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/*
* seqcoordcommand.cpp
* Mothur
*
* Created by Pat Schloss on 5/30/09.
* Copyright 2009 Patrick D. Schloss. All rights reserved.
*
*/
#include "seqsummarycommand.h"
#include "counttable.h"
#include "summary.hpp"
//**********************************************************************************************************************
vector<string> SeqSummaryCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "FastaReport", "none", "none","summary",false,true,true); parameters.push_back(pfasta);
CommandParameter psummary("summary", "InputTypes", "", "", "FastaReport", "none", "none","",false,false,true); parameters.push_back(psummary);
CommandParameter pcontigsreport("contigsreport", "InputTypes", "", "", "FastaReport", "none", "none","",false,false,true); parameters.push_back(pcontigsreport);
CommandParameter palignreport("alignreport", "InputTypes", "", "", "FastaReport", "none", "none","",false,false,true); parameters.push_back(palignreport);
CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pcount);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
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);
abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["summary"] = tempOutNames;
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, "SeqSummaryCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string SeqSummaryCommand::getHelpString(){
try {
string helpString = "";
helpString += "The summary.seqs command reads a fastafile, summary, contigsreport or alignreport file and summarizes it.\n";
helpString += "The summary.seqs command parameters are fasta, name, count, summary, contigsreport, alignreport and processors, fasta, contigsreport, alignreport or summary is required, unless you have a valid current files.\n";
helpString += "The name parameter allows you to enter a name file associated with your fasta file. \n";
helpString += "The count parameter allows you to enter a count file associated with your fasta file. \n";
helpString += "The summary.seqs command should be in the following format: \n";
helpString += "summary.seqs(fasta=yourFastaFile, processors=2) \n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "SeqSummaryCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string SeqSummaryCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "summary") { pattern = "[filename],summary"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "SeqSummaryCommand", "getOutputPattern");
exit(1);
}
}
//***************************************************************************************************************
SeqSummaryCommand::SeqSummaryCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
fastafile = validParameter.validFile(parameters, "fasta");
if (fastafile == "not open") { abort = true; }
else if (fastafile == "not found") { fastafile = ""; }
else { current->setFastaFile(fastafile); }
summaryfile = validParameter.validFile(parameters, "summary");
if (summaryfile == "not open") { abort = true; }
else if (summaryfile == "not found") { summaryfile = ""; }
else { current->setSummaryFile(summaryfile); }
contigsfile = validParameter.validFile(parameters, "contigsreport");
if (contigsfile == "not open") { abort = true; }
else if (contigsfile == "not found") { contigsfile = ""; }
else { current->setContigsReportFile(contigsfile); }
alignfile = validParameter.validFile(parameters, "alignreport");
if (alignfile == "not open") { abort = true; }
else if (alignfile == "not found") { alignfile = ""; }
if ((summaryfile == "") && (fastafile == "") && (contigsfile == "") && (alignfile == "")) {
fastafile = current->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter.\n"); }
else {
summaryfile = current->getSummaryFile();
if (summaryfile != "") { m->mothurOut("Using " + summaryfile + " as input file for the summary parameter.\n"); }
else {
contigsfile = current->getContigsReportFile();
if (contigsfile != "") { m->mothurOut("Using " + contigsfile + " as input file for the contigsreport parameter.\n"); }
else { m->mothurOut("You have no current fasta, summary, contigsreport or alignreport file, one is required.\n"); abort = true; }
}
}
}
if (((fastafile != "") && ((summaryfile != "") || (contigsfile != "") || (alignfile != ""))) ||
((summaryfile != "") && ((fastafile != "") || (contigsfile != "") || (alignfile != ""))) ||
((contigsfile != "") && ((summaryfile != "") || (fastafile != "") || (alignfile != ""))) ||
((alignfile != "") && ((summaryfile != "") || (contigsfile != "") || (fastafile != "")))) {
m->mothurOut("[ERROR]: you may only use one of the following: fasta, summary, contigsreport or alignreport.\n"); abort = true;
}
namefile = validParameter.validFile(parameters, "name");
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { current->setNameFile(namefile); }
countfile = validParameter.validFile(parameters, "count");
if (countfile == "not open") { abort = true; countfile = ""; }
else if (countfile == "not found") { countfile = ""; }
else { current->setCountFile(countfile); }
if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name.\n"); abort = true; }
if (outputdir == ""){ outputdir += util.hasPath(fastafile); }
string temp = validParameter.valid(parameters, "processors"); if (temp == "not found"){ temp = current->getProcessors(); }
processors = current->setProcessors(temp);
}
}
catch(exception& e) {
m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
exit(1);
}
}
//***************************************************************************************************************
int SeqSummaryCommand::execute(){
try{
if (abort) { if (calledHelp) { return 0; } return 2; }
long start = time(nullptr);
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(fastafile));
string outputFile = getOutputFileName("summary",variables);
string nameOrCount = countfile;
if (namefile != "") { nameOrCount = namefile; }
Summary sum(processors);
if (fastafile != "") { sum.summarizeFasta(fastafile, nameOrCount, outputFile); }
else if (summaryfile != "") { sum.summarizeFastaSummary(summaryfile, nameOrCount); }
else if (contigsfile != "") { sum.summarizeContigsSummary(contigsfile, nameOrCount); }
else if (alignfile != "") { sum.summarizeAlignSummary(alignfile, nameOrCount); }
else { m->mothurOut("[ERROR]: Unknown type: you may only use one of the following: fasta, summary, contigsreport or alignreport.\n"); m->setControl_pressed(true); }
if (m->getControl_pressed()) { util.mothurRemove(outputFile); return 0; }
long long size = sum.getTotalSeqs();
long long numUniques = sum.getUniqueSeqs();
vector <long long> ptiles = sum.getDefaults();
if ((fastafile != "") || (summaryfile != "")) {
vector<long long> starts = sum.getStart();
vector<long long> ends = sum.getEnd();
vector<long long> ambigs = sum.getAmbig();
vector<long long> lengths = sum.getLength();
vector<long long> homops = sum.getHomop();
m->mothurOutEndLine();
m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs\n");
m->mothurOut("Minimum:\t" + toString(starts[0]) + "\t" + toString(ends[0]) + "\t" + toString(lengths[0]) + "\t" + toString(ambigs[0]) + "\t" + toString(homops[0]) + "\t" + toString(ptiles[0])); m->mothurOutEndLine();
m->mothurOut("2.5%-tile:\t" + toString(starts[1]) + "\t" + toString(ends[1]) + "\t" + toString(lengths[1]) + "\t" + toString(ambigs[1]) + "\t" + toString(homops[1]) + "\t" + toString(ptiles[1])); m->mothurOutEndLine();
m->mothurOut("25%-tile:\t" + toString(starts[2]) + "\t" + toString(ends[2]) + "\t" + toString(lengths[2]) + "\t" + toString(ambigs[2]) + "\t" + toString(homops[2]) + "\t" + toString(ptiles[2])); m->mothurOutEndLine();
m->mothurOut("Median: \t" + toString(starts[3]) + "\t" + toString(ends[3]) + "\t" + toString(lengths[3]) + "\t" + toString(ambigs[3]) + "\t" + toString(homops[3]) + "\t" + toString(ptiles[3])); m->mothurOutEndLine();
m->mothurOut("75%-tile:\t" + toString(starts[4]) + "\t" + toString(ends[4]) + "\t" + toString(lengths[4]) + "\t" + toString(ambigs[4]) + "\t" + toString(homops[4]) + "\t" + toString(ptiles[4])); m->mothurOutEndLine();
m->mothurOut("97.5%-tile:\t" + toString(starts[5]) + "\t" + toString(ends[5]) + "\t" + toString(lengths[5]) + "\t" + toString(ambigs[5]) + "\t" + toString(homops[5]) + "\t" + toString(ptiles[5])); m->mothurOutEndLine();
m->mothurOut("Maximum:\t" + toString(starts[6]) + "\t" + toString(ends[6]) + "\t" + toString(lengths[6]) + "\t" + toString(ambigs[6]) + "\t" + toString(homops[6]) + "\t" + toString(ptiles[6])); m->mothurOutEndLine();
m->mothurOut("Mean:\t" + toString(starts[7]) + "\t" + toString(ends[7]) + "\t" + toString(lengths[7]) + "\t" + toString(ambigs[7]) + "\t" + toString(homops[7])); m->mothurOutEndLine();
}else if (contigsfile != "") {
vector<long long> ostarts = sum.getOStart();
vector<long long> oends = sum.getOEnd();
vector<long long> length = sum.getLength();
vector<long long> olengths = sum.getOLength();
vector<long long> numns = sum.getNumNs();
vector<long long> mismatches = sum.getMisMatches();
m->mothurOutEndLine();
m->mothurOut("\t\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns\tNumSeqs\n");
m->mothurOut("Minimum:\t" + toString(length[0]) + "\t" + toString(olengths[0]) + "\t" + toString(ostarts[0]) + "\t" + toString(oends[0]) + "\t" + toString(mismatches[0]) + "\t" + toString(numns[0]) + "\t" + toString(ptiles[0])); m->mothurOutEndLine();
m->mothurOut("2.5%-tile:\t" + toString(length[1]) + "\t" + toString(olengths[1]) + "\t" + toString(ostarts[1]) + "\t" + toString(oends[1]) + "\t" + toString(mismatches[1]) + "\t" + toString(numns[1]) + "\t" + toString(ptiles[1])); m->mothurOutEndLine();
m->mothurOut("25%-tile:\t" + toString(length[2]) + "\t" + toString(olengths[2]) + "\t" + toString(ostarts[2]) + "\t" + toString(oends[2]) + "\t" + toString(mismatches[2]) + "\t" + toString(numns[2]) + "\t" + toString(ptiles[2])); m->mothurOutEndLine();
m->mothurOut("Median: \t" + toString(length[3]) + "\t" + toString(olengths[3]) + "\t" + toString(ostarts[3]) + "\t" + toString(oends[3]) + "\t" + toString(mismatches[3]) + "\t" + toString(numns[3]) + "\t" + toString(ptiles[3])); m->mothurOutEndLine();
m->mothurOut("75%-tile:\t" + toString(length[4]) + "\t" + toString(olengths[4]) + "\t" + toString(ostarts[4]) + "\t" + toString(oends[4]) + "\t" + toString(mismatches[4]) + "\t" + toString(numns[4]) + "\t" + toString(ptiles[4])); m->mothurOutEndLine();
m->mothurOut("97.5%-tile:\t" + toString(length[5]) + "\t" + toString(olengths[5]) + "\t" + toString(ostarts[5]) + "\t" + toString(oends[5]) + "\t" + toString(mismatches[5]) + "\t" + toString(numns[5]) + "\t" + toString(ptiles[5])); m->mothurOutEndLine();
m->mothurOut("Maximum:\t" + toString(length[6]) + "\t" + toString(olengths[6]) + "\t" + toString(ostarts[6]) + "\t" + toString(oends[6]) + "\t" + toString(mismatches[6]) + "\t" + toString(numns[6]) + "\t" + toString(ptiles[6])); m->mothurOutEndLine();
m->mothurOut("Mean:\t" + toString(length[7]) + "\t" + toString(olengths[7]) + "\t" + toString(ostarts[7]) + "\t" + toString(oends[7]) + "\t" + toString(mismatches[7]) + "\t" + toString(numns[7]) ); m->mothurOutEndLine();
}else if (alignfile != "") {
vector<long long> sims = sum.getSims();
vector<long long> scores = sum.getScores();
vector<long long> inserts = sum.getNumInserts();
vector<long long> length = sum.getLength();
m->mothurOutEndLine();
m->mothurOut("\t\tLength\tSimBtwnQueryTemplate\tLongestInsert\tSearchScore\tNumSeqs\n");
m->mothurOut("Minimum:\t" + toString(length[0]) + "\t" + toString(sims[0]) + "\t" + toString(inserts[0]) + "\t" + toString(scores[0]) + "\t" + toString(ptiles[0])); m->mothurOutEndLine();
m->mothurOut("2.5%-tile:\t" + toString(length[1]) + "\t" + toString(sims[1]) + "\t" + toString(inserts[1]) + "\t" + toString(scores[1]) + "\t" + toString(ptiles[1])); m->mothurOutEndLine();
m->mothurOut("25%-tile:\t" + toString(length[2]) + "\t" + toString(sims[2]) + "\t" + toString(inserts[2]) + "\t" + toString(scores[2]) + "\t" + toString(ptiles[2])); m->mothurOutEndLine();
m->mothurOut("Median: \t" + toString(length[3]) + "\t" + toString(sims[3]) + "\t" + toString(inserts[3]) + "\t" + toString(scores[3]) + "\t" + toString(ptiles[3])); m->mothurOutEndLine();
m->mothurOut("75%-tile:\t" + toString(length[4]) + "\t" + toString(sims[4]) + "\t" + toString(inserts[4]) + "\t" + toString(scores[4]) + "\t" + toString(ptiles[4])); m->mothurOutEndLine();
m->mothurOut("97.5%-tile:\t" + toString(length[5]) + "\t" + toString(sims[5]) + "\t" + toString(inserts[5]) + "\t" + toString(scores[5]) + "\t" + toString(ptiles[5])); m->mothurOutEndLine();
m->mothurOut("Maximum:\t" + toString(length[6]) + "\t" + toString(sims[6]) + "\t" + toString(inserts[6]) + "\t" + toString(scores[6]) + "\t" + toString(ptiles[6])); m->mothurOutEndLine();
m->mothurOut("Mean:\t" + toString(length[7]) + "\t" + toString(sims[7]) + "\t" + toString(inserts[7]) + "\t" + toString(scores[7])); m->mothurOutEndLine();
}
if (m->getControl_pressed()) { util.mothurRemove(outputFile); return 0; }
if ((namefile == "") && (countfile == "") && (summaryfile == "")) { m->mothurOut("# of Seqs:\t" + toString(numUniques)); m->mothurOutEndLine(); }
else { m->mothurOut("# of unique seqs:\t" + toString(numUniques)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(size)); m->mothurOutEndLine(); }
if (((namefile == "") && (countfile == "")) && (summaryfile == "")) { m->mothurOut("\nIt took " + toString(time(nullptr) - start) + " secs to summarize " + toString(numUniques) + " sequences.\n"); }
else{ m->mothurOut("\nIt took " + toString(time(nullptr) - start) + " secs to summarize " + toString(size) + " sequences.\n"); }
m->mothurOut("\nOutput File Names:\n");
if ((summaryfile == "") && (contigsfile == "") && (alignfile == "")) {
m->mothurOut(outputFile); m->mothurOutEndLine();
outputNames.push_back(outputFile); outputTypes["summary"].push_back(outputFile);
//set fasta file as new current fastafile
string currentName = "";
itTypes = outputTypes.find("summary");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setSummaryFile(currentName); }
}
}
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "SeqSummaryCommand", "execute");
exit(1);
}
}
//***************************************************************************************************************
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