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("screen.seqs");
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;
182 vector<unsigned long int> MPIPos;
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 for(int i = 1; i < processors; i++) {
221 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
222 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
225 //figure out how many sequences you have to align
226 numSeqsPerProcessor = numFastaSeqs / processors;
227 int startIndex = pid * numSeqsPerProcessor;
228 if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
231 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBad, outMPIBadAccnos, MPIPos, badSeqNames);
233 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); MPI_File_close(&outMPIBad); return 0; }
235 for (int i = 1; i < processors; i++) {
239 MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
240 /*for (int j = 0; j < badSize; j++) {
242 MPI_Recv(&length, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status); //recv the length of the name
243 char* buf2 = new char[length]; //make space to recieve it
244 MPI_Recv(buf2, length, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); //get name
246 string tempBuf = buf2;
247 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
250 badSeqNames.insert(tempBuf);
253 }else{ //you are a child process
254 MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
255 MPIPos.resize(numFastaSeqs+1);
256 MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
258 //figure out how many sequences you have to align
259 numSeqsPerProcessor = numFastaSeqs / processors;
260 int startIndex = pid * numSeqsPerProcessor;
261 if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; }
264 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBad, outMPIBadAccnos, MPIPos, badSeqNames);
266 if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBad); MPI_File_close(&outMPIBadAccnos); return 0; }
269 int badSize = badSeqNames.size();
270 MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
273 set<string>::iterator it;
274 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
276 int length = name.length();
277 char* buf2 = new char[length];
278 memcpy(buf2, name.c_str(), length);
280 MPI_Send(&length, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
281 MPI_Send(buf2, length, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
286 MPI_File_close(&inMPI);
287 MPI_File_close(&outMPIGood);
288 MPI_File_close(&outMPIBad);
289 MPI_File_close(&outMPIBadAccnos);
290 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
293 vector<unsigned long int> positions = divideFile(fastafile, processors);
295 for (int i = 0; i < (positions.size()-1); i++) {
296 lines.push_back(new linePair(positions[i], positions[(i+1)]));
299 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
301 numFastaSeqs = driver(lines[0], goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
303 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
306 processIDS.resize(0);
308 numFastaSeqs = createProcesses(goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
310 rename((goodSeqFile + toString(processIDS[0]) + ".temp").c_str(), goodSeqFile.c_str());
311 rename((badSeqFile + toString(processIDS[0]) + ".temp").c_str(), badSeqFile.c_str());
312 rename((badAccnosFile + toString(processIDS[0]) + ".temp").c_str(), badAccnosFile.c_str());
314 //append alignment and report files
315 for(int i=1;i<processors;i++){
316 appendFiles((goodSeqFile + toString(processIDS[i]) + ".temp"), goodSeqFile);
317 remove((goodSeqFile + toString(processIDS[i]) + ".temp").c_str());
319 appendFiles((badSeqFile + toString(processIDS[i]) + ".temp"), badSeqFile);
320 remove((badSeqFile + toString(processIDS[i]) + ".temp").c_str());
322 appendFiles((badAccnosFile + toString(processIDS[i]) + ".temp"), badAccnosFile);
323 remove((badAccnosFile + toString(processIDS[i]) + ".temp").c_str());
326 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
328 //read badSeqs in because root process doesnt know what other "bad" seqs the children found
330 int ableToOpen = openInputFile(badAccnosFile, inBad, "no error");
332 if (ableToOpen == 0) {
335 while (!inBad.eof()) {
336 inBad >> tempName; gobble(inBad);
337 badSeqNames.insert(tempName);
343 numFastaSeqs = driver(lines[0], goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
345 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
352 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
354 if (pid == 0) { //only one process should fix files
356 //read accnos file with all names in it, process 0 just has its names
357 MPI_File inMPIAccnos;
360 char inFileName[1024];
361 strcpy(inFileName, badAccnosFile.c_str());
363 MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos); //comm, filename, mode, info, filepointer
364 MPI_File_get_size(inMPIAccnos, &size);
366 char* buffer = new char[size];
367 MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status);
369 string tempBuf = buffer;
370 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size); }
371 istringstream iss (tempBuf,istringstream::in);
374 MPI_File_close(&inMPIAccnos);
379 iss >> tempName; gobble(iss);
380 badSeqNames.insert(tempName);
384 if(namefile != "" && groupfile != "") {
385 screenNameGroupFile(badSeqNames);
386 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
387 }else if(namefile != "") {
388 screenNameGroupFile(badSeqNames);
389 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
390 }else if(groupfile != "") { screenGroupFile(badSeqNames); } // this screens just the group
392 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
394 if(alignreport != "") { screenAlignReport(badSeqNames); }
396 if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
402 m->mothurOutEndLine();
403 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
404 m->mothurOut(goodSeqFile); m->mothurOutEndLine();
405 m->mothurOut(badSeqFile); m->mothurOutEndLine();
406 m->mothurOut(badAccnosFile); m->mothurOutEndLine();
407 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
408 m->mothurOutEndLine();
409 m->mothurOutEndLine();
411 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
412 m->mothurOutEndLine();
416 catch(exception& e) {
417 m->errorOut(e, "ScreenSeqsCommand", "execute");
422 //***************************************************************************************************************
424 int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
427 openInputFile(namefile, inputNames);
428 set<string> badSeqGroups;
429 string seqName, seqList, group;
430 set<string>::iterator it;
432 string goodNameFile = outputDir + getRootName(getSimpleName(namefile)) + "good" + getExtension(namefile);
433 string badNameFile = outputDir + getRootName(getSimpleName(namefile)) + "bad" + getExtension(namefile);
435 outputNames.push_back(goodNameFile); outputNames.push_back(badNameFile);
437 ofstream goodNameOut; openOutputFile(goodNameFile, goodNameOut);
438 ofstream badNameOut; openOutputFile(badNameFile, badNameOut);
440 while(!inputNames.eof()){
441 if (m->control_pressed) { goodNameOut.close(); badNameOut.close(); inputNames.close(); remove(goodNameFile.c_str()); remove(badNameFile.c_str()); return 0; }
443 inputNames >> seqName >> seqList;
444 it = badSeqNames.find(seqName);
446 if(it != badSeqNames.end()){
447 badSeqNames.erase(it);
448 badNameOut << seqName << '\t' << seqList << endl;
451 for(int i=0;i<seqList.length();i++){
452 if(seqList[i] == ','){
453 badSeqGroups.insert(seqList.substr(start,i-start));
457 badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
461 goodNameOut << seqName << '\t' << seqList << endl;
469 //we were unable to remove some of the bad sequences
470 if (badSeqNames.size() != 0) {
471 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
472 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
473 m->mothurOutEndLine();
479 ifstream inputGroups;
480 openInputFile(groupfile, inputGroups);
482 string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
483 string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
485 outputNames.push_back(goodGroupFile); outputNames.push_back(badGroupFile);
487 ofstream goodGroupOut; openOutputFile(goodGroupFile, goodGroupOut);
488 ofstream badGroupOut; openOutputFile(badGroupFile, badGroupOut);
490 while(!inputGroups.eof()){
491 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; }
493 inputGroups >> seqName >> group;
495 it = badSeqGroups.find(seqName);
497 if(it != badSeqGroups.end()){
498 badSeqGroups.erase(it);
499 badGroupOut << seqName << '\t' << group << endl;
502 goodGroupOut << seqName << '\t' << group << endl;
507 goodGroupOut.close();
510 //we were unable to remove some of the bad sequences
511 if (badSeqGroups.size() != 0) {
512 for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
513 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
514 m->mothurOutEndLine();
522 catch(exception& e) {
523 m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
528 //***************************************************************************************************************
530 int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
532 ifstream inputGroups;
533 openInputFile(groupfile, inputGroups);
534 string seqName, group;
535 set<string>::iterator it;
537 string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
538 string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
540 outputNames.push_back(goodGroupFile); outputNames.push_back(badGroupFile);
542 ofstream goodGroupOut; openOutputFile(goodGroupFile, goodGroupOut);
543 ofstream badGroupOut; openOutputFile(badGroupFile, badGroupOut);
545 while(!inputGroups.eof()){
546 if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
548 inputGroups >> seqName >> group;
549 it = badSeqNames.find(seqName);
551 if(it != badSeqNames.end()){
552 badSeqNames.erase(it);
553 badGroupOut << seqName << '\t' << group << endl;
556 goodGroupOut << seqName << '\t' << group << endl;
561 if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
563 //we were unable to remove some of the bad sequences
564 if (badSeqNames.size() != 0) {
565 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
566 m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
567 m->mothurOutEndLine();
572 goodGroupOut.close();
575 if (m->control_pressed) { remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); }
581 catch(exception& e) {
582 m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
587 //***************************************************************************************************************
589 int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
591 ifstream inputAlignReport;
592 openInputFile(alignreport, inputAlignReport);
593 string seqName, group;
594 set<string>::iterator it;
596 string goodAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "good" + getExtension(alignreport);
597 string badAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "bad" + getExtension(alignreport);
599 outputNames.push_back(goodAlignReportFile); outputNames.push_back(badAlignReportFile);
601 ofstream goodAlignReportOut; openOutputFile(goodAlignReportFile, goodAlignReportOut);
602 ofstream badAlignReportOut; openOutputFile(badAlignReportFile, badAlignReportOut);
604 while (!inputAlignReport.eof()) { // need to copy header
605 char c = inputAlignReport.get();
606 goodAlignReportOut << c;
607 badAlignReportOut << c;
608 if (c == 10 || c == 13){ break; }
611 while(!inputAlignReport.eof()){
612 if (m->control_pressed) { goodAlignReportOut.close(); badAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
614 inputAlignReport >> seqName;
615 it = badSeqNames.find(seqName);
617 while (!inputAlignReport.eof()) { // need to copy header
618 char c = inputAlignReport.get();
620 if (c == 10 || c == 13){ break; }
623 if(it != badSeqNames.end()){
624 badSeqNames.erase(it);
625 badAlignReportOut << seqName << '\t' << line;
628 goodAlignReportOut << seqName << '\t' << line;
630 gobble(inputAlignReport);
633 if (m->control_pressed) { goodAlignReportOut.close(); badAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
635 //we were unable to remove some of the bad sequences
636 if (badSeqNames.size() != 0) {
637 for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
638 m->mothurOut("Your file does not include the sequence " + *it + " please correct.");
639 m->mothurOutEndLine();
643 inputAlignReport.close();
644 goodAlignReportOut.close();
645 badAlignReportOut.close();
647 if (m->control_pressed) { remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
652 catch(exception& e) {
653 m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
658 //**********************************************************************************************************************
660 int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badFName, string badAccnosFName, string filename, set<string>& badSeqNames){
663 openOutputFile(goodFName, goodFile);
666 openOutputFile(badFName, badFile);
668 ofstream badAccnosFile;
669 openOutputFile(badAccnosFName, badAccnosFile);
672 openInputFile(filename, inFASTA);
674 inFASTA.seekg(filePos->start);
681 if (m->control_pressed) { return 0; }
683 Sequence currSeq(inFASTA); gobble(inFASTA);
684 if (currSeq.getName() != "") {
685 bool goodSeq = 1; // innocent until proven guilty
686 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos()) { goodSeq = 0; }
687 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos()) { goodSeq = 0; }
688 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases()) { goodSeq = 0; }
689 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer()) { goodSeq = 0; }
690 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases()) { goodSeq = 0; }
691 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases()) { goodSeq = 0; }
694 currSeq.printSequence(goodFile);
697 currSeq.printSequence(badFile);
698 badAccnosFile << currSeq.getName() << endl;
699 badSeqNames.insert(currSeq.getName());
704 unsigned long int pos = inFASTA.tellg();
705 if ((pos == -1) || (pos >= filePos->end)) { break; }
708 if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
711 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
717 badAccnosFile.close();
721 catch(exception& e) {
722 m->errorOut(e, "ScreenSeqsCommand", "driver");
726 //**********************************************************************************************************************
728 int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badFile, MPI_File& badAccnosFile, vector<unsigned long int>& MPIPos, set<string>& badSeqNames){
730 string outputString = "";
731 MPI_Status statusGood;
732 MPI_Status statusBad;
733 MPI_Status statusBadAccnos;
736 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
738 for(int i=0;i<num;i++){
740 if (m->control_pressed) { return 0; }
743 int length = MPIPos[start+i+1] - MPIPos[start+i];
745 char* buf4 = new char[length];
746 memcpy(buf4, outputString.c_str(), length);
748 MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
750 string tempBuf = buf4; delete buf4;
751 if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
752 istringstream iss (tempBuf,istringstream::in);
754 Sequence currSeq(iss);
757 if (currSeq.getName() != "") {
758 bool goodSeq = 1; // innocent until proven guilty
759 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos()) { goodSeq = 0; }
760 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos()) { goodSeq = 0; }
761 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases()) { goodSeq = 0; }
762 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer()) { goodSeq = 0; }
763 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases()) { goodSeq = 0; }
764 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases()) { goodSeq = 0; }
767 outputString = ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
770 length = outputString.length();
771 char* buf2 = new char[length];
772 memcpy(buf2, outputString.c_str(), length);
774 MPI_File_write_shared(goodFile, buf2, length, MPI_CHAR, &statusGood);
778 outputString = ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
780 //print bad seq to fasta
781 length = outputString.length();
782 char* buf2 = new char[length];
783 memcpy(buf2, outputString.c_str(), length);
785 MPI_File_write_shared(badFile, buf2, length, MPI_CHAR, &statusBad);
788 badSeqNames.insert(currSeq.getName());
790 //write to bad accnos file
791 outputString = currSeq.getName() + "\n";
793 length = outputString.length();
794 char* buf3 = new char[length];
795 memcpy(buf3, outputString.c_str(), length);
797 MPI_File_write_shared(badAccnosFile, buf3, length, MPI_CHAR, &statusBadAccnos);
805 catch(exception& e) {
806 m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
811 /**************************************************************************************************/
813 int ScreenSeqsCommand::createProcesses(string goodFileName, string badFileName, string badAccnos, string filename, set<string>& badSeqNames) {
815 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
819 //loop through and create all the processes you want
820 while (process != processors) {
824 processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
827 num = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
829 //pass numSeqs to parent
831 string tempFile = filename + toString(getpid()) + ".num.temp";
832 openOutputFile(tempFile, out);
837 }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
840 //force parent to wait until all the processes are done
841 for (int i=0;i<processors;i++) {
842 int temp = processIDS[i];
846 for (int i = 0; i < processIDS.size(); i++) {
848 string tempFile = filename + toString(processIDS[i]) + ".num.temp";
849 openInputFile(tempFile, in);
850 if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
851 in.close(); remove(tempFile.c_str());
857 catch(exception& e) {
858 m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
863 //***************************************************************************************************************