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Created vsearchFileParser class to encapsulate code
Issue #169
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,142 @@ | ||
| // | ||
| // vsearchfileparser.cpp | ||
| // Mothur | ||
| // | ||
| // Created by Sarah Westcott on 10/13/15. | ||
| // Copyright (c) 2015 Schloss Lab. All rights reserved. | ||
| // | ||
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| #include "vsearchfileparser.h" | ||
| #include "deconvolutecommand.h" | ||
| #include "sequence.hpp" | ||
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| /***********************************************************************/ | ||
| VsearchFileParser::VsearchFileParser(string f){ | ||
| try { | ||
| m = MothurOut::getInstance(); | ||
| fastafile = f; | ||
| namefile = ""; | ||
| countfile = ""; | ||
| } | ||
| catch(exception& e) { | ||
| m->errorOut(e, "VsearchFileParser", "VsearchFileParser"); | ||
| exit(1); | ||
| } | ||
| } | ||
| /***********************************************************************/ | ||
| VsearchFileParser::VsearchFileParser(string f, string nameOrCount, string format) { | ||
| try { | ||
| m = MothurOut::getInstance(); | ||
| fastafile = f; | ||
| namefile = ""; | ||
| countfile = ""; | ||
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| if (format == "name") { namefile = nameOrCount; } | ||
| else if (format == "count") { countfile = nameOrCount; } | ||
| else { m->mothurOut("[ERROR]: " + format + " is not a valid file format for the VsearchFileParser, quitting.\n"); m->control_pressed = true; } | ||
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| } | ||
| catch(exception& e) { | ||
| m->errorOut(e, "VsearchFileParser", "VsearchFileParser"); | ||
| exit(1); | ||
| } | ||
| } | ||
| /***********************************************************************/ | ||
| string VsearchFileParser::getVsearchFile() { | ||
| try { | ||
| //Run unique.seqs on the data if a name or count file is not given | ||
| map<string, int> nameMap; | ||
| if ((namefile == "") && (countfile == "")) { countfile = getNamesFile(fastafile); } | ||
| else if (namefile != "") { nameMap = m->readNames(namefile); } | ||
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| if (countfile != "") { CountTable countTable; countTable.readTable(countfile, false, false); nameMap = countTable.getNameMap(); } | ||
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| if (m->control_pressed) { return 0; } | ||
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| //Remove gap characters from each sequence if needed | ||
| //Append the number of sequences that each unique sequence represents to the end of the fasta file name | ||
| //Sorts by abundance | ||
| string vsearchFastafile = createVsearchFasta(fastafile, nameMap); nameMap.clear(); | ||
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| return vsearchFastafile; | ||
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| } | ||
| catch(exception& e) { | ||
| m->errorOut(e, "VsearchFileParser", "getVsearchFile"); | ||
| exit(1); | ||
| } | ||
| } | ||
| /**********************************************************************/ | ||
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| string VsearchFileParser::createVsearchFasta(string inputFile, map<string, int>& nameMap){ | ||
| try { | ||
| string vsearchFasta = m->getSimpleName(fastafile) + ".sorted.fasta.temp"; | ||
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| vector<seqPriorityNode> seqs; | ||
| map<string, int>::iterator it; | ||
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| ifstream in; | ||
| m->openInputFile(inputFile, in); | ||
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| while (!in.eof()) { | ||
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| if (m->control_pressed) { in.close(); return vsearchFasta; } | ||
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| Sequence seq(in); m->gobble(in); | ||
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| it = nameMap.find(seq.getName()); | ||
| if (it == nameMap.end()) { | ||
| m->mothurOut("[ERROR]: " + seq.getName() + " is not in your name or countfile, quitting.\n"); m->control_pressed = true; | ||
| }else { | ||
| seqPriorityNode temp(it->second, seq.getUnaligned(), it->first); | ||
| seqs.push_back(temp); | ||
| nameMap.erase(it); | ||
| } | ||
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| } | ||
| in.close(); | ||
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| m->printVsearchFile(seqs, vsearchFasta); | ||
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| return vsearchFasta; | ||
| } | ||
| catch(exception& e) { | ||
| m->errorOut(e, "VsearchFileParser", "createVsearchFasta"); | ||
| exit(1); | ||
| } | ||
| } | ||
| /*************************************************************************/ | ||
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| string VsearchFileParser::getNamesFile(string& inputFile){ | ||
| try { | ||
| string nameFile = ""; | ||
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| m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine(); | ||
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| //use unique.seqs to create new name and fastafile | ||
| string inputString = "fasta=" + inputFile + ", format=count"; | ||
| m->mothurOut("/******************************************/"); m->mothurOutEndLine(); | ||
| m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); | ||
| m->mothurCalling = true; | ||
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| Command* uniqueCommand = new DeconvoluteCommand(inputString); | ||
| uniqueCommand->execute(); | ||
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| map<string, vector<string> > filenames = uniqueCommand->getOutputFiles(); | ||
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| delete uniqueCommand; | ||
| m->mothurCalling = false; | ||
| m->mothurOut("/******************************************/"); m->mothurOutEndLine(); | ||
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| countfile = filenames["count"][0]; | ||
| fastafile = filenames["fasta"][0]; | ||
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| return nameFile; | ||
| } | ||
| catch(exception& e) { | ||
| m->errorOut(e, "VsearchFileParser", "getNamesFile"); | ||
| exit(1); | ||
| } | ||
| } | ||
| /***********************************************************************/ | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| // | ||
| // vsearchfileparser.h | ||
| // Mothur | ||
| // | ||
| // Created by Sarah Westcott on 10/13/15. | ||
| // Copyright (c) 2015 Schloss Lab. All rights reserved. | ||
| // | ||
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| #ifndef __Mothur__vsearchfileparser__ | ||
| #define __Mothur__vsearchfileparser__ | ||
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| #include "mothurout.h" | ||
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| /**************************************************************************************************/ | ||
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| class VsearchFileParser { | ||
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| public: | ||
| VsearchFileParser(string f); | ||
| VsearchFileParser(string f, string n, string format); | ||
| ~VsearchFileParser(){} | ||
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| string getVsearchFile(); | ||
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| private: | ||
| MothurOut* m; | ||
| string fastafile, namefile, countfile; | ||
| string getNamesFile(string& inputFile); | ||
| string createVsearchFasta(string, map<string, int>&); | ||
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| }; | ||
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| /**************************************************************************************************/ | ||
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| #endif /* defined(__Mothur__vsearchfileparser__) */ |