finished shhh.seqs command, fixed bug with remove.groups and get.groups that caused...

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index 69e905e6bc93e401a242f695577b95019be191c3..162d3be9e69d0f86f7e4f2122c3c914b613392c3 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -76,10 +76,15 @@ Sequence::Sequence(istringstream& fastaString){
                        
                        while (!fastaString.eof())      {       char c = fastaString.get();  if (c == 10 || c == 13){ break;    }       } // get rest of line if there's any crap there
                        
-                       sequence = getSequenceString(fastaString);              
+                       int numAmbig = 0;
+                       sequence = getSequenceString(fastaString, numAmbig);
+                       
                        setAligned(sequence);   
                        //setUnaligned removes any gap characters for us                                                
-                       setUnaligned(sequence);         
+                       setUnaligned(sequence); 
+                       
+                       if ((numAmbig / (float) numBases) > 0.25) { m->mothurOut("[WARNING]: We found more than 25% of the bases in sequence " + name + " to be ambiguous. Mothur is not setup to process protein sequences."); m->mothurOutEndLine(); }
+               
                }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaString.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
                
        }
@@ -118,10 +123,14 @@ Sequence::Sequence(istringstream& fastaString, string JustUnaligned){
                        
                        while (!fastaString.eof())      {       char c = fastaString.get();  if (c == 10 || c == 13){ break;    }       } // get rest of line if there's any crap there
                        
-                       sequence = getSequenceString(fastaString);              
+                       int numAmbig = 0;
+                       sequence = getSequenceString(fastaString, numAmbig);
                        
                        //setUnaligned removes any gap characters for us                                                
-                       setUnaligned(sequence);         
+                       setUnaligned(sequence); 
+                       
+                       if ((numAmbig / (float) numBases) > 0.25) { m->mothurOut("[WARNING]: We found more than 25% of the bases in sequence " + name + " to be ambiguous. Mothur is not setup to process protein sequences."); m->mothurOutEndLine(); }
+                       
                }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaString.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
                
        }
@@ -163,11 +172,15 @@ Sequence::Sequence(ifstream& fastaFile){
                        //read real sequence
                        while (!fastaFile.eof())        {       char c = fastaFile.get(); if (c == 10 || c == 13){  break;      }       } // get rest of line if there's any crap there
                        
-                       sequence = getSequenceString(fastaFile);                
-       
+                       int numAmbig = 0;
+                       sequence = getSequenceString(fastaFile, numAmbig);
+                       
                        setAligned(sequence);   
                        //setUnaligned removes any gap characters for us                                                
                        setUnaligned(sequence); 
+                       
+                       if ((numAmbig / (float) numBases) > 0.25) { m->mothurOut("[WARNING]: We found more than 25% of the bases in sequence " + name + " to be ambiguous. Mothur is not setup to process protein sequences."); m->mothurOutEndLine(); }
+                       
                }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
 
        }
@@ -205,10 +218,14 @@ Sequence::Sequence(ifstream& fastaFile, string JustUnaligned){
                        //read real sequence
                        while (!fastaFile.eof())        {       char c = fastaFile.get(); if (c == 10 || c == 13){       break; }       } // get rest of line if there's any crap there
                        
-                       sequence = getSequenceString(fastaFile);                
+                       int numAmbig = 0;
+                       sequence = getSequenceString(fastaFile, numAmbig);
                        
                        //setUnaligned removes any gap characters for us                                                
                        setUnaligned(sequence); 
+                       
+                       if ((numAmbig / (float) numBases) > 0.25) { m->mothurOut("[WARNING]: We found more than 25% of the bases in sequence " + name + " to be ambiguous. Mothur is not setup to process protein sequences."); m->mothurOutEndLine(); }
+                       
                }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
                
        }
@@ -219,10 +236,11 @@ Sequence::Sequence(ifstream& fastaFile, string JustUnaligned){
 }
 
 //********************************************************************************************************************
-string Sequence::getSequenceString(ifstream& fastaFile) {
+string Sequence::getSequenceString(ifstream& fastaFile, int& numAmbig) {
        try {
                char letter;
                string sequence = "";   
+               numAmbig = 0;
                
                while(fastaFile){
                        letter= fastaFile.get();
@@ -233,8 +251,9 @@ string Sequence::getSequenceString(ifstream& fastaFile) {
                        else if(isprint(letter)){
                                letter = toupper(letter);
                                if(letter == 'U'){letter = 'T';}
-                               if(letter != '.' && letter != '-' && letter != 'A' && letter != 'T' && letter != 'G'  && letter != 'C'){
+                               if(letter != '.' && letter != '-' && letter != 'A' && letter != 'T' && letter != 'G'  && letter != 'C' && letter != 'N'){
                                        letter = 'N';
+                                       numAmbig++;
                                }
                                sequence += letter;
                        }
@@ -270,10 +289,11 @@ string Sequence::getCommentString(ifstream& fastaFile) {
        }
 }
 //********************************************************************************************************************
-string Sequence::getSequenceString(istringstream& fastaFile) {
+string Sequence::getSequenceString(istringstream& fastaFile, int& numAmbig) {
        try {
                char letter;
-               string sequence = "";   
+               string sequence = "";
+               numAmbig = 0;
                
                while(!fastaFile.eof()){
                        letter= fastaFile.get();
@@ -285,6 +305,10 @@ string Sequence::getSequenceString(istringstream& fastaFile) {
                        else if(isprint(letter)){
                                letter = toupper(letter);
                                if(letter == 'U'){letter = 'T';}
+                               if(letter != '.' && letter != '-' && letter != 'A' && letter != 'T' && letter != 'G'  && letter != 'C' && letter != 'N'){
+                                       letter = 'N';
+                                       numAmbig++;
+                               }
                                sequence += letter;
                        }
                }