From ac4d6a2ac10c8feb043aa11582a769b6093c5941 Mon Sep 17 00:00:00 2001
From: Sarah Westcott <mothur.westcott@gmail.com>
Date: Fri, 14 Dec 2012 07:21:44 -0500
Subject: [PATCH] fixed outputName creator, added debugging to readblast
---
command.hpp | 9 +++++++--
readblast.cpp | 11 +++++++----
readblast.h | 6 +++---
3 files changed, 17 insertions(+), 9 deletions(-)
diff --git a/command.hpp b/command.hpp
index 2ba35ab..7ed03f1 100644
--- a/command.hpp
+++ b/command.hpp
@@ -74,8 +74,13 @@ class Command {
m->mothurOut("[ERROR]: Did not provide variable for " + pieces[i] + ".\n"); m->control_pressed = true;
}else {
if (it->second != "") {
- if (it->first != "[filename]") { filename += it->second + "."; }
- else { filename += it->second; }
+ if (it->first == "[filename]") { filename += it->second; }
+ else if (it->first == "[extension]") {
+ if (filename.length() > 0) { //rip off last "."
+ filename = filename.substr(0, filename.length()-1);
+ }
+ filename += it->second + ".";
+ }else { filename += it->second + "."; }
}
}
}else {
diff --git a/readblast.cpp b/readblast.cpp
index 5f24415..e98b69c 100644
--- a/readblast.cpp
+++ b/readblast.cpp
@@ -110,8 +110,9 @@ int ReadBlast::read(NameAssignment* nameMap) {
}
}
}else { m->mothurOut("Error in your blast file, cannot read."); m->mothurOutEndLine(); exit(1); }
-
-
+string outDistFilem = "../kathryn/blastDist.dist";
+ ofstream outMDist;
+ m->openOutputFile(outDistFilem, outMDist);
//read file
while(!fileHandle.eof()){
@@ -193,6 +194,7 @@ int ReadBlast::read(NameAssignment* nameMap) {
PDistCell value(itA->second, distance);
matrix->addCell(it->first, value);
}
+ outMDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
}else{
outDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
}
@@ -324,8 +326,8 @@ int ReadBlast::readNames(NameAssignment* nameMap) {
ifstream in;
m->openInputFile(blastfile, in);
- //ofstream outName;
- //m->openOutputFile((blastfile + ".tempOutNames"), outName);
+ ofstream outName;
+ m->openOutputFile((blastfile + ".tempOutNames"), outName);
//read first line
in >> prevName;
@@ -349,6 +351,7 @@ int ReadBlast::readNames(NameAssignment* nameMap) {
if (name != prevName) {
prevName = name;
nameMap->push_back(name);
+ outName << name << '\t' << name << endl;
num++;
}
}
diff --git a/readblast.h b/readblast.h
index ef5ff9a..97ce6c7 100644
--- a/readblast.h
+++ b/readblast.h
@@ -27,9 +27,9 @@ public:
int read(NameAssignment*);
SparseDistanceMatrix* getDistMatrix() { return matrix; }
- vector<seqDist> getOverlapMatrix() { return overlap; }
- string getOverlapFile() { return overlapFile; }
- string getDistFile() { return distFile; }
+ vector<seqDist> getOverlapMatrix() { return overlap; }
+ string getOverlapFile() { return overlapFile; }
+ string getDistFile() { return distFile; }
private:
string blastfile, overlapFile, distFile;
--
2.39.5