/mothur

Permalink
Browse files

Updated to latest version of vsearch 

Adjust of new output files
  • Loading branch information...
1 parent 4eda402 commit 88e0da27828f93b5de047f2183086245808d85d8 @mothur-westcott mothur-westcott committed Jul 20, 2016
Unified Split
Showing with 31 additions and 15 deletions.
  1. +31 −15 source/commands/chimeravsearchcommand.cpp
View
46 source/commands/chimeravsearchcommand.cpp
@@ -589,6 +589,7 @@ int ChimeraVsearchCommand::execute(){
//you provided a groupfile
string groupFile = "";
bool hasGroup = false;
+ int numSeqs = 0;
if (groupFileNames.size() != 0) { groupFile = groupFileNames[s]; hasGroup = true; }
else if (hasCount) {
CountTable ct;
@@ -605,7 +606,7 @@ int ChimeraVsearchCommand::execute(){
}else { nameFile = getNamesFile(fastaFileNames[s]); }
map<string, string> seqs;
- readFasta(fastaFileNames[s], seqs); if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
+ numSeqs = readFasta(fastaFileNames[s], seqs); if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
//read namefile
vector<seqPriorityNode> nameMapCount;
@@ -658,9 +659,8 @@ int ChimeraVsearchCommand::execute(){
m->openOutputFile(outputFileName, out); out.close();
m->openOutputFile(accnosFileName, out1); out1.close();
if (chimealns) { m->openOutputFile(alnsFileName, out2); out2.close(); }
- int totalSeqs = 0;
- if(processors == 1) { totalSeqs = driverGroups(outputFileName, newFasta, accnosFileName, alnsFileName, newCountFile, 0, groups.size(), groups);
+ if(processors == 1) { driverGroups(outputFileName, newFasta, accnosFileName, alnsFileName, newCountFile, 0, groups.size(), groups);
if (hasCount && dups) {
CountTable c; c.readTable(nameFile, true, false);
@@ -679,15 +679,15 @@ int ChimeraVsearchCommand::execute(){
c.printTable(newCountFile);
}
- }else{ totalSeqs = createProcessesGroups(outputFileName, newFasta, accnosFileName, alnsFileName, newCountFile, groups, nameFile, groupFile, fastaFileNames[s]); }
+ }else{ createProcessesGroups(outputFileName, newFasta, accnosFileName, alnsFileName, newCountFile, groups, nameFile, groupFile, fastaFileNames[s]); }
if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
if (!dups) {
int totalChimeras = deconvoluteResults(uniqueNames, outputFileName, accnosFileName, alnsFileName);
- m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(totalSeqs) + " sequences. " + toString(totalChimeras) + " chimeras were found."); m->mothurOutEndLine();
+ m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(uniqueNames.size()) + " sequences. " + toString(totalChimeras) + " chimeras were found."); m->mothurOutEndLine();
m->mothurOut("The number of sequences checked may be larger than the number of unique sequences because some sequences are found in several samples."); m->mothurOutEndLine();
}else {
@@ -721,11 +721,10 @@ int ChimeraVsearchCommand::execute(){
}else{
if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
- int numSeqs = 0;
int numChimeras = 0;
- if(processors == 1){ numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); }
- else{ numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); }
+ if(processors == 1){ driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); }
+ else{ createProcesses(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); }
//add headings
ofstream out;
@@ -828,15 +827,17 @@ int ChimeraVsearchCommand::deconvoluteResults(map<string, string>& uniqueNames,
ofstream out;
m->openOutputFile(outputFileName+".temp", out); out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
- out << "Score\tQuery\tParentA\tParentB\tIdQM\tIdQA\tIdQB\tIdAB\tIdQT\tLY\tLN\tLA\tRY\tRN\tRA\tDiv\tYN\n";
+ //out << "Score\tQuery\tParentA\tParentB\tIdQM\tIdQA\tIdQB\tIdAB\tIdQT\tLY\tLN\tLA\tRY\tRN\tRA\tDiv\tYN\n";
float temp1;
- string parent1, parent2, temp2, temp3, temp4, temp5, temp6, temp7, temp8, temp9, temp10, temp11, temp12, temp13, flag;
+ string parent1, parent2, parent3, temp2, temp3, temp4, temp5, temp6, temp7, temp8, temp9, temp10, temp11, temp12, temp13, flag;
name = "";
namesInFile.clear();
//assumptions - in file each read will always look like - if uchime source is updated, revisit this code.
/* 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
0.000000 F11Fcsw_33372/ab=18/ * * * * * * * * * * * * * * N
+ 0.0000 GQY1XT001C296C;size=356; * * * * * * * * 0 0 0 0 0 0 * N
+ 0.0469 GQY1XT001CPCVN;size=154; GQY1XT001C296C;size=356; GQY1XT001C44N8;size=323; GQY1XT001C44N8;size=323; 93.8 91.5 92.3 92.6 92.3 4 0 7 9 3 7 1.5 N
0.018300 F11Fcsw_14980/ab=16/ F11Fcsw_1915/ab=35/ F11Fcsw_6032/ab=42/ 79.9 78.7 78.2 78.7 79.2 3 0 5 11 10 20 1.46 N
*/
@@ -849,6 +850,7 @@ int ChimeraVsearchCommand::deconvoluteResults(map<string, string>& uniqueNames,
in >> name; m->gobble(in);
in >> parent1; m->gobble(in);
in >> parent2; m->gobble(in);
+ in >> parent3; m->gobble(in);
in >> temp2 >> temp3 >> temp4 >> temp5 >> temp6 >> temp7 >> temp8 >> temp9 >> temp10 >> temp11 >> temp12 >> temp13 >> flag;
m->gobble(in);
@@ -912,6 +914,20 @@ int ChimeraVsearchCommand::deconvoluteResults(map<string, string>& uniqueNames,
else { out << itUnique->second << restOfName << '\t'; }
}else { out << parent2 << '\t'; }
+ //parse parent3 names
+ if (parent3 != "*") {
+ restOfName = "";
+ pos = parent3.find_first_of(';');
+ if (pos != string::npos) {
+ restOfName = parent3.substr(pos);
+ parent3 = parent3.substr(0, pos);
+ }
+
+ itUnique = uniqueNames.find(parent3);
+ if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parentC "+ parent3 + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { out << itUnique->second << restOfName << '\t'; }
+ }else { out << parent3 << '\t'; }
+
out << temp2 << '\t' << temp3 << '\t' << temp4 << '\t' << temp5 << '\t' << temp6 << '\t' << temp7 << '\t' << temp8 << '\t' << temp9 << '\t' << temp10 << '\t' << temp11 << '\t' << temp12 << temp13 << '\t' << flag << endl;
}
}
@@ -1045,16 +1061,18 @@ int ChimeraVsearchCommand::readFasta(string filename, map<string, string>& seqs)
ifstream in;
m->openInputFile(filename, in);
+ int num = 0;
while (!in.eof()) {
if (m->control_pressed) { in.close(); return 0; }
Sequence seq(in); m->gobble(in);
- seqs[seq.getName()] = seq.getAligned();
+ seqs[seq.getName()] = seq.getUnaligned();
+ num++;
}
in.close();
- return 0;
+ return num;
}
catch(exception& e) {
m->errorOut(e, "ChimeraVsearchCommand", "readFasta");
@@ -1362,7 +1380,6 @@ int ChimeraVsearchCommand::driver(string outputFName, string filename, string ac
ofstream out;
m->openOutputFile(accnos, out);
- int num = 0;
numChimeras = 0;
while(!in.eof()) {
@@ -1376,7 +1393,6 @@ int ChimeraVsearchCommand::driver(string outputFName, string filename, string ac
name = name.substr(0, name.find_last_of(';'));
out << name << endl; numChimeras++;
- num++;
}
in.close();
out.close();
@@ -1385,7 +1401,7 @@ int ChimeraVsearchCommand::driver(string outputFName, string filename, string ac
//if (templatefile != "self") { m->mothurRemove(filename); }
- return num;
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "ChimeraVsearchCommand", "driver");

0 comments on commit 88e0da2

Please sign in to comment.