); } // this screens just the group
423 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
425 if(alignreport != "") { screenAlignReport(badSeqNames); }
427 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
433 m->mothurOutEndLine();
434 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
435 m->mothurOut(goodSeqFile); m->mothurOutEndLine();
436 m->mothurOut(badSeqFile); m->mothurOutEndLine();
437 m->mothurOut(badAccnosFile); m->mothurOutEndLine();
438 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
439 m->mothurOutEndLine();
440 m->mothurOutEndLine();
442 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
443 m->mothurOutEndLine();
447 catch(exception& e) {
448 m->errorOut(e, "ScreenSeqsCommand", "execute");
453 //***************************************************************************************************************
455 int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
458 openInputFile(namefile, inputNames);
459 set<string> badSeqGroups;
460 string seqName, seqList, group;
461 set<string>::iterator it;
463 string goodNameFile = outputDir + getRootName(getSimpleName(namefile)) + "good" + getExtension(namefile);
464 string badNameFile = outputDir + getRootName(getSimpleName(namefile)) + "bad" + getExtension(namefile);
466 outputNames.push_back(goodNameFile); outputNames.push_back(badNameFile);
468 ofstream goodNameOut; openOutputFile(goodNameFile, goodNameOut);
469 ofstream badNameOut; openOutputFile(badNameFile, badNameOut);
471 while(!inputNames.eof()){
472 if (m->control_pressed) { goodNameOut.close(); badNameOut.close(); inputNames.close(); remove(goodNameFile.c_str()); remove(badNameFile.c_str()); return 0; }
474 inputNames >> seqName >> seqList;
475 it = badSeqNames.find(seqName);
477 if(it != badSeqNames.end()){
478 badSeqNames.erase(it);
479 badNameOut << seqName << '\t' << seqList << endl;
482 for(int i=0;i<seqList.length();i++){
483 if(seqList[i] == ','){
484 badSeqGroups.insert(seqList.substr(start,i-start));
488 badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
492 goodNameOut << seqName << '\t' << seqList << endl;
500 //we were unable to remove some of the bad sequences
501 if (badSeqNames.size() != 0) {
502 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
503 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
504 m->mothurOutEndLine();
510 ifstream inputGroups;
511 openInputFile(groupfile, inputGroups);
513 string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
514 string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
516 outputNames.push_back(goodGroupFile); outputNames.push_back(badGroupFile);
518 ofstream goodGroupOut; openOutputFile(goodGroupFile, goodGroupOut);
519 ofstream badGroupOut; openOutputFile(badGroupFile, badGroupOut);
521 while(!inputGroups.eof()){
522 if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str()); remove(badNameFile.c_str()); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
524 inputGroups >> seqName >> group;
526 it = badSeqGroups.find(seqName);
528 if(it != badSeqGroups.end()){
529 badSeqGroups.erase(it);
530 badGroupOut << seqName << '\t' << group << endl;
533 goodGroupOut << seqName << '\t' << group << endl;
538 goodGroupOut.close();
541 //we were unable to remove some of the bad sequences
542 if (badSeqGroups.size() != 0) {
543 for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
544 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
545 m->mothurOutEndLine();
553 catch(exception& e) {
554 m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
559 //***************************************************************************************************************
561 int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
563 ifstream inputGroups;
564 openInputFile(groupfile, inputGroups);
565 string seqName, group;
566 set<string>::iterator it;
568 string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
569 string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
571 outputNames.push_back(goodGroupFile); outputNames.push_back(badGroupFile);
573 ofstream goodGroupOut; openOutputFile(goodGroupFile, goodGroupOut);
574 ofstream badGroupOut; openOutputFile(badGroupFile, badGroupOut);
576 while(!inputGroups.eof()){
577 if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
579 inputGroups >> seqName >> group;
580 it = badSeqNames.find(seqName);
582 if(it != badSeqNames.end()){
583 badSeqNames.erase(it);
584 badGroupOut << seqName << '\t' << group << endl;
587 goodGroupOut << seqName << '\t' << group << endl;
592 if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
594 //we were unable to remove some of the bad sequences
595 if (badSeqNames.size() != 0) {
596 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
597 m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
598 m->mothurOutEndLine();
603 goodGroupOut.close();
606 if (m->control_pressed) { remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); }
612 catch(exception& e) {
613 m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
618 //***************************************************************************************************************
620 int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
622 ifstream inputAlignReport;
623 openInputFile(alignreport, inputAlignReport);
624 string seqName, group;
625 set<string>::iterator it;
627 string goodAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "good" + getExtension(alignreport);
628 string badAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "bad" + getExtension(alignreport);
630 outputNames.push_back(goodAlignReportFile); outputNames.push_back(badAlignReportFile);
632 ofstream goodAlignReportOut; openOutputFile(goodAlignReportFile, goodAlignReportOut);
633 ofstream badAlignReportOut; openOutputFile(badAlignReportFile, badAlignReportOut);
635 while (!inputAlignReport.eof()) { // need to copy header
636 char c = inputAlignReport.get();
637 goodAlignReportOut << c;
638 badAlignReportOut << c;
639 if (c == 10 || c == 13){ break; }
642 while(!inputAlignReport.eof()){
643 if (m->control_pressed) { goodAlignReportOut.close(); badAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
645 inputAlignReport >> seqName;
646 it = badSeqNames.find(seqName);
648 while (!inputAlignReport.eof()) { // need to copy header
649 char c = inputAlignReport.get();
651 if (c == 10 || c == 13){ break; }
654 if(it != badSeqNames.end()){
655 badSeqNames.erase(it);
656 badAlignReportOut << seqName << '\t' << line;
659 goodAlignReportOut << seqName << '\t' << line;
661 gobble(inputAlignReport);
664 if (m->control_pressed) { goodAlignReportOut.close(); badAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
666 //we were unable to remove some of the bad sequences
667 if (badSeqNames.size() != 0) {
668 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
669 m->mothurOut("Your file does not include the sequence " + *it + " please correct.");
670 m->mothurOutEndLine();
674 inputAlignReport.close();
675 goodAlignReportOut.close();
676 badAlignReportOut.close();
678 if (m->control_pressed) { remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
683 catch(exception& e) {
684 m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
689 //**********************************************************************************************************************
691 int ScreenSeqsCommand::driver(linePair* line, string goodFName, string badFName, string badAccnosFName, string filename, set<string>& badSeqNames){
694 openOutputFile(goodFName, goodFile);
697 openOutputFile(badFName, badFile);
699 ofstream badAccnosFile;
700 openOutputFile(badAccnosFName, badAccnosFile);
703 openInputFile(filename, inFASTA);
705 inFASTA.seekg(line->start);
707 for(int i=0;i<line->numSeqs;i++){
709 if (m->control_pressed) { return 0; }
711 Sequence currSeq(inFASTA);
712 if (currSeq.getName() != "") {
713 bool goodSeq = 1; // innocent until proven guilty
714 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos()) { goodSeq = 0; }
715 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos()) { goodSeq = 0; }
716 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases()) { goodSeq = 0; }
717 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer()) { goodSeq = 0; }
718 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases()) { goodSeq = 0; }
719 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases()) { goodSeq = 0; }
722 currSeq.printSequence(goodFile);
725 currSeq.printSequence(badFile);
726 badAccnosFile << currSeq.getName() << endl;
727 badSeqNames.insert(currSeq.getName());
737 badAccnosFile.close();
741 catch(exception& e) {
742 m->errorOut(e, "ScreenSeqsCommand", "driver");
746 //**********************************************************************************************************************
748 int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badFile, MPI_File& badAccnosFile, vector<long>& MPIPos, set<string>& badSeqNames){
750 string outputString = "";
751 MPI_Status statusGood;
752 MPI_Status statusBad;
753 MPI_Status statusBadAccnos;
756 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
758 for(int i=0;i<num;i++){
760 if (m->control_pressed) { return 0; }
763 int length = MPIPos[start+i+1] - MPIPos[start+i];
765 char* buf4 = new char[length];
766 memcpy(buf4, outputString.c_str(), length);
768 MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
770 string tempBuf = buf4; delete buf4;
771 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
772 istringstream iss (tempBuf,istringstream::in);
774 Sequence currSeq(iss);
777 if (currSeq.getName() != "") {
778 bool goodSeq = 1; // innocent until proven guilty
779 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos()) { goodSeq = 0; }
780 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos()) { goodSeq = 0; }
781 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases()) { goodSeq = 0; }
782 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer()) { goodSeq = 0; }
783 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases()) { goodSeq = 0; }
784 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases()) { goodSeq = 0; }
787 outputString = ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
790 length = outputString.length();
791 char* buf2 = new char[length];
792 memcpy(buf2, outputString.c_str(), length);
794 MPI_File_write_shared(goodFile, buf2, length, MPI_CHAR, &statusGood);
798 outputString = ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
800 //print bad seq to fasta
801 length = outputString.length();
802 char* buf2 = new char[length];
803 memcpy(buf2, outputString.c_str(), length);
805 MPI_File_write_shared(badFile, buf2, length, MPI_CHAR, &statusBad);
808 badSeqNames.insert(currSeq.getName());
810 //write to bad accnos file
811 outputString = currSeq.getName() + "\n";
813 length = outputString.length();
814 char* buf3 = new char[length];
815 memcpy(buf3, outputString.c_str(), length);
817 MPI_File_write_shared(badAccnosFile, buf3, length, MPI_CHAR, &statusBadAccnos);
825 catch(exception& e) {
826 m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
831 /**************************************************************************************************/
833 int ScreenSeqsCommand::createProcesses(string goodFileName, string badFileName, string badAccnos, string filename, set<string>& badSeqNames) {
835 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
839 //loop through and create all the processes you want
840 while (process != processors) {
844 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
847 exitCommand = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
849 }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
852 //force parent to wait until all the processes are done
853 for (int i=0;i<processors;i++) {
854 int temp = processIDS[i];
861 catch(exception& e) {
862 m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
867 //***************************************************************************************************************