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A7730EFE13967241007433A3 /* countseqscommand.cpp */,
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+ A77EBD2E1523709100ED407C /* createdatabasecommand.cpp */,
A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */,
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A7E9B6C612D37EC400DA6239 /* degapseqscommand.h */,
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A7C3DC0F14FE469500FE1924 /* trialSwap2.cpp in Sources */,
A76CDD821510F143004C8458 /* prcseqscommand.cpp in Sources */,
+ A77EBD2F1523709100ED407C /* createdatabasecommand.cpp in Sources */,
);
runOnlyForDeploymentPostprocessing = 0;
};
*
*/
-#include "mothur.h"
+
#include "command.hpp"
#include "classify.h"
#include "referencedb.h"
//This function calls the appropriate command fucntions based on user input.
Command* CommandFactory::getCommand(string commandName, string optionString){
try {
+
delete command; //delete the old command
//user has opted to redirect output from dir where input files are located to some other place
--- /dev/null
+//
+// createdatabasecommand.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 3/28/12.
+// Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "createdatabasecommand.h"
+#include "sequence.hpp"
+#include "inputdata.h"
+
+//**********************************************************************************************************************
+vector<string> CreateDatabaseCommand::setParameters(){
+ try {
+ CommandParameter pfasta("repfasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pname("repname", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
+ CommandParameter pcontaxonomy("contaxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcontaxonomy);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ 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, "CreateDatabaseCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string CreateDatabaseCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The create.database command reads a listfile, *.cons.taxonomy, *.rep.fasta, *.rep.names and optional groupfile, and creates a database file.\n";
+ helpString += "The create.database command parameters are repfasta, list, repname, contaxonomy, group and label. List, repfasta, repnames, and contaxonomy are required. \n";
+
+ helpString += "The create.database command should be in the following format: \n";
+ helpString += "create.database(repfasta=yourFastaFileFromGetOTURep, repname=yourNameFileFromGetOTURep, contaxonomy=yourConTaxFileFromClassifyOTU, list=yourListFile) \n";
+ helpString += "Example: create.database(repfasta=final.an.0.03.rep.fasta, name=final.an.0.03.rep.names, list=fina.an.list, label=0.03, contaxonomy=final.an.0.03.cons.taxonomy) \n";
+ helpString += "Note: No spaces between parameter labels (i.e. repfasta), '=' and parameters (i.e.yourFastaFileFromGetOTURep).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CreateDatabaseCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
--- /dev/null
+#ifndef Mothur_createdatabasecommand_h
+#define Mothur_createdatabasecommand_h
+
+//
+// createdatabasecommand.h
+// Mothur
+//
+// Created by Sarah Westcott on 3/28/12.
+// Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "command.hpp"
+#include "listvector.hpp"
+
+class CreateDatabaseCommand : public Command {
+public:
+ CreateDatabaseCommand(string);
+ CreateDatabaseCommand();
+ ~CreateDatabaseCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "create.database"; }
+ string getCommandCategory() { return "OTU-Based Approaches"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Create.database"; }
+ string getDescription() { return "creates database file that includes, abundances across groups, representative sequences, and taxonomy for each OTU"; }
+
+
+ int execute() {};
+ void help() { m->mothurOut(getHelpString()); }
+
+private:
+
+ bool abort;
+ string listfile, groupfile, repfastafile, repnamesfile, constaxonomyfile, label, outputDir;
+
+ vector<string> outputNames;
+
+ int readFasta();
+ int readNames();
+ int readTax();
+ int processList(ListVector*&);
+
+};
+
+
+
+
+#endif
m->mothurOut("[ERROR]: You did not set any options. Please provide an oligos or ecoli file, or set start or end.\n"); abort = true;
}
- if ((oligosfile == "") && (ecolifile == "") && (start < 0) && (end != -1)) { m->mothurOut("[ERROR]: Invalid start value.\n"); abort = true; }
+ if ((oligosfile == "") && (ecolifile == "") && (start < 0) && (end == -1)) { m->mothurOut("[ERROR]: Invalid start value.\n"); abort = true; }
if ((ecolifile != "") && (start != -1) && (end != -1)) {
m->mothurOut("[ERROR]: You provided an ecoli file , but set the start or end parameters. Unsure what you intend. When you provide the ecoli file, mothur thinks you want to use the start and end of the sequence in the ecoli file.\n"); abort = true;
else{
//are you aligned
if (aligned) {
- if (!keepprimer) { currSeq.padToPos(mapAligned[primerEnd]); }
- else { currSeq.padToPos(mapAligned[primerStart]); }
+ if (!keepprimer) { currSeq.filterToPos(mapAligned[primerEnd]); }
+ else { currSeq.filterToPos(mapAligned[primerStart]); }
}else {
if (!keepprimer) { currSeq.setAligned(currSeq.getUnaligned().substr(primerEnd)); }
else { currSeq.setAligned(currSeq.getUnaligned().substr(primerStart)); }
else{
//are you aligned
if (aligned) {
- if (!keepprimer) { currSeq.padFromPos(mapAligned[primerStart]); }
- else { currSeq.padFromPos(mapAligned[primerEnd]); }
+ if (!keepprimer) { currSeq.filterFromPos(mapAligned[primerStart]); }
+ else { currSeq.filterFromPos(mapAligned[primerEnd]); }
}
else {
if (!keepprimer) { currSeq.setAligned(currSeq.getUnaligned().substr(0, primerStart)); }
else if (currSeq.getAligned().length() != length) {
m->mothurOut("[ERROR]: seqs are not the same length as ecoli seq. When using ecoli option your sequences must be aligned and the same length as the ecoli sequence.\n"); m->control_pressed = true; break;
}else {
- currSeq.padToPos(start);
- currSeq.padFromPos(end);
+ currSeq.filterToPos(start);
+ currSeq.filterFromPos(end);
}
}else{ //using start and end to trim
//make sure the seqs are aligned
lengths.insert(currSeq.getAligned().length());
if (lengths.size() > 1) { m->mothurOut("[ERROR]: seqs are not aligned. When using start and end your sequences must be aligned.\n"); m->control_pressed = true; break; }
else {
- if (start != -1) { currSeq.padToPos(start); }
+ if (start != -1) { currSeq.filterToPos(start); }
if (end != -1) {
if (end > currSeq.getAligned().length()) { m->mothurOut("[ERROR]: end is longer than your sequence length, aborting.\n"); m->control_pressed = true; break; }
else {
- currSeq.padFromPos(end);
+ currSeq.filterFromPos(end);
}
}
}
if(numParentSeqs > 1 && ignoreChimeras == 1) { ignoreSeq = 1; }
else { ignoreSeq = 0; }
- Compare minCompare = getErrors(query, referenceSeqs[closestRefIndex]);
+ Compare minCompare;
+ getErrors(query, referenceSeqs[closestRefIndex], minCompare);
if(namesFileName != ""){
it = weights.find(query.getName());
//***************************************************************************************************************
-Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){
+int SeqErrorCommand::getErrors(Sequence query, Sequence reference, Compare& errors){
try {
if(query.getAlignLength() != reference.getAlignLength()){
m->mothurOut("Warning: " + toString(query.getName()) + " and " + toString(reference.getName()) + " are different lengths\n");
string r = reference.getAligned();
int started = 0;
- Compare errors;
+ //Compare errors;
for(int i=0;i<alignLength;i++){
// cout << r[i] << '\t' << q[i] << '\t';
errors.queryName = query.getName();
errors.refName = reference.getName();
- return errors;
+ //return errors;
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "SeqErrorCommand", "getErrors");
*
*/
-#include "mothur.h"
#include "command.hpp"
#include "sequence.hpp"
#include "referencedb.h"
-struct Compare {
- int AA, AT, AG, AC, TA, TT, TG, TC, GA, GT, GG, GC, CA, CT, CG, CC, NA, NT, NG, NC, Ai, Ti, Gi, Ci, Ni, dA, dT, dG, dC;
- string refName, queryName, sequence;
- double errorRate;
- int weight, matches, mismatches, total;
-
- Compare(){
- AA=0; AT=0; AG=0; AC=0;
- TA=0; TT=0; TG=0; TC=0;
- GA=0; GT=0; GG=0; GC=0;
- CA=0; CT=0; CG=0; CC=0;
- NA=0; NT=0; NG=0; NC=0;
- Ai=0; Ti=0; Gi=0; Ci=0; Ni=0;
- dA=0; dT=0; dG=0; dC=0;
- refName = "";
- queryName = "";
- weight = 1;
- matches = 0;
- mismatches = 0;
- total = 0;
- errorRate = 1.0000;
- sequence = "";
- }
-};
class SeqErrorCommand : public Command {
public:
SeqErrorCommand(string);
SeqErrorCommand();
- ~SeqErrorCommand() {}
+ ~SeqErrorCommand(){}
vector<string> setParameters();
string getCommandName() { return "seq.error"; }
unsigned long long start;
unsigned long long end;
linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
+ ~linePair(){}
};
+ struct Compare {
+ int AA, AT, AG, AC, TA, TT, TG, TC, GA, GT, GG, GC, CA, CT, CG, CC, NA, NT, NG, NC, Ai, Ti, Gi, Ci, Ni, dA, dT, dG, dC;
+ string refName, queryName, sequence;
+ double errorRate;
+ int weight, matches, mismatches, total;
+
+ Compare(){
+ AA=0; AT=0; AG=0; AC=0;
+ TA=0; TT=0; TG=0; TC=0;
+ GA=0; GT=0; GG=0; GC=0;
+ CA=0; CT=0; CG=0; CC=0;
+ NA=0; NT=0; NG=0; NC=0;
+ Ai=0; Ti=0; Gi=0; Ci=0; Ni=0;
+ dA=0; dT=0; dG=0; dC=0;
+ refName = "";
+ queryName = "";
+ weight = 1;
+ matches = 0;
+ mismatches = 0;
+ total = 0;
+ errorRate = 1.0000;
+ sequence = "";
+ }
+ ~Compare(){};
+ };
+
vector<int> processIDS; //processid
vector<linePair> lines;
vector<linePair> qLines;
void getReferences();
map<string,int> getWeights();
- Compare getErrors(Sequence, Sequence);
+ int getErrors(Sequence, Sequence, Compare&);
void printErrorHeader(ofstream&);
void printErrorData(Compare, int, ofstream&, ofstream&);
void printSubMatrix();
startPos = start;
}
+//********************************************************************************************************************
+
+int Sequence::filterToPos(int start){
+
+ if (start > aligned.length()) { start = aligned.length(); m->mothurOut("[ERROR]: start to large.\n"); }
+
+ for(int j = 0; j < start-1; j++) {
+ aligned[j] = '.';
+ }
+
+ setUnaligned(aligned);
+
+ return 0;
+
+}
+//********************************************************************************************************************
+int Sequence::filterFromPos(int end){
+
+ if (end > aligned.length()) { end = aligned.length(); m->mothurOut("[ERROR]: end to large.\n"); }
+
+ for(int j = end; j < aligned.length(); j++) {
+ aligned[j] = '.';
+ }
+
+ setUnaligned(aligned);
+
+ return 0;
+}
//********************************************************************************************************************
int Sequence::getEndPos(){
//********************************************************************************************************************
void Sequence::padFromPos(int end){
-
+ cout << end << '\t' << endPos << endl;
for(int j = end; j < endPos; j++) {
aligned[j] = '.';
}
int getEndPos();
void padToPos(int);
void padFromPos(int);
+ int filterToPos(int); //any character before the pos is changed to . and aligned and unaligned strings changed
+ int filterFromPos(int); //any character after the pos is changed to . and aligned and unaligned strings changed
int getAlignLength();
int getAmbigBases();
void removeAmbigBases();
int j=4; //need to get past the first four bases
while(qualities[i][j] != -1){
- //cout << i << '\t' << j << '\t' << qualities[i][j] << endl;
qualityFile << qualities[i][j] << ' ';
+ if (j > qualities[i].size()) { break; }
j++;
-
}
qualityFile << endl;
}
projects / mothur.git / commitdiff