1 #ifndef SEQSUMMARYCOMMAND_H
2 #define SEQSUMMARYCOMMAND_H
8 * Created by Pat Schloss on 5/30/09.
9 * Copyright 2009 Patrick D. Schloss. All rights reserved.
14 #include "command.hpp"
15 #include "sequence.hpp"
17 /**************************************************************************************************/
19 class SeqSummaryCommand : public Command {
21 SeqSummaryCommand(string);
23 ~SeqSummaryCommand(){}
25 vector<string> setParameters();
26 string getCommandName() { return "summary.seqs"; }
27 string getCommandCategory() { return "Sequence Processing"; }
29 string getHelpString();
30 string getOutputPattern(string);
31 string getCitation() { return "http://www.mothur.org/wiki/Summary.seqs"; }
32 string getDescription() { return "summarize the quality of sequences in an unaligned or aligned fasta file"; }
35 void help() { m->mothurOut(getHelpString()); }
38 string fastafile, outputDir, namefile, countfile;
40 vector<string> outputNames;
41 map<string, int> nameMap;
44 unsigned long long start;
45 unsigned long long end;
46 linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
49 vector<linePair*> lines;
50 vector<int> processIDS;
52 int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string);
53 int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string, linePair*);
56 int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<unsigned long long>&);
62 /**************************************************************************************************/
63 //custom data structure for threads to use.
64 // This is passed by void pointer so it can be any data type
65 // that can be passed using a single void pointer (LPVOID).
67 vector<int> startPosition;
68 vector<int> endPosition;
69 vector<int> seqLength;
70 vector<int> ambigBases;
71 vector<int> longHomoPolymer;
74 unsigned long long start;
75 unsigned long long end;
79 map<string, int> nameMap;
83 seqSumData(string f, string sf, MothurOut* mout, unsigned long long st, unsigned long long en, bool na, map<string, int> nam) {
95 /**************************************************************************************************/
96 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
98 static DWORD WINAPI MySeqSumThreadFunction(LPVOID lpParam){
99 seqSumData* pDataArray;
100 pDataArray = (seqSumData*)lpParam;
104 pDataArray->m->openOutputFile(pDataArray->sumFile, outSummary);
107 pDataArray->m->openInputFile(pDataArray->filename, in);
109 //print header if you are process 0
110 if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
111 outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs" << endl;
113 }else { //this accounts for the difference in line endings.
114 in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
117 for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
121 if (pDataArray->m->control_pressed) { in.close(); outSummary.close(); pDataArray->count = 1; return 1; }
123 Sequence current(in); pDataArray->m->gobble(in);
125 if (current.getName() != "") {
128 if (pDataArray->hasNameMap){
129 //make sure this sequence is in the namefile, else error
130 map<string, int>::iterator it = pDataArray->nameMap.find(current.getName());
132 if (it == pDataArray->nameMap.end()) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " is not in your name or count file, please correct."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
133 else { num = it->second; }
136 //for each sequence this sequence represents
137 for (int i = 0; i < num; i++) {
138 pDataArray->startPosition.push_back(current.getStartPos());
139 pDataArray->endPosition.push_back(current.getEndPos());
140 pDataArray->seqLength.push_back(current.getNumBases());
141 pDataArray->ambigBases.push_back(current.getAmbigBases());
142 pDataArray->longHomoPolymer.push_back(current.getLongHomoPolymer());
145 outSummary << current.getName() << '\t';
146 outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
147 outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
148 outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
158 catch(exception& e) {
159 pDataArray->m->errorOut(e, "SeqSummaryCommand", "MySeqSumThreadFunction");
170 /**************************************************************************************************/