5 * Created by Sarah Westcott on 7/8/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "getseqscommand.h"
11 #include "sequence.hpp"
12 #include "listvector.hpp"
14 //**********************************************************************************************************************
16 GetSeqsCommand::GetSeqsCommand(string option) {
20 //allow user to run help
21 if(option == "help") { help(); abort = true; }
24 //valid paramters for this command
25 string Array[] = {"fasta","name", "group", "alignreport", "accnos", "dups", "list","taxonomy","outputdir","inputdir"};
26 vector<string> myArray (Array, Array+(sizeof(Array)/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 output directory command factory will send this info to us in the output parameter
40 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
42 //if the user changes the input directory command factory will send this info to us in the output parameter
43 string inputDir = validParameter.validFile(parameters, "inputdir", false);
44 if (inputDir == "not found"){ inputDir = ""; }
47 it = parameters.find("alignreport");
48 //user has given a template file
49 if(it != parameters.end()){
50 path = hasPath(it->second);
51 //if the user has not given a path then, add inputdir. else leave path alone.
52 if (path == "") { parameters["alignreport"] = inputDir + it->second; }
55 it = parameters.find("fasta");
56 //user has given a template file
57 if(it != parameters.end()){
58 path = hasPath(it->second);
59 //if the user has not given a path then, add inputdir. else leave path alone.
60 if (path == "") { parameters["fasta"] = inputDir + it->second; }
63 it = parameters.find("accnos");
64 //user has given a template file
65 if(it != parameters.end()){
66 path = hasPath(it->second);
67 //if the user has not given a path then, add inputdir. else leave path alone.
68 if (path == "") { parameters["accnos"] = inputDir + it->second; }
71 it = parameters.find("list");
72 //user has given a template file
73 if(it != parameters.end()){
74 path = hasPath(it->second);
75 //if the user has not given a path then, add inputdir. else leave path alone.
76 if (path == "") { parameters["list"] = inputDir + it->second; }
79 it = parameters.find("name");
80 //user has given a template file
81 if(it != parameters.end()){
82 path = hasPath(it->second);
83 //if the user has not given a path then, add inputdir. else leave path alone.
84 if (path == "") { parameters["name"] = inputDir + it->second; }
87 it = parameters.find("group");
88 //user has given a template file
89 if(it != parameters.end()){
90 path = hasPath(it->second);
91 //if the user has not given a path then, add inputdir. else leave path alone.
92 if (path == "") { parameters["group"] = inputDir + it->second; }
95 it = parameters.find("taxonomy");
96 //user has given a template file
97 if(it != parameters.end()){
98 path = hasPath(it->second);
99 //if the user has not given a path then, add inputdir. else leave path alone.
100 if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
105 //check for required parameters
106 accnosfile = validParameter.validFile(parameters, "accnos", true);
107 if (accnosfile == "not open") { abort = true; }
108 else if (accnosfile == "not found") { accnosfile = ""; m->mothurOut("You must provide an accnos file."); m->mothurOutEndLine(); abort = true; }
110 fastafile = validParameter.validFile(parameters, "fasta", true);
111 if (fastafile == "not open") { abort = true; }
112 else if (fastafile == "not found") { fastafile = ""; }
114 namefile = validParameter.validFile(parameters, "name", true);
115 if (namefile == "not open") { abort = true; }
116 else if (namefile == "not found") { namefile = ""; }
118 groupfile = validParameter.validFile(parameters, "group", true);
119 if (groupfile == "not open") { abort = true; }
120 else if (groupfile == "not found") { groupfile = ""; }
122 alignfile = validParameter.validFile(parameters, "alignreport", true);
123 if (alignfile == "not open") { abort = true; }
124 else if (alignfile == "not found") { alignfile = ""; }
126 listfile = validParameter.validFile(parameters, "list", true);
127 if (listfile == "not open") { abort = true; }
128 else if (listfile == "not found") { listfile = ""; }
130 taxfile = validParameter.validFile(parameters, "taxonomy", true);
131 if (taxfile == "not open") { abort = true; }
132 else if (taxfile == "not found") { taxfile = ""; }
134 string usedDups = "true";
135 string temp = validParameter.validFile(parameters, "dups", false); if (temp == "not found") { temp = "false"; usedDups = ""; }
138 if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; }
140 if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; }
145 catch(exception& e) {
146 m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
150 //**********************************************************************************************************************
152 void GetSeqsCommand::help(){
154 m->mothurOut("The get.seqs command reads an .accnos file and any of the following file types: fasta, name, group, list, taxonomy or alignreport file.\n");
155 m->mothurOut("It outputs a file containing only the sequences in the .accnos file.\n");
156 m->mothurOut("The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy, alignreport and dups. You must provide accnos and at least one of the other parameters.\n");
157 m->mothurOut("The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n");
158 m->mothurOut("The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
159 m->mothurOut("Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n");
160 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
162 catch(exception& e) {
163 m->errorOut(e, "GetSeqsCommand", "help");
168 //**********************************************************************************************************************
170 int GetSeqsCommand::execute(){
173 if (abort == true) { return 0; }
175 //get names you want to keep
178 if (m->control_pressed) { return 0; }
180 //read through the correct file and output lines you want to keep
181 if (namefile != "") { readName(); }
182 if (fastafile != "") { readFasta(); }
183 if (groupfile != "") { readGroup(); }
184 if (alignfile != "") { readAlign(); }
185 if (listfile != "") { readList(); }
186 if (taxfile != "") { readTax(); }
188 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
190 if (outputNames.size() != 0) {
191 m->mothurOutEndLine();
192 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
193 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
194 m->mothurOutEndLine();
200 catch(exception& e) {
201 m->errorOut(e, "GetSeqsCommand", "execute");
206 //**********************************************************************************************************************
207 int GetSeqsCommand::readFasta(){
209 if (outputDir == "") { outputDir += hasPath(fastafile); }
210 string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "pick" + getExtension(fastafile);
212 openOutputFile(outputFileName, out);
216 openInputFile(fastafile, in);
219 bool wroteSomething = false;
223 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
225 Sequence currSeq(in);
226 name = currSeq.getName();
229 //if this name is in the accnos file
230 if (names.count(name) != 0) {
231 wroteSomething = true;
233 currSeq.printSequence(out);
241 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
242 outputNames.push_back(outputFileName);
247 catch(exception& e) {
248 m->errorOut(e, "GetSeqsCommand", "readFasta");
252 //**********************************************************************************************************************
253 int GetSeqsCommand::readList(){
255 if (outputDir == "") { outputDir += hasPath(listfile); }
256 string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + "pick" + getExtension(listfile);
258 openOutputFile(outputFileName, out);
261 openInputFile(listfile, in);
263 bool wroteSomething = false;
267 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
269 //read in list vector
272 //make a new list vector
274 newList.setLabel(list.getLabel());
277 for (int i = 0; i < list.getNumBins(); i++) {
279 //parse out names that are in accnos file
280 string binnames = list.get(i);
282 string newNames = "";
283 while (binnames.find_first_of(',') != -1) {
284 string name = binnames.substr(0,binnames.find_first_of(','));
285 binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
287 //if that name is in the .accnos file, add it
288 if (names.count(name) != 0) { newNames += name + ","; }
292 if (names.count(binnames) != 0) { newNames += binnames + ","; }
294 //if there are names in this bin add to new list
295 if (newNames != "") {
296 newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
297 newList.push_back(newNames);
301 //print new listvector
302 if (newList.getNumBins() != 0) {
303 wroteSomething = true;
312 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
313 outputNames.push_back(outputFileName);
318 catch(exception& e) {
319 m->errorOut(e, "GetSeqsCommand", "readList");
323 //**********************************************************************************************************************
324 int GetSeqsCommand::readName(){
326 if (outputDir == "") { outputDir += hasPath(namefile); }
327 string outputFileName = outputDir + getRootName(getSimpleName(namefile)) + "pick" + getExtension(namefile);
329 openOutputFile(outputFileName, out);
333 openInputFile(namefile, in);
334 string name, firstCol, secondCol;
336 bool wroteSomething = false;
341 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
347 if (dups) { hold = secondCol; }
349 vector<string> parsedNames;
350 //parse second column saving each name
351 while (secondCol.find_first_of(',') != -1) {
352 name = secondCol.substr(0,secondCol.find_first_of(','));
353 secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
354 parsedNames.push_back(name);
357 //get name after last ,
358 parsedNames.push_back(secondCol);
360 vector<string> validSecond;
361 for (int i = 0; i < parsedNames.size(); i++) {
362 if (names.count(parsedNames[i]) != 0) {
363 validSecond.push_back(parsedNames[i]);
367 if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
368 for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); }
369 out << firstCol << '\t' << hold << endl;
370 wroteSomething = true;
372 //if the name in the first column is in the set then print it and any other names in second column also in set
373 if (names.count(firstCol) != 0) {
375 wroteSomething = true;
377 out << firstCol << '\t';
379 //you know you have at least one valid second since first column is valid
380 for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
381 out << validSecond[validSecond.size()-1] << endl;
384 //make first name in set you come to first column and then add the remaining names to second column
386 //you want part of this row
387 if (validSecond.size() != 0) {
389 wroteSomething = true;
391 out << validSecond[0] << '\t';
393 //you know you have at least one valid second since first column is valid
394 for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
395 out << validSecond[validSecond.size()-1] << endl;
404 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
405 outputNames.push_back(outputFileName);
410 catch(exception& e) {
411 m->errorOut(e, "GetSeqsCommand", "readName");
416 //**********************************************************************************************************************
417 int GetSeqsCommand::readGroup(){
419 if (outputDir == "") { outputDir += hasPath(groupfile); }
420 string outputFileName = outputDir + getRootName(getSimpleName(groupfile)) + "pick" + getExtension(groupfile);
422 openOutputFile(outputFileName, out);
426 openInputFile(groupfile, in);
429 bool wroteSomething = false;
433 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
436 in >> name; //read from first column
437 in >> group; //read from second column
439 //if this name is in the accnos file
440 if (names.count(name) != 0) {
441 wroteSomething = true;
443 out << name << '\t' << group << endl;
451 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
452 outputNames.push_back(outputFileName);
457 catch(exception& e) {
458 m->errorOut(e, "GetSeqsCommand", "readGroup");
462 //**********************************************************************************************************************
463 int GetSeqsCommand::readTax(){
465 if (outputDir == "") { outputDir += hasPath(taxfile); }
466 string outputFileName = outputDir + getRootName(getSimpleName(taxfile)) + "pick" + getExtension(taxfile);
468 openOutputFile(outputFileName, out);
471 openInputFile(taxfile, in);
474 bool wroteSomething = false;
478 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
480 in >> name; //read from first column
481 in >> tax; //read from second column
483 //if this name is in the accnos file
484 if (names.count(name) != 0) {
485 wroteSomething = true;
487 out << name << '\t' << tax << endl;
495 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
496 outputNames.push_back(outputFileName);
501 catch(exception& e) {
502 m->errorOut(e, "GetSeqsCommand", "readTax");
506 //**********************************************************************************************************************
507 //alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name
508 int GetSeqsCommand::readAlign(){
510 if (outputDir == "") { outputDir += hasPath(alignfile); }
511 string outputFileName = outputDir + getRootName(getSimpleName(alignfile)) + "pick.align.report";
513 openOutputFile(outputFileName, out);
517 openInputFile(alignfile, in);
520 bool wroteSomething = false;
522 //read column headers
523 for (int i = 0; i < 16; i++) {
524 if (!in.eof()) { in >> junk; out << junk << '\t'; }
531 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
534 in >> name; //read from first column
536 //if this name is in the accnos file
537 if (names.count(name) != 0) {
538 wroteSomething = true;
543 for (int i = 0; i < 15; i++) {
544 if (!in.eof()) { in >> junk; out << junk << '\t'; }
549 }else {//still read just don't do anything with it
551 for (int i = 0; i < 15; i++) {
552 if (!in.eof()) { in >> junk; }
562 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
563 outputNames.push_back(outputFileName);
568 catch(exception& e) {
569 m->errorOut(e, "GetSeqsCommand", "readAlign");
573 //**********************************************************************************************************************
575 int GetSeqsCommand::readAccnos(){
579 openInputFile(accnosfile, in);
594 catch(exception& e) {
595 m->errorOut(e, "GetSeqsCommand", "readAccnos");
600 //**********************************************************************************************************************