[med-svn] [mothur] 01/08: New upstream version 1.38.1.1
Andreas Tille
tille at debian.org
Sat Dec 10 08:38:29 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository mothur.
commit a2de24813620009cbb47e3d7651fa129bed36d99
Author: Andreas Tille <tille at debian.org>
Date: Sat Dec 10 06:32:37 2016 +0100
New upstream version 1.38.1.1
---
.gitignore | 1 +
Makefile | 4 +-
Mothur.xcodeproj/project.pbxproj | 94 ++++----
source/commandfactory.cpp | 17 +-
source/commands/clustercommand.cpp | 41 ++--
source/commands/clustercommand.h | 2 +-
source/commands/clusterdoturcommand.cpp | 16 +-
source/commands/clusterdoturcommand.h | 2 +-
source/commands/clustersplitcommand.cpp | 35 +--
source/commands/clustersplitcommand.h | 2 +-
source/commands/command.hpp | 8 +-
source/commands/getmimarkspackagecommand.cpp | 2 +-
source/commands/helpcommand.cpp | 325 ++++++++++++++++++++++++++-
source/commands/helpcommand.h | 8 +-
source/commands/makecontigscommand.cpp | 5 +-
source/commands/makefilecommand.cpp | 42 ++--
source/commands/makefilecommand.h | 2 +-
source/commands/makegroupcommand.cpp | 2 +-
source/commands/mergecountcommand.cpp | 226 +++++++++++++++++++
source/commands/mergecountcommand.hpp | 48 ++++
source/commands/mergegroupscommand.cpp | 5 +
source/commands/parselistscommand.cpp | 23 +-
source/commands/seqerrorcommand.cpp | 5 +
source/commands/sracommand.cpp | 11 +-
source/commands/trimflowscommand.cpp | 2 +
source/commands/trimseqscommand.cpp | 1 +
source/datastructures/counttable.cpp | 24 +-
source/datastructures/counttable.h | 5 +-
source/mothurout.cpp | 4 +-
29 files changed, 792 insertions(+), 170 deletions(-)
diff --git a/.gitignore b/.gitignore
index 522f8a2..4e1c84e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -14,6 +14,7 @@ TARGET_BUILD_DIRTARGET_BUILD_DIR
nbproject/
mothur
Mothur.1
+DerivedData/
*.stdout
diff --git a/Makefile b/Makefile
index a49ad17..88e837f 100644
--- a/Makefile
+++ b/Makefile
@@ -15,8 +15,8 @@ USEBOOST ?= yes
BOOST_LIBRARY_DIR="\"Enter_your_boost_library_path_here\""
BOOST_INCLUDE_DIR="\"Enter_your_boost_include_path_here\""
MOTHUR_FILES="\"Enter_your_default_path_here\""
-RELEASE_DATE = "\"7/20/2016\""
-VERSION = "\"1.38.0\""
+RELEASE_DATE = "\"8/9/2016\""
+VERSION = "\"1.38.1\""
ifeq ($(strip $(64BIT_VERSION)),yes)
CXXFLAGS += -DBIT_VERSION
diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index a4d9cc1..48a38e6 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -379,6 +379,8 @@
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7B2181FE17AD777B00286E6A /* classifysvmsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = classifysvmsharedcommand.cpp; path = source/commands/classifysvmsharedcommand.cpp; sourceTree = SOURCE_ROOT; };
7B2181FF17AD777B00286E6A /* classifysvmsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = classifysvmsharedcommand.h; path = source/commands/classifysvmsharedcommand.h; sourceTree = SOURCE_ROOT; };
7B21820117AD77BD00286E6A /* svm.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = svm.cpp; path = source/svm/svm.cpp; sourceTree = SOURCE_ROOT; };
7B21820217AD77BD00286E6A /* svm.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; name = svm.hpp; path = source/svm/svm.hpp; sourceTree = SOURCE_ROOT; };
- 7E6BE10812F710D8007ADDBE /* refchimeratest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = refchimeratest.h; path = source/refchimeratest.h; sourceTree = "<group>"; };
- 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = refchimeratest.cpp; path = source/refchimeratest.cpp; sourceTree = "<group>"; };
+ 7E6BE10812F710D8007ADDBE /* refchimeratest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = refchimeratest.h; path = source/refchimeratest.h; sourceTree = SOURCE_ROOT; };
+ 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = refchimeratest.cpp; path = source/refchimeratest.cpp; sourceTree = SOURCE_ROOT; };
7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = eachgapdistignorens.h; path = source/calculators/eachgapdistignorens.h; sourceTree = SOURCE_ROOT; };
83F25B0A163B031200ABE73D /* forest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = forest.cpp; path = source/randomforest/forest.cpp; sourceTree = SOURCE_ROOT; };
83F25B0B163B031200ABE73D /* forest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = forest.h; path = source/randomforest/forest.h; sourceTree = SOURCE_ROOT; };
@@ -931,8 +935,8 @@
A7730EFE13967241007433A3 /* countseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; name = countseqscommand.cpp; path = source/commands/countseqscommand.cpp; sourceTree = SOURCE_ROOT; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
A774101214695AF60098E6AC /* shhhseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = shhhseqscommand.h; path = source/commands/shhhseqscommand.h; sourceTree = SOURCE_ROOT; };
A774101314695AF60098E6AC /* shhhseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = shhhseqscommand.cpp; path = source/commands/shhhseqscommand.cpp; sourceTree = SOURCE_ROOT; };
- A774104614696F320098E6AC /* myseqdist.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = myseqdist.cpp; path = source/myseqdist.cpp; sourceTree = "<group>"; };
- A774104714696F320098E6AC /* myseqdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = myseqdist.h; path = source/myseqdist.h; sourceTree = "<group>"; };
+ A774104614696F320098E6AC /* myseqdist.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = myseqdist.cpp; path = source/myseqdist.cpp; sourceTree = SOURCE_ROOT; };
+ A774104714696F320098E6AC /* myseqdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = myseqdist.h; path = source/myseqdist.h; sourceTree = SOURCE_ROOT; };
A77410F414697C300098E6AC /* seqnoise.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = seqnoise.cpp; path = source/seqnoise.cpp; sourceTree = "<group>"; };
A77410F514697C300098E6AC /* seqnoise.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = seqnoise.h; path = source/seqnoise.h; sourceTree = "<group>"; };
A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = getcommandinfocommand.h; path = source/commands/getcommandinfocommand.h; sourceTree = SOURCE_ROOT; };
@@ -1964,12 +1968,14 @@
A7E6F69D17427D06006775E2 /* makelookupcommand.cpp */,
A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */,
A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */,
- 48705ABF19BE32C50075E977 /* mergesfffilecommand.cpp */,
- 48705AC019BE32C50075E977 /* mergesfffilecommand.h */,
+ 48910D411D5243E500F60EDB /* mergecountcommand.cpp */,
+ 48910D421D5243E500F60EDB /* mergecountcommand.hpp */,
A7E9B75412D37EC400DA6239 /* mergefilecommand.h */,
A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */,
A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */,
A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */,
+ 48705AC019BE32C50075E977 /* mergesfffilecommand.h */,
+ 48705ABF19BE32C50075E977 /* mergesfffilecommand.cpp */,
A799314816CBD0BC0017E888 /* mergetaxsummarycommand.h */,
A799314A16CBD0CD0017E888 /* mergetaxsummarycommand.cpp */,
A7E9B75812D37EC400DA6239 /* metastatscommand.h */,
@@ -2666,6 +2672,7 @@
481FB6881AC1B8B80076CFF3 /* weightedlinkage.cpp in Sources */,
480E8DB21CAB1F5E00A0D137 /* vsearchfileparser.cpp in Sources */,
481FB61E1AC1B7AC0076CFF3 /* unifracweightedcommand.cpp in Sources */,
+ 48910D441D5243E500F60EDB /* mergecountcommand.cpp in Sources */,
481FB5951AC1B71B0076CFF3 /* chimerabellerophoncommand.cpp in Sources */,
481FB68D1AC1BA9E0076CFF3 /* classify.cpp in Sources */,
481FB65F1AC1B8450076CFF3 /* myseqdist.cpp in Sources */,
@@ -3011,6 +3018,7 @@
A7E9B8C512D37EC400DA6239 /* fileoutput.cpp in Sources */,
A7E9B8C612D37EC400DA6239 /* filterseqscommand.cpp in Sources */,
A7E9B8C812D37EC400DA6239 /* flowdata.cpp in Sources */,
+ 48910D431D5243E500F60EDB /* mergecountcommand.cpp in Sources */,
A7E9B8C912D37EC400DA6239 /* formatcolumn.cpp in Sources */,
A7E9B8CA12D37EC400DA6239 /* formatphylip.cpp in Sources */,
A7E9B8CB12D37EC400DA6239 /* fullmatrix.cpp in Sources */,
@@ -3326,8 +3334,8 @@
GCC_MODEL_TUNING = G5;
GCC_OPTIMIZATION_LEVEL = 0;
GCC_PREPROCESSOR_DEFINITIONS = (
- "VERSION=\"\\\"1.37.1\\\"\"",
- "RELEASE_DATE=\"\\\"04/11/2016\\\"\"",
+ "VERSION=\"\\\"1.38.1\\\"\"",
+ "RELEASE_DATE=\"\\\"08/9/2016\\\"\"",
"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
);
GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
@@ -3361,8 +3369,8 @@
GCC_MODEL_TUNING = G5;
GCC_OPTIMIZATION_LEVEL = 0;
GCC_PREPROCESSOR_DEFINITIONS = (
- "VERSION=\"\\\"1.37.1\\\"\"",
- "RELEASE_DATE=\"\\\"04/11/2016\\\"\"",
+ "VERSION=\"\\\"1.38.1\\\"\"",
+ "RELEASE_DATE=\"\\\"8/9/2016\\\"\"",
"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
);
GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
@@ -3439,8 +3447,8 @@
GCC_MODEL_TUNING = "";
GCC_OPTIMIZATION_LEVEL = 0;
GCC_PREPROCESSOR_DEFINITIONS = (
- "VERSION=\"\\\"1.37.6\\\"\"",
- "RELEASE_DATE=\"\\\"06/20/2016\\\"\"",
+ "VERSION=\"\\\"1.38.1\\\"\"",
+ "RELEASE_DATE=\"\\\"8/9/2016\\\"\"",
"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
);
GCC_VERSION = "";
diff --git a/source/commandfactory.cpp b/source/commandfactory.cpp
index bec2db3..259ad5c 100644
--- a/source/commandfactory.cpp
+++ b/source/commandfactory.cpp
@@ -152,6 +152,7 @@
#include "biominfocommand.h"
#include "renamefilecommand.h"
#include "chimeravsearchcommand.h"
+#include "mergecountcommand.hpp"
//needed for testing project
//CommandFactory* CommandFactory::_uniqueInstance;
@@ -327,6 +328,7 @@ CommandFactory::CommandFactory(){
commands["biom.info"] = "biom.info";
commands["set.seed"] = "set.seed";
commands["rename.file"] = "rename.file";
+ commands["merge.count"] = "merge.count";
}
@@ -526,6 +528,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
else if(commandName == "corr.axes") { command = new CorrAxesCommand(optionString); }
else if(commandName == "remove.rare") { command = new RemoveRareCommand(optionString); }
else if(commandName == "merge.groups") { command = new MergeGroupsCommand(optionString); }
+ else if(commandName == "merge.count") { command = new MergeCountCommand(optionString); }
else if(commandName == "amova") { command = new AmovaCommand(optionString); }
else if(commandName == "homova") { command = new HomovaCommand(optionString); }
else if(commandName == "mantel") { command = new MantelCommand(optionString); }
@@ -699,6 +702,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
else if(commandName == "corr.axes") { pipecommand = new CorrAxesCommand(optionString); }
else if(commandName == "remove.rare") { pipecommand = new RemoveRareCommand(optionString); }
else if(commandName == "merge.groups") { pipecommand = new MergeGroupsCommand(optionString); }
+ else if(commandName == "merge.count") { pipecommand = new MergeCountCommand(optionString); }
else if(commandName == "amova") { pipecommand = new AmovaCommand(optionString); }
else if(commandName == "homova") { pipecommand = new HomovaCommand(optionString); }
else if(commandName == "mantel") { pipecommand = new MantelCommand(optionString); }
@@ -858,6 +862,7 @@ Command* CommandFactory::getCommand(string commandName){
else if(commandName == "corr.axes") { shellcommand = new CorrAxesCommand(); }
else if(commandName == "remove.rare") { shellcommand = new RemoveRareCommand(); }
else if(commandName == "merge.groups") { shellcommand = new MergeGroupsCommand(); }
+ else if(commandName == "merge.count") { shellcommand = new MergeCountCommand(); }
else if(commandName == "amova") { shellcommand = new AmovaCommand(); }
else if(commandName == "homova") { shellcommand = new HomovaCommand(); }
else if(commandName == "mantel") { shellcommand = new MantelCommand(); }
@@ -973,11 +978,15 @@ bool CommandFactory::isValidCommand(string command, string noError) {
/***********************************************************************/
void CommandFactory::printCommands(ostream& out) {
try {
- out << "Valid commands are: ";
- for (it = commands.begin(); it != commands.end(); it++) {
- out << it->first << ",";
+ it = commands.begin();
+ out << "Valid commands are: " << it->first << ", ";
+ it++;
+ out << it->first;
+ it++;
+ for (; it != commands.end(); it++) {
+ out << ", " << it->first;
}
- out << endl;
+ out << "." << endl;
}
catch(exception& e) {
m->errorOut(e, "CommandFactory", "printCommands");
diff --git a/source/commands/clustercommand.cpp b/source/commands/clustercommand.cpp
index 1b35740..652355d 100644
--- a/source/commands/clustercommand.cpp
+++ b/source/commands/clustercommand.cpp
@@ -30,8 +30,7 @@ vector<string> ClusterCommand::setParameters(){
CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshowabund);
CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming);
CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim);
- CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
- CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
+ CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
//CommandParameter padjust("adjust", "String", "", "F", "", "", "","",false,false); parameters.push_back(padjust);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
@@ -49,7 +48,7 @@ vector<string> ClusterCommand::setParameters(){
string ClusterCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The cluster command parameter options are phylip, column, name, count, method, cuttoff, hard, precision, sim, showabund and timing. Fasta or Phylip or column and name are required.\n";
+ helpString += "The cluster command parameter options are phylip, column, name, count, method, cutoff, precision, sim, showabund and timing. Fasta or Phylip or column and name are required.\n";
//helpString += "The adjust parameter is used to handle missing distances. If you set a cutoff, adjust=f by default. If not, adjust=t by default. Adjust=f, means ignore missing distances and adjust cutoff as needed with the average neighbor method. Adjust=t, will treat missing distances as 1.0. You can also set the value the missing distances should be set to, adjust=0.5 would give missing distances a value of 0.5.\n";
helpString += "The phylip and column parameter allow you to enter your distance file. \n";
helpString += "The fasta parameter allows you to enter your fasta file for use with the agc or dgc methods. \n";
@@ -249,21 +248,11 @@ ClusterCommand::ClusterCommand(string option) {
if (temp == "not found") { temp = "100"; }
//saves precision legnth for formatting below
length = temp.length();
- m->mothurConvert(temp, precision);
-
- temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "T"; }
- hard = m->isTrue(temp);
+ m->mothurConvert(temp, precision);
temp = validParameter.validFile(parameters, "sim", false); if (temp == "not found") { temp = "F"; }
sim = m->isTrue(temp);
- //bool cutoffSet = false;
- temp = validParameter.validFile(parameters, "cutoff", false);
- if (temp == "not found") { temp = "10"; }
- //else { cutoffSet = true; }
- m->mothurConvert(temp, cutoff);
- cutoff += (5 / (precision * 10.0));
-
//temp = validParameter.validFile(parameters, "adjust", false); if (temp == "not found") { temp = "F"; }
//if (m->isNumeric1(temp)) { m->mothurConvert(temp, adjust); }
//else if (m->isTrue(temp)) { adjust = 1.0; }
@@ -283,6 +272,13 @@ ClusterCommand::ClusterCommand(string option) {
#else
if ((method == "agc") || (method == "dgc")) { m->mothurOut("[ERROR]: The agc and dgc clustering methods are not available for Windows, aborting\n."); abort = true; }
#endif
+
+ //bool cutoffSet = false;
+ temp = validParameter.validFile(parameters, "cutoff", false);
+ if (temp == "not found") { temp = "10"; }
+ //else { cutoffSet = true; }
+ m->mothurConvert(temp, cutoff);
+
showabund = validParameter.validFile(parameters, "showabund", false);
if (showabund == "not found") { showabund = "T"; }
@@ -314,9 +310,7 @@ int ClusterCommand::execute(){
else if (countfile != "") { inputString += ", count=" + countfile; }
inputString += ", precision=" + toString(precision);
inputString += ", method=" + method;
- if (hard) { inputString += ", hard=T"; }
- else { inputString += ", hard=F"; }
- if (sim) { inputString += ", sim=T"; }
+ if (sim) { inputString += ", sim=T"; }
else { inputString += ", sim=F"; }
@@ -688,12 +682,7 @@ int ClusterCommand::runMothurCluster(){
cluster->update(cutoff);
float dist = matrix->getSmallDist();
- float rndDist;
- if (hard) {
- rndDist = m->ceilDist(dist, precision);
- }else{
- rndDist = m->roundDist(dist, precision);
- }
+ float rndDist = m->ceilDist(dist, precision);
if(previousDist <= 0.0000 && dist != previousDist){
printData("unique", counts);
@@ -732,10 +721,8 @@ int ClusterCommand::runMothurCluster(){
}
listFile.close();
- if (saveCutoff != cutoff) {
- if (hard) { saveCutoff = m->ceilDist(saveCutoff, precision); }
- else { saveCutoff = m->roundDist(saveCutoff, precision); }
-
+ if (saveCutoff != cutoff) {
+ saveCutoff = m->ceilDist(saveCutoff, precision);
m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine();
}
diff --git a/source/commands/clustercommand.h b/source/commands/clustercommand.h
index e55cf3d..d4f0c8c 100644
--- a/source/commands/clustercommand.h
+++ b/source/commands/clustercommand.h
@@ -52,7 +52,7 @@ private:
RAbundVector oldRAbund;
ListVector oldList;
- bool abort, hard, sim;
+ bool abort, sim;
string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile, countfile, fastafile, inputDir, vsearchLocation;
double cutoff;
diff --git a/source/commands/clusterdoturcommand.cpp b/source/commands/clusterdoturcommand.cpp
index b4a4fda..695e9a7 100644
--- a/source/commands/clusterdoturcommand.cpp
+++ b/source/commands/clusterdoturcommand.cpp
@@ -19,7 +19,6 @@ vector<string> ClusterDoturCommand::setParameters(){
CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff);
CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "","",false,false); parameters.push_back(pmethod);
- CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
@@ -39,7 +38,7 @@ string ClusterDoturCommand::getHelpString(){
try {
string helpString = "";
helpString += "The cluster.classic command clusters using the algorithm from dotur. \n";
- helpString += "The cluster.classic command parameter options are phylip, name, count, method, cuttoff, hard, sim, precision. Phylip is required, unless you have a valid current file.\n";
+ helpString += "The cluster.classic command parameter options are phylip, name, count, method, cuttoff, sim, precision. Phylip is required, unless you have a valid current file.\n";
helpString += "The cluster.classic command should be in the following format: \n";
helpString += "cluster.classic(phylip=yourDistanceMatrix, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
helpString += "The acceptable cluster methods are furthest, nearest, weighted and average. If no method is provided then average is assumed.\n";
@@ -183,11 +182,7 @@ ClusterDoturCommand::ClusterDoturCommand(string option) {
temp = validParameter.validFile(parameters, "cutoff", false);
if (temp == "not found") { temp = "10"; }
- m->mothurConvert(temp, cutoff);
- cutoff += (5 / (precision * 10.0));
-
- temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "T"; }
- hard = m->isTrue(temp);
+ m->mothurConvert(temp, cutoff);
temp = validParameter.validFile(parameters, "sim", false); if (temp == "not found") { temp = "F"; }
sim = m->isTrue(temp);
@@ -280,12 +275,7 @@ int ClusterDoturCommand::execute(){
cluster->update(cutoff);
float dist = cluster->getSmallDist();
- float rndDist;
- if (hard) {
- rndDist = m->ceilDist(dist, precision);
- }else{
- rndDist = m->roundDist(dist, precision);
- }
+ float rndDist = m->ceilDist(dist, precision);
if(previousDist <= 0.0000 && dist != previousDist){
printData("unique", counts);
diff --git a/source/commands/clusterdoturcommand.h b/source/commands/clusterdoturcommand.h
index 1cf1e1d..9bc4775 100644
--- a/source/commands/clusterdoturcommand.h
+++ b/source/commands/clusterdoturcommand.h
@@ -37,7 +37,7 @@ public:
void help() { m->mothurOut(getHelpString()); }
private:
- bool abort, hard, sim;
+ bool abort, sim;
string method, fileroot, tag, outputDir, phylipfile, namefile, countfile;
double cutoff;
int precision, length;
diff --git a/source/commands/clustersplitcommand.cpp b/source/commands/clustersplitcommand.cpp
index 2362d7f..dd68d51 100644
--- a/source/commands/clustersplitcommand.cpp
+++ b/source/commands/clustersplitcommand.cpp
@@ -31,7 +31,6 @@ vector<string> ClusterSplitCommand::setParameters(){
CommandParameter pcutoff("cutoff", "Number", "", "0.25", "", "", "","",false,false,true); parameters.push_back(pcutoff);
CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted-agc-dgc", "average", "", "", "","",false,false,true); parameters.push_back(pmethod);
- CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
CommandParameter pislist("islist", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pislist);
CommandParameter pclassic("classic", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pclassic);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
@@ -51,7 +50,7 @@ vector<string> ClusterSplitCommand::setParameters(){
string ClusterSplitCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The cluster.split command parameter options are file, fasta, phylip, column, name, count, cutoff, precision, method, splitmethod, taxonomy, taxlevel, showabund, timing, hard, large, cluster, processors. Fasta or Phylip or column and name are required.\n";
+ helpString += "The cluster.split command parameter options are file, fasta, phylip, column, name, count, cutoff, precision, method, splitmethod, taxonomy, taxlevel, showabund, timing, large, cluster, processors. Fasta or Phylip or column and name are required.\n";
helpString += "The cluster.split command can split your files in 3 ways. Splitting by distance file, by classification, or by classification also using a fasta file. \n";
helpString += "For the distance file method, you need only provide your distance file and mothur will split the file into distinct groups. \n";
helpString += "For the classification method, you need to provide your distance file and taxonomy file, and set the splitmethod to classify. \n";
@@ -325,9 +324,6 @@ ClusterSplitCommand::ClusterSplitCommand(string option) {
length = temp.length();
m->mothurConvert(temp, precision);
- temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "T"; }
- hard = m->isTrue(temp);
-
temp = validParameter.validFile(parameters, "large", false); if (temp == "not found") { temp = "F"; }
large = m->isTrue(temp);
@@ -346,11 +342,6 @@ ClusterSplitCommand::ClusterSplitCommand(string option) {
//not using file option and don't have fasta method with classic
if (((splitmethod != "fasta") && classic) && (file == "")) { m->mothurOut("[ERROR]: splitmethod must be fasta to use cluster.classic, or you must use the file option.\n"); abort=true; }
-
- cutoffNotSet = false;
- temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { cutoffNotSet = true; temp = "0.25"; }
- m->mothurConvert(temp, cutoff);
- cutoff += (5 / (precision * 10.0));
temp = validParameter.validFile(parameters, "taxlevel", false); if (temp == "not found") { temp = "3"; }
m->mothurConvert(temp, taxLevelCutoff);
@@ -369,6 +360,10 @@ ClusterSplitCommand::ClusterSplitCommand(string option) {
if ((method == "agc") || (method == "dgc")) { m->mothurOut("[ERROR]: The agc and dgc clustering methods are not available for Windows, aborting\n."); abort = true; }
#endif
+ cutoffNotSet = false;
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { cutoffNotSet = true; temp = "0.25"; }
+ m->mothurConvert(temp, cutoff);
+
if ((splitmethod == "distance") || (splitmethod == "classify") || (splitmethod == "fasta")) { }
else { m->mothurOut("[ERROR]: " + splitmethod + " is not a valid splitting method. Valid splitting algorithms are distance, classify or fasta."); m->mothurOutEndLine(); abort = true; }
@@ -1147,13 +1142,8 @@ string ClusterSplitCommand::clusterClassicFile(string thisDistFile, string thisN
cluster->update(cutoff);
float dist = cluster->getSmallDist();
- float rndDist;
- if (hard) {
- rndDist = m->ceilDist(dist, precision);
- }else{
- rndDist = m->roundDist(dist, precision);
- }
-
+ float rndDist = m->ceilDist(dist, precision);
+
if(previousDist <= 0.0000 && dist != previousDist){
oldList.setLabel("unique");
oldList.print(listFile);
@@ -1286,12 +1276,7 @@ string ClusterSplitCommand::clusterFile(string thisDistFile, string thisNamefile
cluster->update(saveCutoff);
float dist = matrix->getSmallDist();
- float rndDist;
- if (hard) {
- rndDist = m->ceilDist(dist, precision);
- }else{
- rndDist = m->roundDist(dist, precision);
- }
+ float rndDist = m->ceilDist(dist, precision);
if(previousDist <= 0.0000 && dist != previousDist){
oldList.setLabel("unique");
@@ -1336,9 +1321,7 @@ string ClusterSplitCommand::clusterFile(string thisDistFile, string thisNamefile
}
if (saveCutoff != cutoff) {
- if (hard) { saveCutoff = m->ceilDist(saveCutoff, precision); }
- else { saveCutoff = m->roundDist(saveCutoff, precision); }
-
+ saveCutoff = m->ceilDist(saveCutoff, precision);
m->mothurOut("Cutoff was " + toString(cutoff) + " changed cutoff to " + toString(saveCutoff)); m->mothurOutEndLine();
}
diff --git a/source/commands/clustersplitcommand.h b/source/commands/clustersplitcommand.h
index 811c27f..5396409 100644
--- a/source/commands/clustersplitcommand.h
+++ b/source/commands/clustersplitcommand.h
@@ -51,7 +51,7 @@ private:
string file, method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, countfile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile, inputDir, vsearchLocation;
double cutoff, splitcutoff;
int precision, length, processors, taxLevelCutoff;
- bool print_start, abort, hard, large, classic, runCluster, deleteFiles, isList, cutoffNotSet;
+ bool print_start, abort, large, classic, runCluster, deleteFiles, isList, cutoffNotSet;
time_t start;
ofstream outList, outRabund, outSabund;
diff --git a/source/commands/command.hpp b/source/commands/command.hpp
index 3718652..bb23311 100644
--- a/source/commands/command.hpp
+++ b/source/commands/command.hpp
@@ -87,7 +87,13 @@ class Command {
if (filename.length() > 0) { //rip off last "."
filename = filename.substr(0, filename.length()-1);
}
- filename += it->second + ".";
+ filename += it->second + ".";
+ }else if ((it->first == "[group]") || (it->first == "[tag]")) {
+ string group = it->second;
+ for (int j = 0; j < group.length(); j++) {
+ if (group[j] == '-') { group[j] = '_'; }
+ }
+ filename += group + ".";
}else { filename += it->second + "."; }
}
}
diff --git a/source/commands/getmimarkspackagecommand.cpp b/source/commands/getmimarkspackagecommand.cpp
index e05d42c..f298eca 100644
--- a/source/commands/getmimarkspackagecommand.cpp
+++ b/source/commands/getmimarkspackagecommand.cpp
@@ -589,7 +589,7 @@ set<string> GetMIMarksPackageCommand::createGroupNames(Oligos& oligos) {
//overwrite global oligos - assume fastq data like make.contigs
Oligos oligos;
if ((fileOption == 3) || (fileOption == 5)) { oligos.read(oligosfile, false); } //like make.contigs
- else { oligos.read(oligosfile); }
+ else { oligos.read(oligosfile, false); }
map<int, oligosPair> barcodes = oligos.getPairedBarcodes();
map<int, oligosPair> primers = oligos.getPairedPrimers();
diff --git a/source/commands/helpcommand.cpp b/source/commands/helpcommand.cpp
index ef54dae..8716567 100644
--- a/source/commands/helpcommand.cpp
+++ b/source/commands/helpcommand.cpp
@@ -8,19 +8,334 @@
*/
#include "helpcommand.h"
+#include "command.hpp"
+#include "clustercommand.h"
+#include "collectcommand.h"
+#include "collectsharedcommand.h"
+#include "getgroupcommand.h"
+#include "getlabelcommand.h"
+#include "rarefactcommand.h"
+#include "summarycommand.h"
+#include "summarysharedcommand.h"
+#include "rarefactsharedcommand.h"
+#include "quitcommand.h"
+#include "helpcommand.h"
+#include "commandfactory.hpp"
+#include "deconvolutecommand.h"
+#include "parsimonycommand.h"
+#include "unifracunweightedcommand.h"
+#include "unifracweightedcommand.h"
+#include "libshuffcommand.h"
+#include "heatmapcommand.h"
+#include "heatmapsimcommand.h"
+#include "filterseqscommand.h"
+#include "venncommand.h"
+#include "nocommands.h"
+#include "binsequencecommand.h"
+#include "getoturepcommand.h"
+#include "treegroupscommand.h"
+#include "distancecommand.h"
+#include "aligncommand.h"
+#include "matrixoutputcommand.h"
+#include "getsabundcommand.h"
+#include "getrabundcommand.h"
+#include "seqsummarycommand.h"
+#include "screenseqscommand.h"
+#include "reversecommand.h"
+#include "trimseqscommand.h"
+#include "mergefilecommand.h"
+#include "listseqscommand.h"
+#include "getseqscommand.h"
+#include "removeseqscommand.h"
+#include "systemcommand.h"
+#include "secondarystructurecommand.h"
+#include "getsharedotucommand.h"
+#include "getlistcountcommand.h"
+#include "classifyseqscommand.h"
+#include "phylotypecommand.h"
+#include "mgclustercommand.h"
+#include "preclustercommand.h"
+#include "pcoacommand.h"
+#include "otuhierarchycommand.h"
+#include "setdircommand.h"
+#include "parselistscommand.h"
+#include "chimeraccodecommand.h"
+#include "chimeracheckcommand.h"
+#include "chimeraslayercommand.h"
+#include "chimerapintailcommand.h"
+#include "chimerabellerophoncommand.h"
+#include "chimerauchimecommand.h"
+#include "setlogfilecommand.h"
+#include "phylodiversitycommand.h"
+#include "makegroupcommand.h"
+#include "chopseqscommand.h"
+#include "clearcutcommand.h"
+#include "catchallcommand.h"
+#include "splitabundcommand.h"
+#include "clustersplitcommand.h"
+#include "classifyotucommand.h"
+#include "degapseqscommand.h"
+#include "getrelabundcommand.h"
+#include "sensspeccommand.h"
+#include "sffinfocommand.h"
+#include "seqerrorcommand.h"
+#include "normalizesharedcommand.h"
+#include "metastatscommand.h"
+#include "splitgroupscommand.h"
+#include "clusterfragmentscommand.h"
+#include "getlineagecommand.h"
+#include "removelineagecommand.h"
+#include "parsefastaqcommand.h"
+#include "deuniqueseqscommand.h"
+#include "pairwiseseqscommand.h"
+#include "clusterdoturcommand.h"
+#include "subsamplecommand.h"
+#include "removegroupscommand.h"
+#include "getgroupscommand.h"
+#include "indicatorcommand.h"
+#include "consensusseqscommand.h"
+#include "trimflowscommand.h"
+#include "corraxescommand.h"
+#include "shhhercommand.h"
+#include "pcacommand.h"
+#include "nmdscommand.h"
+#include "removerarecommand.h"
+#include "mergegroupscommand.h"
+#include "amovacommand.h"
+#include "homovacommand.h"
+#include "mantelcommand.h"
+#include "makefastqcommand.h"
+#include "anosimcommand.h"
+#include "getcurrentcommand.h"
+#include "setcurrentcommand.h"
+#include "sharedcommand.h"
+#include "getcommandinfocommand.h"
+#include "deuniquetreecommand.h"
+#include "countseqscommand.h"
+#include "countgroupscommand.h"
+#include "summarytaxcommand.h"
+#include "chimeraperseuscommand.h"
+#include "shhhseqscommand.h"
+#include "summaryqualcommand.h"
+#include "otuassociationcommand.h"
+#include "sortseqscommand.h"
+#include "classifytreecommand.h"
+#include "cooccurrencecommand.h"
+#include "pcrseqscommand.h"
+#include "createdatabasecommand.h"
+#include "makebiomcommand.h"
+#include "getcoremicrobiomecommand.h"
+#include "listotulabelscommand.h"
+#include "getotulabelscommand.h"
+#include "removeotulabelscommand.h"
+#include "makecontigscommand.h"
+#include "sffmultiplecommand.h"
+#include "classifysvmsharedcommand.h"
+#include "classifyrfsharedcommand.h"
+#include "filtersharedcommand.h"
+#include "primerdesigncommand.h"
+#include "getdistscommand.h"
+#include "removedistscommand.h"
+#include "mergetaxsummarycommand.h"
+#include "getmetacommunitycommand.h"
+#include "sparcccommand.h"
+#include "makelookupcommand.h"
+#include "renameseqscommand.h"
+#include "makelefsecommand.h"
+#include "lefsecommand.h"
+#include "kruskalwalliscommand.h"
+#include "sracommand.h"
+#include "mergesfffilecommand.h"
+#include "getmimarkspackagecommand.h"
+#include "mimarksattributescommand.h"
+#include "setseedcommand.h"
+#include "makefilecommand.h"
+#include "biominfocommand.h"
+#include "renamefilecommand.h"
+#include "chimeravsearchcommand.h"
+#include "mergecountcommand.hpp"
+
//**********************************************************************************************************************
HelpCommand::HelpCommand(string option) {
- validCommands = CommandFactory::getInstance();
+ validCommands = CommandFactory::getInstance();
+
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ commandName = option;
+
}
//**********************************************************************************************************************
int HelpCommand::execute(){
try {
- validCommands->printCommands(cout);
- m->mothurOut("For more information about a specific command type 'commandName(help)' i.e. 'read.dist(help)'"); m->mothurOutEndLine();
-
- m->mothurOutEndLine(); m->mothurOut("For further assistance please refer to the Mothur manual on our wiki at http://www.mothur.org/wiki, or contact Pat Schloss at mothur.bugs at gmail.com.\n");
+ if (commandName != "") {
+ if (validCommands->isValidCommand(commandName)) {
+ Command* command;
+ string optionString = "help";
+
+ if(commandName == "cluster") { command = new ClusterCommand(optionString); }
+ else if(commandName == "unique.seqs") { command = new DeconvoluteCommand(optionString); }
+ else if(commandName == "parsimony") { command = new ParsimonyCommand(optionString); }
+ else if(commandName == "help") { command = new HelpCommand(optionString); }
+ else if(commandName == "quit") { command = new QuitCommand(optionString); }
+ else if(commandName == "collect.single") { command = new CollectCommand(optionString); }
+ else if(commandName == "collect.shared") { command = new CollectSharedCommand(optionString); }
+ else if(commandName == "rarefaction.single") { command = new RareFactCommand(optionString); }
+ else if(commandName == "rarefaction.shared") { command = new RareFactSharedCommand(optionString); }
+ else if(commandName == "summary.single") { command = new SummaryCommand(optionString); }
+ else if(commandName == "summary.shared") { command = new SummarySharedCommand(optionString); }
+ else if(commandName == "unifrac.weighted") { command = new UnifracWeightedCommand(optionString); }
+ else if(commandName == "unifrac.unweighted") { command = new UnifracUnweightedCommand(optionString); }
+ else if(commandName == "get.group") { command = new GetgroupCommand(optionString); }
+ else if(commandName == "get.label") { command = new GetlabelCommand(optionString); }
+ else if(commandName == "get.sabund") { command = new GetSAbundCommand(optionString); }
+ else if(commandName == "get.rabund") { command = new GetRAbundCommand(optionString); }
+ else if(commandName == "libshuff") { command = new LibShuffCommand(optionString); }
+ else if(commandName == "heatmap.bin") { command = new HeatMapCommand(optionString); }
+ else if(commandName == "heatmap.sim") { command = new HeatMapSimCommand(optionString); }
+ else if(commandName == "filter.seqs") { command = new FilterSeqsCommand(optionString); }
+ else if(commandName == "venn") { command = new VennCommand(optionString); }
+ else if(commandName == "bin.seqs") { command = new BinSeqCommand(optionString); }
+ else if(commandName == "get.oturep") { command = new GetOTURepCommand(optionString); }
+ else if(commandName == "tree.shared") { command = new TreeGroupCommand(optionString); }
+ else if(commandName == "dist.shared") { command = new MatrixOutputCommand(optionString); }
+ else if(commandName == "dist.seqs") { command = new DistanceCommand(optionString); }
+ else if(commandName == "align.seqs") { command = new AlignCommand(optionString); }
+ else if(commandName == "summary.seqs") { command = new SeqSummaryCommand(optionString); }
+ else if(commandName == "screen.seqs") { command = new ScreenSeqsCommand(optionString); }
+ else if(commandName == "reverse.seqs") { command = new ReverseSeqsCommand(optionString); }
+ else if(commandName == "trim.seqs") { command = new TrimSeqsCommand(optionString); }
+ else if(commandName == "trim.flows") { command = new TrimFlowsCommand(optionString); }
+ else if(commandName == "shhh.flows") { command = new ShhherCommand(optionString); }
+ else if(commandName == "list.seqs") { command = new ListSeqsCommand(optionString); }
+ else if(commandName == "get.seqs") { command = new GetSeqsCommand(optionString); }
+ else if(commandName == "remove.seqs") { command = new RemoveSeqsCommand(optionString); }
+ else if(commandName == "merge.files") { command = new MergeFileCommand(optionString); }
+ else if(commandName == "system") { command = new SystemCommand(optionString); }
+ else if(commandName == "align.check") { command = new AlignCheckCommand(optionString); }
+ else if(commandName == "get.sharedseqs") { command = new GetSharedOTUCommand(optionString); }
+ else if(commandName == "get.otulist") { command = new GetListCountCommand(optionString); }
+ else if(commandName == "classify.seqs") { command = new ClassifySeqsCommand(optionString); }
+ else if(commandName == "chimera.ccode") { command = new ChimeraCcodeCommand(optionString); }
+ else if(commandName == "chimera.check") { command = new ChimeraCheckCommand(optionString); }
+ else if(commandName == "chimera.slayer") { command = new ChimeraSlayerCommand(optionString); }
+ else if(commandName == "chimera.uchime") { command = new ChimeraUchimeCommand(optionString); }
+ else if(commandName == "chimera.pintail") { command = new ChimeraPintailCommand(optionString); }
+ else if(commandName == "chimera.bellerophon") { command = new ChimeraBellerophonCommand(optionString); }
+ else if(commandName == "chimera.vsearch") { command = new ChimeraVsearchCommand(optionString); }
+ else if(commandName == "phylotype") { command = new PhylotypeCommand(optionString); }
+ else if(commandName == "mgcluster") { command = new MGClusterCommand(optionString); }
+ else if(commandName == "pre.cluster") { command = new PreClusterCommand(optionString); }
+ else if(commandName == "pcoa") { command = new PCOACommand(optionString); }
+ else if(commandName == "pca") { command = new PCACommand(optionString); }
+ else if(commandName == "nmds") { command = new NMDSCommand(optionString); }
+ else if(commandName == "otu.hierarchy") { command = new OtuHierarchyCommand(optionString); }
+ else if(commandName == "set.dir") { command = new SetDirectoryCommand(optionString); }
+ else if(commandName == "set.logfile") { command = new SetLogFileCommand(optionString); }
+ else if(commandName == "parse.list") { command = new ParseListCommand(optionString); }
+ else if(commandName == "phylo.diversity") { command = new PhyloDiversityCommand(optionString); }
+ else if(commandName == "make.group") { command = new MakeGroupCommand(optionString); }
+ else if(commandName == "chop.seqs") { command = new ChopSeqsCommand(optionString); }
+ else if(commandName == "clearcut") { command = new ClearcutCommand(optionString); }
+ else if(commandName == "catchall") { command = new CatchAllCommand(optionString); }
+ else if(commandName == "split.abund") { command = new SplitAbundCommand(optionString); }
+ else if(commandName == "cluster.split") { command = new ClusterSplitCommand(optionString); }
+ else if(commandName == "classify.otu") { command = new ClassifyOtuCommand(optionString); }
+ else if(commandName == "degap.seqs") { command = new DegapSeqsCommand(optionString); }
+ else if(commandName == "get.relabund") { command = new GetRelAbundCommand(optionString); }
+ else if(commandName == "sens.spec") { command = new SensSpecCommand(optionString); }
+ else if(commandName == "seq.error") { command = new SeqErrorCommand(optionString); }
+ else if(commandName == "sffinfo") { command = new SffInfoCommand(optionString); }
+ else if(commandName == "normalize.shared") { command = new NormalizeSharedCommand(optionString); }
+ else if(commandName == "metastats") { command = new MetaStatsCommand(optionString); }
+ else if(commandName == "split.groups") { command = new SplitGroupCommand(optionString); }
+ else if(commandName == "cluster.fragments") { command = new ClusterFragmentsCommand(optionString); }
+ else if(commandName == "get.lineage") { command = new GetLineageCommand(optionString); }
+ else if(commandName == "remove.lineage") { command = new RemoveLineageCommand(optionString); }
+ else if(commandName == "get.groups") { command = new GetGroupsCommand(optionString); }
+ else if(commandName == "remove.groups") { command = new RemoveGroupsCommand(optionString); }
+ else if((commandName == "get.otus") || (commandName == "get.otulabels")) { command = new GetOtuLabelsCommand(optionString); }
+ else if((commandName == "remove.otus") || (commandName == "remove.otulabels")) { command = new RemoveOtuLabelsCommand(optionString); }
+ else if((commandName == "list.otus") ||(commandName == "list.otulabels")) { command = new ListOtuLabelsCommand(optionString); }
+ else if(commandName == "fastq.info") { command = new ParseFastaQCommand(optionString); }
+ else if(commandName == "deunique.seqs") { command = new DeUniqueSeqsCommand(optionString); }
+ else if(commandName == "pairwise.seqs") { command = new PairwiseSeqsCommand(optionString); }
+ else if(commandName == "cluster.classic") { command = new ClusterDoturCommand(optionString); }
+ else if(commandName == "sub.sample") { command = new SubSampleCommand(optionString); }
+ else if(commandName == "indicator") { command = new IndicatorCommand(optionString); }
+ else if(commandName == "consensus.seqs") { command = new ConsensusSeqsCommand(optionString); }
+ else if(commandName == "corr.axes") { command = new CorrAxesCommand(optionString); }
+ else if(commandName == "remove.rare") { command = new RemoveRareCommand(optionString); }
+ else if(commandName == "merge.groups") { command = new MergeGroupsCommand(optionString); }
+ else if(commandName == "merge.count") { command = new MergeCountCommand(optionString); }
+ else if(commandName == "amova") { command = new AmovaCommand(optionString); }
+ else if(commandName == "homova") { command = new HomovaCommand(optionString); }
+ else if(commandName == "mantel") { command = new MantelCommand(optionString); }
+ else if(commandName == "make.fastq") { command = new MakeFastQCommand(optionString); }
+ else if(commandName == "get.current") { command = new GetCurrentCommand(optionString); }
+ else if(commandName == "set.current") { command = new SetCurrentCommand(optionString); }
+ else if(commandName == "anosim") { command = new AnosimCommand(optionString); }
+ else if(commandName == "make.shared") { command = new SharedCommand(optionString); }
+ else if(commandName == "get.commandinfo") { command = new GetCommandInfoCommand(optionString); }
+ else if(commandName == "deunique.tree") { command = new DeuniqueTreeCommand(optionString); }
+ else if((commandName == "count.seqs") || (commandName == "make.table")) { command = new CountSeqsCommand(optionString); }
+ else if(commandName == "count.groups") { command = new CountGroupsCommand(optionString); }
+ else if(commandName == "summary.tax") { command = new SummaryTaxCommand(optionString); }
+ else if(commandName == "summary.qual") { command = new SummaryQualCommand(optionString); }
+ else if(commandName == "chimera.perseus") { command = new ChimeraPerseusCommand(optionString); }
+ else if(commandName == "shhh.seqs") { command = new ShhhSeqsCommand(optionString); }
+ else if(commandName == "otu.association") { command = new OTUAssociationCommand(optionString); }
+ else if(commandName == "sort.seqs") { command = new SortSeqsCommand(optionString); }
+ else if(commandName == "classify.tree") { command = new ClassifyTreeCommand(optionString); }
+ else if(commandName == "cooccurrence") { command = new CooccurrenceCommand(optionString); }
+ else if(commandName == "pcr.seqs") { command = new PcrSeqsCommand(optionString); }
+ else if(commandName == "create.database") { command = new CreateDatabaseCommand(optionString); }
+ else if(commandName == "make.biom") { command = new MakeBiomCommand(optionString); }
+ else if(commandName == "get.coremicrobiome") { command = new GetCoreMicroBiomeCommand(optionString); }
+ else if(commandName == "make.contigs") { command = new MakeContigsCommand(optionString); }
+ else if(commandName == "sff.multiple") { command = new SffMultipleCommand(optionString); }
+ else if(commandName == "classify.svm") { command = new ClassifySvmSharedCommand(optionString); }
+ else if(commandName == "classify.rf") { command = new ClassifyRFSharedCommand(optionString); }
+ else if(commandName == "filter.shared") { command = new FilterSharedCommand(optionString); }
+ else if(commandName == "primer.design") { command = new PrimerDesignCommand(optionString); }
+ else if(commandName == "get.dists") { command = new GetDistsCommand(optionString); }
+ else if(commandName == "remove.dists") { command = new RemoveDistsCommand(optionString); }
+ else if(commandName == "merge.taxsummary") { command = new MergeTaxSummaryCommand(optionString); }
+ else if(commandName == "get.communitytype") { command = new GetMetaCommunityCommand(optionString); }
+ else if(commandName == "sparcc") { command = new SparccCommand(optionString); }
+ else if(commandName == "make.lookup") { command = new MakeLookupCommand(optionString); }
+ else if(commandName == "rename.seqs") { command = new RenameSeqsCommand(optionString); }
+ else if(commandName == "make.lefse") { command = new MakeLefseCommand(optionString); }
+ else if(commandName == "lefse") { command = new LefseCommand(optionString); }
+ else if(commandName == "kruskal.wallis") { command = new KruskalWallisCommand(optionString); }
+ else if(commandName == "make.sra") { command = new SRACommand(optionString); }
+ else if(commandName == "merge.sfffiles") { command = new MergeSfffilesCommand(optionString); }
+ else if(commandName == "get.mimarkspackage") { command = new GetMIMarksPackageCommand(optionString); }
+ else if(commandName == "mimarks.attributes") { command = new MimarksAttributesCommand(optionString); }
+ else if(commandName == "set.seed") { command = new SetSeedCommand(optionString); }
+ else if(commandName == "make.file") { command = new MakeFileCommand(optionString); }
+ else if(commandName == "biom.info") { command = new BiomInfoCommand(optionString); }
+ else if(commandName == "rename.file") { command = new RenameFileCommand(optionString); }
+ else { command = new NoCommand(optionString); }
+
+ command->execute();
+ delete command;
+
+ }else {
+ m->mothurOut("[ERROR]: " + commandName + " is not a valid command."); m->mothurOutEndLine();
+ validCommands->printCommands(cout);
+ }
+ }else {
+ validCommands->printCommands(cout);
+ m->mothurOut("For more information about a specific command type 'commandName(help)' i.e. 'cluster(help)'"); m->mothurOutEndLine();
+ }
+
+ m->mothurOutEndLine(); m->mothurOut("For further assistance please refer to the Mothur manual on our wiki at http://www.mothur.org/wiki, or contact Pat Schloss at mothur.bugs at gmail.com.\n");
return 0;
}
diff --git a/source/commands/helpcommand.h b/source/commands/helpcommand.h
index aedb7b5..dc1462a 100644
--- a/source/commands/helpcommand.h
+++ b/source/commands/helpcommand.h
@@ -25,7 +25,7 @@ public:
string getCommandName() { return "help"; }
string getCommandCategory() { return "Hidden"; }
string getHelpString() { return "For more information about a specific command type 'commandName(help)' i.e. 'cluster(help)'"; }
- string getOutputPattern(string) { return ""; }
+ string getOutputPattern(string) { return ""; }
string getCitation() { return "no citation"; }
string getDescription() { return "help"; }
@@ -35,7 +35,11 @@ public:
private:
CommandFactory* validCommands;
- vector<string> outputNames;
+ vector<string> outputNames;
+
+ bool abort, calledHelp;
+
+ string commandName;
};
diff --git a/source/commands/makecontigscommand.cpp b/source/commands/makecontigscommand.cpp
index ff8ba86..68f449e 100644
--- a/source/commands/makecontigscommand.cpp
+++ b/source/commands/makecontigscommand.cpp
@@ -769,7 +769,7 @@ unsigned long long MakeContigsCommand::processSingleFileOption(map<string, int>&
ofstream out;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(it->first));
- cout << variables["[filename]"] << endl;
+ //cout << variables["[filename]"] << endl;
string thisGroupName = getOutputFileName("group",variables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
m->openOutputFile(thisGroupName, out);
@@ -2652,6 +2652,7 @@ int MakeContigsCommand::setLines(vector<string> fasta, vector<string> qual, vect
unsigned long long size;
//get num bytes in file
+ fasta[1] = m->getFullPathName(fasta[1]);
pFile = fopen (fasta[1].c_str(),"rb");
if (pFile==NULL) perror ("Error opening file");
else{
@@ -2723,6 +2724,7 @@ int MakeContigsCommand::setLines(vector<string> fasta, vector<string> qual, vect
unsigned long long size;
//get num bytes in file
+ qual[0] = m->getFullPathName(qual[0]);
pFile = fopen (qual[0].c_str(),"rb");
if (pFile==NULL) perror ("Error opening file");
else{
@@ -2781,6 +2783,7 @@ int MakeContigsCommand::setLines(vector<string> fasta, vector<string> qual, vect
FILE * pFile2;
//get num bytes in file
+ qual[1] = m->getFullPathName(qual[1]);
pFile2 = fopen (qual[1].c_str(),"rb");
if (pFile2==NULL) perror ("Error opening file");
else{
diff --git a/source/commands/makefilecommand.cpp b/source/commands/makefilecommand.cpp
index 83b7606..92f580f 100644
--- a/source/commands/makefilecommand.cpp
+++ b/source/commands/makefilecommand.cpp
@@ -14,6 +14,7 @@ vector<string> MakeFileCommand::setParameters(){
CommandParameter ptype("type", "Multiple", "fastq-gz", "fastq", "", "", "","",false,false); parameters.push_back(ptype);
CommandParameter pnumcols("numcols", "Multiple", "2-3", "3", "", "", "","",false,false, true); parameters.push_back(pnumcols);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
+ CommandParameter pprefix("prefix", "String", "", "", "", "", "","",false,false); parameters.push_back(pprefix);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
@@ -31,10 +32,11 @@ string MakeFileCommand::getHelpString(){
try {
string helpString = "";
helpString += "The make.file command takes a input directory and creates a file file containing the fastq or gz files in the directory.\n";
- helpString += "The make.fastq command parameters are inputdir, numcols and type. inputdir is required.\n";
+ helpString += "The make.file command parameters are inputdir, numcols, type and prefix. inputdir is required.\n";
helpString += "May create more than one file. Mothur will attempt to match paired files. \n";
helpString += "The type parameter allows you to set the type of files to look for. Options are fastq or gz. Default=fastq. \n";
helpString += "The numcols parameter allows you to set number of columns you mothur to make in the file. Default=3, meaning groupName forwardFastq reverseFastq. The groupName is made from the beginning part of the forwardFastq file. Everything up to the first '_' or if no '_' is found then the root of the forwardFastq filename.\n";
+ helpString += "The prefix parameter allows you to enter your own prefix for the output filename. Default=stability.";
helpString += "The make.file command should be in the following format: \n";
helpString += "make.file(inputdir=yourInputDirectory). \n";
helpString += "Example make.group(inputdir=fastqFiles)\n";
@@ -51,7 +53,7 @@ string MakeFileCommand::getOutputPattern(string type) {
try {
string pattern = "";
- if (type == "file") { pattern = "[filename],[tag],file"; }
+ if (type == "file") { pattern = "[filename],[tag],files-[filename],files"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
@@ -126,6 +128,8 @@ MakeFileCommand::MakeFileCommand(string option) {
if ((temp != "2") && (temp != "3")) { m->mothurOut(temp + " is not a valid numcols. Options are 2 or 3. I will use 3."); m->mothurOutEndLine(); temp = "3"; }
m->mothurConvert(temp, numCols);
+ prefix = validParameter.validFile(parameters, "prefix", false); if (prefix == "not found") { prefix = "stability"; }
+
}
}
catch(exception& e) {
@@ -177,23 +181,17 @@ int MakeFileCommand::execute(){
}
if (numDiffs > 1) { singles.push_back(fastqFiles[i]); lastFile = fastqFiles[i]; }
else { //only one diff = paired files
- int pos = simpleName1.find("R1");
- int pos2 = simpleName2.find("R2");
- if ((pos != string::npos) && (pos2 != string::npos)){
- vector<string> temp;
- if (numCols == 3) {
- string groupName = "noGroup"+toString(i);
- int posUnderscore = fastqFiles[i].find_first_of('_');
- if (posUnderscore == string::npos) { groupName = m->getSimpleName(m->getRootName(fastqFiles[i])); }
- else{ groupName = m->getSimpleName(fastqFiles[i].substr(0, posUnderscore)); }
- temp.push_back(groupName);
- }
- temp.push_back(fastqFiles[i]); temp.push_back(fastqFiles[i+1]); lastFile = fastqFiles[i+1];
- paired.push_back(temp);
- i++;
- }else {
- singles.push_back(fastqFiles[i]); lastFile = fastqFiles[i];
+ vector<string> temp;
+ if (numCols == 3) {
+ string groupName = "noGroup"+toString(i);
+ int posUnderscore = fastqFiles[i].find_first_of('_');
+ if (posUnderscore == string::npos) { groupName = m->getSimpleName(m->getRootName(fastqFiles[i])); }
+ else{ groupName = m->getSimpleName(fastqFiles[i].substr(0, posUnderscore)); }
+ temp.push_back(groupName);
}
+ temp.push_back(fastqFiles[i]); temp.push_back(fastqFiles[i+1]); lastFile = fastqFiles[i+1];
+ paired.push_back(temp);
+ i++;
}
}else{
singles.push_back(fastqFiles[i]); lastFile = fastqFiles[i];
@@ -203,8 +201,8 @@ int MakeFileCommand::execute(){
if (singles.size() != 0) {
map<string, string> variables;
- variables["[filename]"] = outputDir + "fileList.";
- variables["[tag]"] = "single";
+ variables["[filename]"] = outputDir + prefix + ".";
+ if (paired.size() != 0) { variables["[tag]"] = "single"; }
string filename = getOutputFileName("file",variables);
ofstream out;
m->openOutputFile(filename, out);
@@ -219,8 +217,8 @@ int MakeFileCommand::execute(){
if (paired.size() != 0) {
map<string, string> variables;
- variables["[filename]"] = outputDir + "fileList.";
- variables["[tag]"] = "paired";
+ variables["[filename]"] = outputDir + prefix + ".";
+ if (singles.size() != 0) { variables["[tag]"] = "paired"; }
string filename = getOutputFileName("file",variables);
ofstream out;
m->openOutputFile(filename, out);
diff --git a/source/commands/makefilecommand.h b/source/commands/makefilecommand.h
index ec05dfb..eb6a7bf 100644
--- a/source/commands/makefilecommand.h
+++ b/source/commands/makefilecommand.h
@@ -32,7 +32,7 @@ public:
private:
- string inputDir, outputDir, typeFile;
+ string inputDir, outputDir, typeFile, prefix;
vector<string> outputNames;
int numCols;
bool abort;
diff --git a/source/commands/makegroupcommand.cpp b/source/commands/makegroupcommand.cpp
index e7b8860..1d9f89d 100644
--- a/source/commands/makegroupcommand.cpp
+++ b/source/commands/makegroupcommand.cpp
@@ -186,7 +186,7 @@ MakeGroupCommand::MakeGroupCommand(string option) {
//prevent giantic file name
map<string, string> variables;
variables["[filename]"] = filename;
- if (fastaFileNames.size() > 3) { variables["[filename]"] = outputDir + "merge"; }
+ if (fastaFileNames.size() > 3) { variables["[filename]"] = "merge"; }
filename = getOutputFileName("group",variables);
//make sure there is at least one valid file left
diff --git a/source/commands/mergecountcommand.cpp b/source/commands/mergecountcommand.cpp
new file mode 100644
index 0000000..42e9917
--- /dev/null
+++ b/source/commands/mergecountcommand.cpp
@@ -0,0 +1,226 @@
+//
+// mergecountcommand.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 8/3/16.
+// Copyright © 2016 Schloss Lab. All rights reserved.
+//
+
+#include "mergecountcommand.hpp"
+#include "counttable.h"
+
+//**********************************************************************************************************************
+vector<string> MergeCountCommand::setParameters(){
+ try {
+ CommandParameter pcount("count", "InputTypes", "", "", "", "", "","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter poutput("output", "String", "", "", "", "", "","",false,true,true); parameters.push_back(poutput);
+ CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeCountCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string MergeCountCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The merge.count command takes a list of count files separated by dashes and merges them into one file.";
+ helpString += "The merge.count command parameters are count and output.";
+ helpString += "Example merge.count(count=final.count_table-new.count_table, output=complete.count_table).";
+ helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputFileName).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeCountCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+MergeCountCommand::MergeCountCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["count"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeCountCommand", "MergeCountCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+MergeCountCommand::MergeCountCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ if(option == "help") {
+ help();
+ abort = true; calledHelp = true;
+ }else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["count"] = tempOutNames;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+
+ string fileList = validParameter.validFile(parameters, "count", false);
+ if(fileList == "not found") { m->mothurOut("[ERROR]: you must enter two or more count file names"); m->mothurOutEndLine(); abort=true; }
+ else{ m->splitAtDash(fileList, fileNames); }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found") { outputDir = ""; }
+
+
+ numInputFiles = fileNames.size();
+ ifstream testFile;
+ if(numInputFiles == 0){
+ m->mothurOut("you must enter two or more file names and you entered " + toString(fileNames.size()) + " file names"); m->mothurOutEndLine();
+ abort=true;
+ }
+ else{
+ for(int i=0;i<numInputFiles;i++){
+ if (inputDir != "") {
+ string path = m->hasPath(fileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { fileNames[i] = inputDir + fileNames[i]; }
+ }
+
+ map<string, string> file; file["file"] = fileNames[i];
+ fileNames[i] = validParameter.validFile(file, "file", true);
+ if(fileNames[i] == "not found"){ abort = true; }
+ }
+ }
+
+ outputFileName = validParameter.validFile(parameters, "output", false);
+ if (outputFileName == "not found") { m->mothurOut("you must enter an output file name"); m->mothurOutEndLine(); abort=true; }
+ else if (outputDir != "") { outputFileName = outputDir + m->getSimpleName(outputFileName); }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeCountCommand", "MergeCountCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int MergeCountCommand::execute(){
+ try {
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ m->mothurRemove(outputFileName);
+
+ //read headers from each file to confirm all contain groupinfo or all do not
+ //Also collect all group names
+ bool allContainGroups = true; bool allNoGroups = true;
+ set<string> allGroups;
+ for(int i = 0; i < numInputFiles; i++) {
+
+ if (m->control_pressed) { return 0; }
+
+ vector<string> thisTablesGroups;
+ CountTable table;
+ bool hasGroups = table.testGroups(fileNames[i], thisTablesGroups);
+
+ if (hasGroups) {
+ allNoGroups = false;
+ for (int j = 0; j < thisTablesGroups.size(); j++) { allGroups.insert(thisTablesGroups[j]); }
+ }else { allContainGroups = false; }
+ }
+ int numGroups = allGroups.size();
+
+ //check to make sure all files are one type - quit if not
+ if (!allContainGroups && !allNoGroups) { m->mothurOut("[ERROR]: your have countfiles that contains group information and count files that do not. These cannot be combined without loss of information, please correct.\n"); m->control_pressed = true; return 0; }
+
+ if (m->control_pressed) { return 0; }
+
+ //Create Blank Table - (set<string>&, map<string, string>&, set<string>&); //seqNames, seqName->group, groupNames
+ set<string> seqNames; map<string, string> seqGroup; set<string> g;
+ CountTable completeTable;
+ completeTable.createTable(seqNames, seqGroup, g);
+
+ //append first one to get headers
+ map<string, int> groupIndex;
+ if (allNoGroups) { m->appendBinaryFiles(fileNames[0], outputFileName); }
+ else { //create groupMap to save time setting abundance vector
+ int count = 0;
+ for (set<string>::iterator it = allGroups.begin(); it != allGroups.end(); it++) {
+ completeTable.addGroup(*it);
+ groupIndex[*it] = count; count++;
+ }
+ }
+
+ //for each file
+ for(int i = 0; i < numInputFiles; i++) {
+
+ if (m->control_pressed) { break; }
+
+ if (allContainGroups) {
+
+ CountTable table; table.readTable(fileNames[i], true, false);
+ vector<string> groups = table.getNamesOfGroups();
+
+ vector<string> seqs = table.getNamesOfSeqs();
+ for (int j = 0; j < seqs.size(); j++) {
+ if (m->control_pressed) { break; }
+ vector<int> abunds = table.getGroupCounts(seqs[j]);
+ vector<int> newAbunds; newAbunds.resize(numGroups, 0);
+ for (int k = 0; k < abunds.size(); k++) {
+ if (abunds[k] != 0) { //we need to set abundance in vector with all groups
+ //groups and abunds are in matching order. we know all groups are in groupIndex from above.
+ int newIndex = groupIndex[groups[k]];
+ newAbunds[newIndex] = abunds[k];
+ }
+ }
+ completeTable.push_back(seqs[j], newAbunds);
+ }
+ }
+ else { m->appendFilesWithoutHeaders(fileNames[i], outputFileName); } //No group info so simple append
+ }
+
+ if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
+
+ //print new table
+ if (allContainGroups) { completeTable.printTable(outputFileName); }
+
+ if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
+
+ //update current count file
+ m->setCountTableFile(outputFileName);
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["merge"].push_back(outputFileName);
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeCountCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
diff --git a/source/commands/mergecountcommand.hpp b/source/commands/mergecountcommand.hpp
new file mode 100644
index 0000000..5edfd4d
--- /dev/null
+++ b/source/commands/mergecountcommand.hpp
@@ -0,0 +1,48 @@
+//
+// mergecountcommand.hpp
+// Mothur
+//
+// Created by Sarah Westcott on 8/3/16.
+// Copyright © 2016 Schloss Lab. All rights reserved.
+//
+
+#ifndef mergecountcommand_hpp
+#define mergecountcommand_hpp
+
+#include "command.hpp"
+
+class MergeCountCommand : public Command {
+
+#ifdef UNIT_TEST
+ //friend class TestMergeCountCommand;
+#endif
+
+public:
+ MergeCountCommand(string);
+ MergeCountCommand();
+ ~MergeCountCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "merge.count"; }
+ string getCommandCategory() { return "General"; }
+
+ string getHelpString();
+ string getOutputPattern(string) { return ""; }
+ string getCitation() { return "http://www.mothur.org/wiki/Merge.count"; }
+ string getDescription() { return "reads count files and combines them into a single count file"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+private:
+
+ bool abort;
+ string outputDir, inputDir, countfile, output, outputFileName;
+ vector<string> outputNames, fileNames;
+ int numInputFiles;
+
+};
+
+
+#endif /* mergecountcommand_hpp */
diff --git a/source/commands/mergegroupscommand.cpp b/source/commands/mergegroupscommand.cpp
index 8d36d2b..7c40ce8 100644
--- a/source/commands/mergegroupscommand.cpp
+++ b/source/commands/mergegroupscommand.cpp
@@ -308,6 +308,11 @@ int MergeGroupsCommand::execute(){
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
}
+
+ itTypes = outputTypes.find("count");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
diff --git a/source/commands/parselistscommand.cpp b/source/commands/parselistscommand.cpp
index cbd5009..6659692 100644
--- a/source/commands/parselistscommand.cpp
+++ b/source/commands/parselistscommand.cpp
@@ -324,14 +324,7 @@ int ParseListCommand::execute(){
/**********************************************************************************************************************/
int ParseListCommand::parse(ListVector* thisList) {
try {
- map<string, string> files;
- map<string, string>::iterator it3;
-
- //set fileroot
- map<string, string> variables;
- variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
- variables["[distance]"] = thisList->getLabel();
-
+
//fill filehandles with neccessary ofstreams
vector<string> gGroups;
if (groupfile != "") { gGroups = groupMap->getNamesOfGroups(); }
@@ -342,11 +335,18 @@ int ParseListCommand::parse(ListVector* thisList) {
map<string, string>::iterator itGroup;
map<string, int> groupNumBins;
+ map<string, string> files;
+
+ //set fileroot
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[distance]"] = thisList->getLabel();
+
for (int i=0; i<gGroups.size(); i++) {
variables["[group]"] = gGroups[i];
string filename = getOutputFileName("list",variables);
ofstream temp;
- m->openOutputFile(filename, temp);
+ m->openOutputFile(filename, temp); temp.close();
files[gGroups[i]] = filename;
outputNames.push_back(filename); outputTypes["list"].push_back(filename);
groupNumBins[gGroups[i]] = 0;
@@ -404,9 +404,10 @@ int ParseListCommand::parse(ListVector* thisList) {
}
//end list vector
- for (it3 = files.begin(); it3 != files.end(); it3++) {
+ for (map<string, string>::iterator it3 = files.begin(); it3 != files.end(); it3++) {
ofstream out;
- m->openOutputFileAppend(files[it3->second], out);
+ string filename = it3->second;
+ m->openOutputFileAppend(filename, out);
out << groupLabels[it3->first] << endl;
out << thisList->getLabel() << '\t' << groupNumBins[it3->first] << groupVector[it3->first] << endl; // label numBins listvector for that group
out.close();
diff --git a/source/commands/seqerrorcommand.cpp b/source/commands/seqerrorcommand.cpp
index f061fd3..a56e943 100644
--- a/source/commands/seqerrorcommand.cpp
+++ b/source/commands/seqerrorcommand.cpp
@@ -1374,6 +1374,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
unsigned long long size;
//get num bytes in file
+ qfilename = m->getFullPathName(qfilename);
pFile = fopen (qfilename.c_str(),"rb");
if (pFile==NULL) perror ("Error opening file");
else{
@@ -1436,6 +1437,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
unsigned long long sizeR;
//get num bytes in file
+ rfilename = m->getFullPathName(rfilename);
rFile = fopen (rfilename.c_str(),"rb");
if (rFile==NULL) perror ("Error opening file");
else{
@@ -1455,6 +1457,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
unsigned long long size;
//get num bytes in file
+ filename = m->getFullPathName(filename);
pFile = fopen (filename.c_str(),"rb");
if (pFile==NULL) perror ("Error opening file");
else{
@@ -1469,6 +1472,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
FILE * qFile;
//get num bytes in file
+ qfilename = m->getFullPathName(qfilename);
qFile = fopen (qfilename.c_str(),"rb");
if (qFile==NULL) perror ("Error opening file");
else{
@@ -1486,6 +1490,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
FILE * rFile;
//get num bytes in file
+ rfilename = m->getFullPathName(rfilename);
rFile = fopen (rfilename.c_str(),"rb");
if (rFile==NULL) perror ("Error opening file");
else{
diff --git a/source/commands/sracommand.cpp b/source/commands/sracommand.cpp
index 14f8475..17fac11 100644
--- a/source/commands/sracommand.cpp
+++ b/source/commands/sracommand.cpp
@@ -1327,15 +1327,19 @@ int SRACommand::mapGroupToFile(map<string, vector<string> >& files, vector<strin
try {
for (int i = 0; i < Groups.size(); i++) {
+ //correct filename issues if group name contains '-' characters
+ string thisGroup = Groups[i];
+ for (int k = 0; k < thisGroup.length(); k++) { if (thisGroup[k] == '-') { thisGroup[k] = '_'; } }
+
for (int j = 0; j < theseFiles.size(); j++) {
string tempName = m->getSimpleName(theseFiles[j]);
//if ((tempName == "GZGO5KL01.F006D146.sff") || (tempName == "G3BMWHG01.F008D021.sff") || (tempName == "GO2JXTW01.M002D125.sff") || (tempName == "GO5715J01.M003D125.sff")) { cout << Groups[i] << '\t' << theseFiles[j] << endl; }
//cout << i << '\t' << j << '\t' << Groups[i] << '\t' << theseFiles[j] << endl;
- int pos = theseFiles[j].find(Groups[i]);
+ int pos = theseFiles[j].find(thisGroup);
if (pos != string::npos) { //you have a potential match, make sure you dont have a case of partial name
- if (theseFiles[j][pos+Groups[i].length()] == '.') { //final.soil.sff vs final.soil2.sff both would match soil.
- map<string, vector<string> >::iterator it = files.find(Groups[i]);
+ if (theseFiles[j][pos+thisGroup.length()] == '.') { //final.soil.sff vs final.soil2.sff both would match soil.
+ map<string, vector<string> >::iterator it = files.find(thisGroup);
if (it == files.end()) {
vector<string> temp; temp.push_back(theseFiles[j]);
files[Groups[i]] = temp;
@@ -1346,6 +1350,7 @@ int SRACommand::mapGroupToFile(map<string, vector<string> >& files, vector<strin
}
}
}
+
return 0;
}
catch(exception& e) {
diff --git a/source/commands/trimflowscommand.cpp b/source/commands/trimflowscommand.cpp
index 445b556..3064c83 100644
--- a/source/commands/trimflowscommand.cpp
+++ b/source/commands/trimflowscommand.cpp
@@ -341,6 +341,7 @@ int TrimFlowsCommand::execute(){
unsigned long long size;
//get num bytes in file
+ barcodePrimerComboFileNames[i][j] = m->getFullPathName(barcodePrimerComboFileNames[i][j]);
pFile = fopen (barcodePrimerComboFileNames[i][j].c_str(),"rb");
if (pFile==NULL) perror ("Error opening file");
else{
@@ -777,6 +778,7 @@ vector<unsigned long long> TrimFlowsCommand::getFlowFileBreaks() {
unsigned long long size;
//get num bytes in file
+ flowFileName = m->getFullPathName(flowFileName);
pFile = fopen (flowFileName.c_str(),"rb");
if (pFile==NULL) perror ("Error opening file");
else{
diff --git a/source/commands/trimseqscommand.cpp b/source/commands/trimseqscommand.cpp
index eb9a73f..037f8ed 100644
--- a/source/commands/trimseqscommand.cpp
+++ b/source/commands/trimseqscommand.cpp
@@ -1646,6 +1646,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
unsigned long long size;
//get num bytes in file
+ qfilename = m->getFullPathName(qfilename);
pFile = fopen (qfilename.c_str(),"rb");
if (pFile==NULL) perror ("Error opening file");
else{
diff --git a/source/datastructures/counttable.cpp b/source/datastructures/counttable.cpp
index 4cd2aa3..cf078fc 100644
--- a/source/datastructures/counttable.cpp
+++ b/source/datastructures/counttable.cpp
@@ -11,6 +11,7 @@
/************************************************************/
int CountTable::createTable(set<string>& n, map<string, string>& g, set<string>& gs) {
try {
+ hasGroups = false;
int numGroups = 0;
groups.clear();
totalGroups.clear();
@@ -81,13 +82,34 @@ int CountTable::createTable(set<string>& n, map<string, string>& g, set<string>&
/************************************************************/
bool CountTable::testGroups(string file) {
try {
+ vector<string> nothing;
+ return testGroups(file, nothing);
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountTable", "testGroups");
+ exit(1);
+ }
+}
+
+/************************************************************/
+bool CountTable::testGroups(string file, vector<string>& groups) {
+ try {
m = MothurOut::getInstance(); hasGroups = false; total = 0;
ifstream in;
m->openInputFile(file, in);
string headers = m->getline(in); m->gobble(in);
vector<string> columnHeaders = m->splitWhiteSpace(headers);
- if (columnHeaders.size() > 2) { hasGroups = true; }
+ if (columnHeaders.size() > 2) {
+ hasGroups = true;
+
+ for (int i = 2; i < columnHeaders.size(); i++) {
+ groups.push_back(columnHeaders[i]);
+ }
+ //sort groups to keep consistent with how we store the groups in groupmap
+ sort(groups.begin(), groups.end());
+ }
+
return hasGroups;
}
catch(exception& e) {
diff --git a/source/datastructures/counttable.h b/source/datastructures/counttable.h
index 64def2e..f9150d1 100644
--- a/source/datastructures/counttable.h
+++ b/source/datastructures/counttable.h
@@ -50,12 +50,13 @@ class CountTable {
//reads and creates smart enough to eliminate groups with zero counts
int createTable(set<string>&, map<string, string>&, set<string>&); //seqNames, seqName->group, groupNames
int createTable(string, string, bool); //namefile, groupfile, createGroup
- int readTable(string, bool, bool);
+ int readTable(string, bool, bool); //file, readGroups, mothurRunning
int printTable(string);
int printHeaders(ofstream&);
int printSeq(ofstream&, string);
- bool testGroups(string file); //used to check if file has group data without reading it.
+ bool testGroups(string file); //used to check if file has group data without reading it
+ bool testGroups(string file, vector<string>&); //used to check if file has group data without reading it, return groups if found.
int copy(CountTable*);
bool hasGroupInfo() { return hasGroups; }
diff --git a/source/mothurout.cpp b/source/mothurout.cpp
index 86d9e52..eadce7e 100644
--- a/source/mothurout.cpp
+++ b/source/mothurout.cpp
@@ -1356,6 +1356,8 @@ vector<bool> MothurOut::isGZ(string filename){
int ableToOpen = openInputFileBinary(filename, fileHandle, gzin, ""); //no error
+ if (debug) { if (ableToOpen == 1) { mothurOut("[DEBUG]: unable to open gz file. \n"); } }
+
if (ableToOpen == 1) { return results; } // results[0] = false; results[1] = false;
else { results[0] = true; }
@@ -2991,7 +2993,7 @@ bool MothurOut::checkGroupName(string name) {
}
if (!goodName) {
- mothurOut("\n[ERROR]: group " + name + " contains illegal characters in the name. Group names cannot include :, -, or / characters. The ':' character is a special character used in trees. Using ':' will result in your tree being unreadable by tree reading software. The '-' character is a special character used by mothur to parse group names. Using the '-' character will prevent you from selecting groups. The '/' character will created unreadable filenames when mothur inclu [...]
+ mothurOut("\n[WARNING]: group " + name + " contains illegal characters in the name. Group names should not include :, -, or / characters. The ':' character is a special character used in trees. Using ':' will result in your tree being unreadable by tree reading software. The '-' character is a special character used by mothur to parse group names. Using the '-' character will prevent you from selecting groups. The '/' character will created unreadable filenames when mothur [...]
}
return goodName;
--
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