Adds sorting to pcr.seqs to force order

#792
mothur · Oct 5, 2021 · 60cc15c · 60cc15c
1 parent f597278
commit 60cc15c
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Showing 4 changed files with 59 additions and 4 deletions.
diff --git a/source/commands/pcrseqscommand.cpp b/source/commands/pcrseqscommand.cpp
@@ -7,6 +7,7 @@
 //
 
 #include "pcrseqscommand.h"
+#include "sortseqscommand.h"
 
 //**********************************************************************************************************************
 vector<string> PcrSeqsCommand::setParameters(){	
@@ -216,8 +217,7 @@ int PcrSeqsCommand::execute(){
 
 		if (abort) { if (calledHelp) { return 0; }  return 2;	}
 
-        long start = time(NULL);
-        fileAligned = true; pairedOligos = false;
+        long start = time(NULL); fileAligned = true; pairedOligos = false;
 
         string thisOutputDir = outputdir;
 		if (outputdir == "") {  thisOutputDir += util.hasPath(fastafile);  }
@@ -317,6 +317,11 @@ int PcrSeqsCommand::execute(){
         }
         if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) {	util.mothurRemove(outputNames[i]); } return 0; }
 
+        itTypes = outputTypes.find("fasta");
+        if (itTypes != outputTypes.end()) {
+            if ((itTypes->second).size() != 0) { preserveOrder((itTypes->second)[0]);  }
+        }
+
         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.\n");
 
 		m->mothurOut("\nOutput File Names: \n");
@@ -1020,6 +1025,55 @@ int PcrSeqsCommand::adjustDots(string goodFasta, map<string, vector<int> > locat
     }
 }
 //***************************************************************************************************************
+void PcrSeqsCommand::preserveOrder(string outputfile){
+    try {
+        string thisOutputDir = outputdir;
+        if (outputdir == "") {  thisOutputDir += util.hasPath(fastafile);  }
+        string orderAccnosFile = thisOutputDir + util.getRootName(util.getSimpleName(fastafile)) + "order.accnos";
+
+        ofstream out; util.openOutputFile(orderAccnosFile, out);
+        ifstream in; util.openInputFile(fastafile, in);
+
+        while (!in.eof()) {
+            if (m->getControl_pressed()) { break; }
+
+            Sequence seq(in); util.gobble(in);
+
+            if (seq.getName() != "") {
+                out << seq.getName() << endl;
+            }
+        }
+        in.close();
+        out.close();
+
+        //run sort.seqs
+        string inputString = "fasta=" + outputfile + ", accnos=" + orderAccnosFile;
+
+        m->mothurOut("/******************************************/\n");
+        m->mothurOut("\nRunning command: sort.seqs(" + inputString + ")\n");
+        current->setMothurCalling(true);
+
+        Command* sortSeqsCommand = new SortSeqsCommand(inputString);
+        sortSeqsCommand->execute();
+
+        string tempFastafile = sortSeqsCommand->getOutputFiles()["fasta"][0];
+        util.mothurRemove(outputfile);
+        util.renameFile(tempFastafile, outputfile);
+        util.mothurRemove(orderAccnosFile);
+
+        delete sortSeqsCommand;
+        current->setMothurCalling(false);
+
+        m->mothurOut("/******************************************/\n");
+
+    }
+    catch(exception& e) {
+        m->errorOut(e, "PcrSeqsCommand", "preserveOrder");
+        exit(1);
+    }
+
+}
+//***************************************************************************************************************
 Sequence PcrSeqsCommand::readEcoli(){
 	try {
 		ifstream in; util.openInputFile(ecolifile, in);

diff --git a/source/commands/pcrseqscommand.h b/source/commands/pcrseqscommand.h
@@ -45,6 +45,7 @@ class PcrSeqsCommand : public Command {
     int writeAccnos(set<string>, string);
     Sequence readEcoli();
 	long long createProcesses(string, string, string, set<string>&);
+    void preserveOrder(string);
     int adjustDots(string goodFasta, map<string, vector<int> > locations, int pstart, int pend, bool, bool);
 };
 

diff --git a/source/commands/sortseqscommand.cpp b/source/commands/sortseqscommand.cpp
@@ -149,7 +149,7 @@ int SortSeqsCommand::execute(){
             vector<string> temp;
             util.readAccnos(accnosfile, temp);
             for (int i = 0; i < temp.size(); i++) {  names[temp[i]] = i;  }
-            m->mothurOut("\nUsing " + accnosfile + " to determine the order. It contains " + toString(temp.size()) + " representative sequences.\n");	
+            m->mothurOut("\nUsing " + accnosfile + " to determine the order. It contains " + toString(temp.size()) + " sequences.\n");	
         }
 
 		if (fastafile != "")		{		readFasta();	}

diff --git a/source/datastructures/counttable.cpp b/source/datastructures/counttable.cpp
@@ -23,7 +23,7 @@ int CountTable::createTable(map<string, string>& g) {
             groups.insert(it->second);
         }
 
-        createTable(names, g, groups);
+        return (createTable(names, g, groups));
 
     }
     catch(exception& e) {