From a688f253166590ee0b256f02e02f47c9cae44fd1 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Tue, 27 Apr 2010 18:53:09 +0000
Subject: [PATCH] added name parameter to phylotype command
---
phylosummary.cpp | 4 ++--
phylotypecommand.cpp | 53 ++++++++++++++++++++++++++++++++++++++++++--
phylotypecommand.h | 5 ++++-
3 files changed, 57 insertions(+), 5 deletions(-)
diff --git a/phylosummary.cpp b/phylosummary.cpp
index 1e8d1bc..a5f67c0 100644
--- a/phylosummary.cpp
+++ b/phylosummary.cpp
@@ -126,8 +126,8 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
tree[currentNode].total++;
currentNode = childPointer->second;
- }else{ //otherwise, create it
- m->mothurOut("Error: cannot find taxonomy in tree for " + seqName + "."); m->mothurOutEndLine();
+ }else{ //otherwise, error
+ m->mothurOut("Warning: cannot find taxon " + taxon + " in reference taxonomy tree at level " + toString(tree[currentNode].level) + " for " + seqName + ". This may cause totals of daughter levels not to add up in summary file."); m->mothurOutEndLine();
seqTaxonomy = "";
}
diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index 1828eb1..d04c960 100644
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -24,7 +24,7 @@ PhylotypeCommand::PhylotypeCommand(string option) {
else {
//valid paramters for this command
- string AlignArray[] = {"taxonomy","cutoff","label","outputdir","inputdir"};
+ string AlignArray[] = {"taxonomy","cutoff","label","name","outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
@@ -50,6 +50,14 @@ PhylotypeCommand::PhylotypeCommand(string option) {
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
}
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
}
taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
@@ -59,6 +67,11 @@ PhylotypeCommand::PhylotypeCommand(string option) {
abort = true;
}else if (taxonomyFileName == "not open") { abort = true; }
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { readNamesFile(); }
+
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
@@ -187,7 +200,15 @@ int PhylotypeCommand::execute(){
//make the names compatable with listvector
string name = "";
- for (int i = 0; i < names.size(); i++) { name += names[i] + ","; }
+ for (int i = 0; i < names.size(); i++) {
+ if (namefile != "") {
+ map<string, string>::iterator itNames = namemap.find(names[i]); //make sure this name is in namefile
+
+ if (itNames != namemap.end()) { name += namemap[names[i]] + ","; } //you found it in namefile
+ else { m->mothurOut(names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); exit(1); }
+
+ }else{ name += names[i] + ","; }
+ }
name = name.substr(0, name.length()-1); //rip off extra ','
//add bin to list vector
@@ -244,4 +265,32 @@ int PhylotypeCommand::execute(){
exit(1);
}
}
+/*****************************************************************/
+int PhylotypeCommand::readNamesFile() {
+ try {
+
+ ifstream in;
+ openInputFile(namefile, in);
+
+ string first, second;
+ map<string, string>::iterator itNames;
+
+ while(!in.eof()) {
+ in >> first >> second; gobble(in);
+
+ itNames = namemap.find(first);
+ if (itNames == namemap.end()) {
+ namemap[first] = second;
+ }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); namemap.clear(); namefile = ""; return 1; }
+ }
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "readNamesFile");
+ exit(1);
+ }
+}
+
/**********************************************************************************************************************/
diff --git a/phylotypecommand.h b/phylotypecommand.h
index b61c039..c5aea71 100644
--- a/phylotypecommand.h
+++ b/phylotypecommand.h
@@ -26,13 +26,16 @@ public:
private:
bool abort, allLines;
- string taxonomyFileName, label, outputDir;
+ string taxonomyFileName, label, outputDir, namefile;
set<string> labels; //holds labels to be used
int cutoff;
+ map<string, string> namemap;
map<int, int> currentNodes;
map<int, int> parentNodes;
map<int, int>::iterator itCurrent;
+
+ int readNamesFile();
};
--
2.39.5