X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.cpp;h=8bf93ce68db55f9b380307feb73d83ecf3700c5d;hb=28d6f2bddc5c0718ae7f63648be3130a35fb0f02;hp=a9463a076cfee738f5171575325a6a92881744d9;hpb=814675616c10a40911886afb9dfe216f0245e3a2;p=mothur.git diff --git a/getseqscommand.cpp b/getseqscommand.cpp index a9463a0..8bf93ce 100644 --- a/getseqscommand.cpp +++ b/getseqscommand.cpp @@ -130,9 +130,15 @@ GetSeqsCommand::GetSeqsCommand(string option) { taxfile = validParameter.validFile(parameters, "taxonomy", true); if (taxfile == "not open") { abort = true; } else if (taxfile == "not found") { taxfile = ""; } - + + string usedDups = "true"; + string temp = validParameter.validFile(parameters, "dups", false); if (temp == "not found") { temp = "false"; usedDups = ""; } + dups = isTrue(temp); 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; } + + if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; } + } } @@ -147,7 +153,8 @@ void GetSeqsCommand::help(){ try { 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"); m->mothurOut("It outputs a file containing only the sequences in the .accnos file.\n"); - m->mothurOut("The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy and alignreport. You must provide accnos and at least one of the other parameters.\n"); + 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"); + 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"); m->mothurOut("The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n"); m->mothurOut("Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n"); m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); @@ -171,8 +178,8 @@ int GetSeqsCommand::execute(){ if (m->control_pressed) { return 0; } //read through the correct file and output lines you want to keep - if (fastafile != "") { readFasta(); } if (namefile != "") { readName(); } + if (fastafile != "") { readFasta(); } if (groupfile != "") { readGroup(); } if (alignfile != "") { readAlign(); } if (listfile != "") { readList(); } @@ -220,7 +227,7 @@ int GetSeqsCommand::readFasta(){ if (name != "") { //if this name is in the accnos file - if (names.count(name) == 1) { + if (names.count(name) != 0) { wroteSomething = true; currSeq.printSequence(out); @@ -280,11 +287,11 @@ int GetSeqsCommand::readList(){ binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length()); //if that name is in the .accnos file, add it - if (names.count(name) == 1) { newNames += name + ","; } + if (names.count(name) != 0) { newNames += name + ","; } } //get last name - if (names.count(binnames) == 1) { newNames += binnames + ","; } + if (names.count(binnames) != 0) { newNames += binnames + ","; } //if there are names in this bin add to new list if (newNames != "") { @@ -338,7 +345,10 @@ int GetSeqsCommand::readName(){ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } in >> firstCol; - in >> secondCol; + in >> secondCol; + + string hold = ""; + if (dups) { hold = secondCol; } vector parsedNames; //parse second column saving each name @@ -353,39 +363,43 @@ int GetSeqsCommand::readName(){ vector validSecond; for (int i = 0; i < parsedNames.size(); i++) { - if (names.count(parsedNames[i]) == 1) { + if (names.count(parsedNames[i]) != 0) { validSecond.push_back(parsedNames[i]); } } - - //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) == 1) { - + if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone + for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); } + out << firstCol << '\t' << hold << endl; wroteSomething = true; - - out << firstCol << '\t'; - - //you know you have at least one valid second since first column is valid - for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; } - out << validSecond[validSecond.size()-1] << endl; - - - //make first name in set you come to first column and then add the remaining names to second column }else { - //you want part of this row - if (validSecond.size() != 0) { + //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) { wroteSomething = true; - out << validSecond[0] << '\t'; - + out << firstCol << '\t'; + //you know you have at least one valid second since first column is valid for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; } out << validSecond[validSecond.size()-1] << endl; + + + //make first name in set you come to first column and then add the remaining names to second column + }else { + //you want part of this row + if (validSecond.size() != 0) { + + wroteSomething = true; + + out << validSecond[0] << '\t'; + + //you know you have at least one valid second since first column is valid + for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; } + out << validSecond[validSecond.size()-1] << endl; + } } } - gobble(in); } in.close(); @@ -429,7 +443,7 @@ int GetSeqsCommand::readGroup(){ in >> group; //read from second column //if this name is in the accnos file - if (names.count(name) == 1) { + if (names.count(name) != 0) { wroteSomething = true; out << name << '\t' << group << endl; @@ -475,7 +489,7 @@ int GetSeqsCommand::readTax(){ in >> tax; //read from second column //if this name is in the accnos file - if (names.count(name) == 1) { + if (names.count(name) != 0) { wroteSomething = true; out << name << '\t' << tax << endl; @@ -530,7 +544,7 @@ int GetSeqsCommand::readAlign(){ in >> name; //read from first column //if this name is in the accnos file - if (names.count(name) == 1) { + if (names.count(name) != 0) { wroteSomething = true; out << name << '\t';