X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.cpp;h=2abe9ef78a8c76354d377087fa7a23deb27b4d25;hb=d205e70ae86dbee2efc2df02f2717975854de6ba;hp=832bb9e70dd6d7addf6cc364b384a8b3de100417;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp index 832bb9e..2abe9ef 100644 --- a/removeseqscommand.cpp +++ b/removeseqscommand.cpp @@ -81,6 +81,7 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option) { //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { vector myArray = setParameters(); @@ -190,19 +191,22 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option) { m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine(); abort = true; } - } + }else { m->setAccnosFile(accnosfile); } fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not open") { abort = true; } + if (fastafile == "not open") { fastafile = ""; abort = true; } else if (fastafile == "not found") { fastafile = ""; } - + else { m->setFastaFile(fastafile); } + namefile = validParameter.validFile(parameters, "name", true); - if (namefile == "not open") { abort = true; } + if (namefile == "not open") { namefile = ""; abort = true; } else if (namefile == "not found") { namefile = ""; } - + else { m->setNameFile(namefile); } + groupfile = validParameter.validFile(parameters, "group", true); if (groupfile == "not open") { abort = true; } - else if (groupfile == "not found") { groupfile = ""; } + else if (groupfile == "not found") { groupfile = ""; } + else { m->setGroupFile(groupfile); } alignfile = validParameter.validFile(parameters, "alignreport", true); if (alignfile == "not open") { abort = true; } @@ -211,15 +215,17 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option) { listfile = validParameter.validFile(parameters, "list", true); if (listfile == "not open") { abort = true; } else if (listfile == "not found") { listfile = ""; } + else { m->setListFile(listfile); } taxfile = validParameter.validFile(parameters, "taxonomy", true); if (taxfile == "not open") { abort = true; } else if (taxfile == "not found") { taxfile = ""; } + else { m->setTaxonomyFile(taxfile); } qualfile = validParameter.validFile(parameters, "qfile", true); if (qualfile == "not open") { abort = true; } else if (qualfile == "not found") { qualfile = ""; } - + else { m->setQualFile(qualfile); } string usedDups = "true"; string temp = validParameter.validFile(parameters, "dups", false); @@ -231,6 +237,10 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option) { if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, group, taxonomy, quality, alignreport or list."); m->mothurOutEndLine(); abort = true; } + if ((fastafile != "") && (namefile == "")) { + vector files; files.push_back(fastafile); + parser.getNameFile(files); + } } } @@ -260,10 +270,8 @@ int RemoveSeqsCommand::execute(){ if (taxfile != "") { readTax(); } if (qualfile != "") { readQual(); } - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } - - m->mothurOut("Removed " + toString(names.size()) + " sequences."); m->mothurOutEndLine(); - + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + if (outputNames.size() != 0) { m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); @@ -327,9 +335,10 @@ int RemoveSeqsCommand::readFasta(){ string name; bool wroteSomething = false; + int removedCount = 0; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } Sequence currSeq(in); name = currSeq.getName(); @@ -340,7 +349,7 @@ int RemoveSeqsCommand::readFasta(){ wroteSomething = true; currSeq.printSequence(out); - } + }else { removedCount++; } } m->gobble(in); } @@ -350,6 +359,8 @@ int RemoveSeqsCommand::readFasta(){ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); } outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName); + m->mothurOut("Removed " + toString(removedCount) + " sequences from your fasta file."); m->mothurOutEndLine(); + return 0; } @@ -373,6 +384,7 @@ int RemoveSeqsCommand::readQual(){ string name; bool wroteSomething = false; + int removedCount = 0; while(!in.eof()){ @@ -404,7 +416,7 @@ int RemoveSeqsCommand::readQual(){ wroteSomething = true; out << name << endl << scores; - } + }else { removedCount++; } m->gobble(in); } @@ -415,6 +427,8 @@ int RemoveSeqsCommand::readQual(){ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); } outputNames.push_back(outputFileName); outputTypes["qfile"].push_back(outputFileName); + m->mothurOut("Removed " + toString(removedCount) + " sequences from your quality file."); m->mothurOutEndLine(); + return 0; } @@ -437,8 +451,12 @@ int RemoveSeqsCommand::readList(){ m->openInputFile(listfile, in); bool wroteSomething = false; + int removedCount = 0; while(!in.eof()){ + + removedCount = 0; + //read in list vector ListVector list(in); @@ -448,7 +466,7 @@ int RemoveSeqsCommand::readList(){ //for each bin for (int i = 0; i < list.getNumBins(); i++) { - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } //parse out names that are in accnos file string binnames = list.get(i); @@ -460,10 +478,12 @@ int RemoveSeqsCommand::readList(){ //if that name is in the .accnos file, add it if (names.count(name) == 0) { newNames += name + ","; } + else { removedCount++; } } //get last name if (names.count(binnames) == 0) { newNames += binnames + ","; } + else { removedCount++; } //if there are names in this bin add to new list if (newNames != "") { @@ -485,7 +505,9 @@ int RemoveSeqsCommand::readList(){ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); } outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName); - + + m->mothurOut("Removed " + toString(removedCount) + " sequences from your list file."); m->mothurOutEndLine(); + return 0; } @@ -509,10 +531,10 @@ int RemoveSeqsCommand::readName(){ string name, firstCol, secondCol; bool wroteSomething = false; - + int removedCount = 0; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> firstCol; m->gobble(in); in >> secondCol; @@ -529,7 +551,9 @@ int RemoveSeqsCommand::readName(){ if ((dups) && (validSecond.size() != parsedNames.size())) { //if dups is true and we want to get rid of anyone, get rid of everyone for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); } + removedCount += parsedNames.size(); }else { + removedCount += parsedNames.size()-validSecond.size(); //if the name in the first column is in the set then print it and any other names in second column also in set if (names.count(firstCol) == 0) { @@ -565,6 +589,8 @@ int RemoveSeqsCommand::readName(){ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); } outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName); + m->mothurOut("Removed " + toString(removedCount) + " sequences from your name file."); m->mothurOutEndLine(); + return 0; } catch(exception& e) { @@ -588,9 +614,10 @@ int RemoveSeqsCommand::readGroup(){ string name, group; bool wroteSomething = false; + int removedCount = 0; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> name; //read from first column in >> group; //read from second column @@ -599,7 +626,7 @@ int RemoveSeqsCommand::readGroup(){ if (names.count(name) == 0) { wroteSomething = true; out << name << '\t' << group << endl; - } + }else { removedCount++; } m->gobble(in); } @@ -609,6 +636,9 @@ int RemoveSeqsCommand::readGroup(){ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); } outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName); + m->mothurOut("Removed " + toString(removedCount) + " sequences from your group file."); m->mothurOutEndLine(); + + return 0; } catch(exception& e) { @@ -630,9 +660,10 @@ int RemoveSeqsCommand::readTax(){ string name, tax; bool wroteSomething = false; + int removedCount = 0; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> name; //read from first column in >> tax; //read from second column @@ -641,7 +672,7 @@ int RemoveSeqsCommand::readTax(){ if (names.count(name) == 0) { wroteSomething = true; out << name << '\t' << tax << endl; - } + }else { removedCount++; } m->gobble(in); } @@ -651,6 +682,8 @@ int RemoveSeqsCommand::readTax(){ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); } outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName); + m->mothurOut("Removed " + toString(removedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine(); + return 0; } catch(exception& e) { @@ -674,6 +707,7 @@ int RemoveSeqsCommand::readAlign(){ string name, junk; bool wroteSomething = false; + int removedCount = 0; //read column headers for (int i = 0; i < 16; i++) { @@ -683,7 +717,7 @@ int RemoveSeqsCommand::readAlign(){ out << endl; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> name; //read from first column @@ -701,6 +735,7 @@ int RemoveSeqsCommand::readAlign(){ out << endl; }else {//still read just don't do anything with it + removedCount++; //read rest for (int i = 0; i < 15; i++) { @@ -717,6 +752,9 @@ int RemoveSeqsCommand::readAlign(){ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine(); } outputTypes["alignreport"].push_back(outputFileName); outputNames.push_back(outputFileName); + m->mothurOut("Removed " + toString(removedCount) + " sequences from your alignreport file."); m->mothurOutEndLine(); + + return 0; }