captured stdout from system command, fixed bug in trim.seqs added error checks for...

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index 48ae1686a35aae2f1a19e980c8b057c827c40021..c7003f4489232b347d6927d718c5d7497d050ae8 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -14,17 +14,74 @@
 
 /**************************************************************************************************/
 
-BlastDB::BlastDB(string tag, float gO, float gE, float m, float mM) : Database(), 
-gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
-       
-       count = 0;
-
-       int randNumber = rand();
-       //int randNumber = 12345;
-       dbFileName = tag + toString(randNumber) + ".template.unaligned.fasta";
-       queryFileName = tag + toString(randNumber) + ".candidate.unaligned.fasta";
-       blastFileName = tag + toString(randNumber) + ".blast";
+BlastDB::BlastDB(string tag, float gO, float gE, float mm, float mM) : Database(), 
+gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
+       try {
+               count = 0;
 
+               int randNumber = rand();
+               //int randNumber = 12345;
+               dbFileName = tag + toString(randNumber) + ".template.unaligned.fasta";
+               queryFileName = tag + toString(randNumber) + ".candidate.unaligned.fasta";
+               blastFileName = tag + toString(randNumber) + ".blast";
+               
+               //make sure blast exists in the write place
+               path = m->argv;
+               string tempPath = path;
+               for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+               path = path.substr(0, (tempPath.find_last_of('m')));
+               
+               string formatdbCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               formatdbCommand = path + "blast/bin/formatdb";  //      format the database, -o option gives us the ability
+#else
+               formatdbCommand = path + "blast\\bin\\formatdb";
+               //wrap entire string in ""
+               formatdbCommand = "\"" + formatdbCommand + "\"";
+#endif
+               
+               //test to make sure formatdb exists
+               ifstream in;
+               formatdbCommand = m->getFullPathName(formatdbCommand);
+               int ableToOpen = m->openInputFile(formatdbCommand, in, "no error"); in.close();
+               if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe to be in the ./blast/bin folder relative to the mothur.exe location."); m->mothurOutEndLine(); m->control_pressed = true; }
+               
+               string blastCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               blastCommand = path + "blast/bin/blastall";     //      format the database, -o option gives us the ability
+#else
+               blastCommand = path + "blast\\bin\\blastall";
+               //wrap entire string in ""
+               blastCommand = "\"" + blastCommand + "\"";
+#endif
+               
+               //test to make sure formatdb exists
+               ifstream in2;
+               blastCommand = m->getFullPathName(blastCommand);
+               ableToOpen = m->openInputFile(blastCommand, in2, "no error"); in2.close();
+               if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " + blastCommand + " file does not exist. mothur requires blastall.exe to be in the ./blast/bin folder relative to the mothur.exe location."); m->mothurOutEndLine(); m->control_pressed = true; }
+               
+               
+               string megablastCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               megablastCommand = path + "blast/bin/megablast";        //      format the database, -o option gives us the ability
+#else
+               megablastCommand = path + "blast\\bin\\megablast";
+               //wrap entire string in ""
+               megablastCommand = "\"" + blastCommmegablastCommandand + "\"";
+#endif
+               
+               //test to make sure formatdb exists
+               ifstream in3;
+               megablastCommand = m->getFullPathName(megablastCommand);
+               ableToOpen = m->openInputFile(megablastCommand, in3, "no error"); in3.close();
+               if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " +  megablastCommand + " file does not exist. mothur requires megablast.exe to be in the ./blast/bin folder relative to the mothur.exe location."); m->mothurOutEndLine(); m->control_pressed = true; }
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "BlastDB", "BlastDB");
+               exit(1);
+       }
 }
 /**************************************************************************************************/
 
@@ -37,6 +94,60 @@ BlastDB::BlastDB() : Database() {
                dbFileName = toString(randNumber) + ".template.unaligned.fasta";
                queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
                blastFileName = toString(randNumber) + ".blast";
+               
+               //make sure blast exists in the write place
+               path = m->argv;
+               string tempPath = path;
+               for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+               path = path.substr(0, (tempPath.find_last_of('m')));
+               
+               string formatdbCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               formatdbCommand = path + "blast/bin/formatdb";  //      format the database, -o option gives us the ability
+#else
+               formatdbCommand = path + "blast\\bin\\formatdb";
+               //wrap entire string in ""
+               formatdbCommand = "\"" + formatdbCommand + "\"";
+#endif
+               
+               //test to make sure formatdb exists
+               ifstream in;
+               formatdbCommand = m->getFullPathName(formatdbCommand);
+               int ableToOpen = m->openInputFile(formatdbCommand, in, "no error"); in.close();
+               if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " +  formatdbCommand + " file does not exist. mothur requires formatdb.exe to be in the ./blast/bin folder relative to the mothur.exe location."); m->mothurOutEndLine(); m->control_pressed = true; }
+               
+               string blastCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               blastCommand = path + "blast/bin/blastall";     //      format the database, -o option gives us the ability
+#else
+               blastCommand = path + "blast\\bin\\blastall";
+               //wrap entire string in ""
+               blastCommand = "\"" + blastCommand + "\"";
+#endif
+               
+               //test to make sure formatdb exists
+               ifstream in2;
+               blastCommand = m->getFullPathName(blastCommand);
+               ableToOpen = m->openInputFile(blastCommand, in2, "no error"); in2.close();
+               if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " + blastCommand + " file does not exist. mothur requires blastall.exe to be in the ./blast/bin folder relative to the mothur.exe location."); m->mothurOutEndLine(); m->control_pressed = true; }
+               
+               
+               string megablastCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               megablastCommand = path + "blast/bin/megablast";        //      format the database, -o option gives us the ability
+#else
+               megablastCommand = path + "blast\\bin\\megablast";
+               //wrap entire string in ""
+               megablastCommand = "\"" + blastCommmegablastCommandand + "\"";
+#endif
+               
+               //test to make sure formatdb exists
+               ifstream in3;
+               megablastCommand = m->getFullPathName(megablastCommand);
+               ableToOpen = m->openInputFile(megablastCommand, in3, "no error"); in3.close();
+               if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " + megablastCommand + " file does not exist. mothur requires megablast.exe to be in the ./blast/bin folder relative to the mothur.exe location."); m->mothurOutEndLine(); m->control_pressed = true; }
+               
+               
        }
        catch(exception& e) {
                m->errorOut(e, "BlastDB", "BlastDB");