*/
#include "clusterfragmentscommand.h"
+#include "needlemanoverlap.hpp"
//**********************************************************************************************************************
//sort by unaligned
return better;
}
//**********************************************************************************************************************
+vector<string> ClusterFragmentsCommand::getValidParameters(){
+ try {
+ string AlignArray[] = {"fasta","name","diffs","percent","outputdir","inputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterFragmentsCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ClusterFragmentsCommand::ClusterFragmentsCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterFragmentsCommand", "ClusterFragmentsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ClusterFragmentsCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterFragmentsCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ClusterFragmentsCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterFragmentsCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
- string Array[] = {"fasta","name","outputdir","inputdir"};
+ string Array[] = {"fasta","name","diffs","percent","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = 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 = ""; }
if (namefile == "not found") { namefile = ""; }
else if (namefile == "not open") { abort = true; }
else { readNameFile(); }
+
+ string temp;
+ temp = validParameter.validFile(parameters, "diffs", false); if (temp == "not found"){ temp = "0"; }
+ convert(temp, diffs);
+
+ temp = validParameter.validFile(parameters, "percent", false); if (temp == "not found"){ temp = "0"; }
+ convert(temp, percent);
+
}
}
try {
m->mothurOut("The cluster.fragments command groups sequences that are part of a larger sequence.\n");
m->mothurOut("The cluster.fragments command outputs a new fasta and name file.\n");
- m->mothurOut("The cluster.fragments command parameters are fasta and name. The fasta parameter is required. \n");
+ m->mothurOut("The cluster.fragments command parameters are fasta, name, diffs and percent. The fasta parameter is required. \n");
m->mothurOut("The names parameter allows you to give a list of seqs that are identical. This file is 2 columns, first column is name or representative sequence, second column is a list of its identical sequences separated by commas.\n");
+ m->mothurOut("The diffs parameter allows you to set the number of differences allowed, default=0. \n");
+ m->mothurOut("The percent parameter allows you to set percentage of differences allowed, default=0. percent=2 means if the number of difference is less than or equal to two percent of the length of the fragment, then cluster.\n");
+ m->mothurOut("You may use diffs and percent at the same time to say something like: If the number or differences is greater than 1 or more than 2% of the fragment length, don't merge. \n");
m->mothurOut("The cluster.fragments command should be in the following format: \n");
m->mothurOut("cluster.fragments(fasta=yourFastaFile, names=yourNamesFile) \n");
m->mothurOut("Example cluster.fragments(fasta=amazon.fasta).\n");
int ClusterFragmentsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int start = time(NULL);
if (alignSeqs[j].active) { //this sequence has not been merged yet
string jBases = alignSeqs[j].seq.getUnaligned();
-
- int pos = iBases.find(jBases);
-
- if (pos != string::npos) {
+
+ if (isFragment(iBases, jBases)) {
//merge
alignSeqs[i].names += ',' + alignSeqs[j].names;
alignSeqs[i].numIdentical += alignSeqs[j].numIdentical;
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(newFastaFile); m->mothurOutEndLine();
m->mothurOut(newNamesFile); m->mothurOutEndLine();
+ outputNames.push_back(newFastaFile); outputNames.push_back(newNamesFile); outputTypes["fasta"].push_back(newFastaFile); outputTypes["name"].push_back(newNamesFile);
m->mothurOutEndLine();
return 0;
exit(1);
}
}
-
+//***************************************************************************************************************
+bool ClusterFragmentsCommand::isFragment(string seq1, string seq2){
+ try {
+ bool fragment = false;
+
+ //exact match
+ int pos = seq1.find(seq2);
+ if (pos != string::npos) { return true; }
+ //no match, no diffs wanted
+ else if ((diffs == 0) && (percent == 0)) { return false; }
+ else { //try aligning and see if you can find it
+
+ //find number of acceptable differences for this sequence fragment
+ int totalDiffs;
+ if (diffs == 0) { //you didnt set diffs you want a percentage
+ totalDiffs = floor((seq2.length() * (percent / 100.0)));
+ }else if (percent == 0) { //you didn't set percent you want diffs
+ totalDiffs = diffs;
+ }else if ((percent != 0) && (diffs != 0)) { //you want both, set total diffs to smaller of 2
+ totalDiffs = diffs;
+ int percentDiff = floor((seq2.length() * (percent / 100.0)));
+ if (percentDiff < totalDiffs) { totalDiffs = percentDiff; }
+ }
+
+ Alignment* alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (seq1.length()+totalDiffs+1));
+
+ //use needleman to align
+ alignment->align(seq2, seq1);
+ string tempSeq2 = alignment->getSeqAAln();
+ string temp = alignment->getSeqBAln();
+
+ delete alignment;
+
+ //chop gap ends
+ int startPos = 0;
+ int endPos = tempSeq2.length()-1;
+ for (int i = 0; i < tempSeq2.length(); i++) { if (isalpha(tempSeq2[i])) { startPos = i; break; } }
+ for (int i = tempSeq2.length()-1; i >= 0; i--) { if (isalpha(tempSeq2[i])) { endPos = i; break; } }
+
+ //count number of diffs
+ int numDiffs = 0;
+ for (int i = startPos; i <= endPos; i++) {
+ if (tempSeq2[i] != temp[i]) { numDiffs++; }
+ }
+
+ if (numDiffs <= totalDiffs) { fragment = true; }
+
+ }
+
+ return fragment;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterFragmentsCommand", "isFragment");
+ exit(1);
+ }
+}
/**************************************************************************************************/
int ClusterFragmentsCommand::readFASTA(){
try {
projects / mothur.git / blobdiff