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//
// summary.hpp
// Mothur
//
// Created by Sarah Westcott on 3/27/17.
// Copyright © 2017 Schloss Lab. All rights reserved.
//
#ifndef summary_hpp
#define summary_hpp
#include "mothurout.h"
#include "sequence.hpp"
#include "counttable.h"
class Summary {
public:
#ifdef UNIT_TEST
friend class TestSummary;
#endif
Summary(int p) { processors = p; m = MothurOut::getInstance(); total = 0; numUniques = 0; hasNameOrCount = false; nameCountNumUniques = 0; type = "count"; }
~Summary() = default;
long long summarizeFasta(string f, string n, string o); //provide fasta file to summarize (paralellized) and optional nameorCountfile and optional outputfile for individual seqs info. To skip nameCount or output file, n="" and / or o=""
long long summarizeFasta(string f, string o); //provide fasta file to summarize (paralellized) and optional outputfile for individual seqs info. To skip output file, o=""
long long summarizeFastaSummary(string f); //provide summary of fasta file to summarize (paralellized)
long long summarizeFastaSummary(string f, string n); //provide summary of fasta file and name or count file to summarize (paralellized)
long long summarizeContigsSummary(string f); //provide summary of contigs summary file to summarize (paralellized)
long long summarizeContigsSummary(string f, string n); //provide summary of contigs summary file and name or count file to summarize (paralellized)
long long summarizeAlignSummary(string f); //provide summary of contigs summary file to summarize (paralellized)
long long summarizeAlignSummary(string f, string n); //provide summary of contigs summary file and name or count file to summarize (paralellized)
vector<long long> getDefaults();
//fasta and summary
vector<long long> getStart() { return (getValues(startPosition)); } //returns vector of 8 locations. (min, 2.5, 25, 50, 75, 97.5, max, mean)
long long getStart(double value) { return (getValue(startPosition, value)); } //2.5 = 2.5% of sequences of sequences start before, 25 = location 25% of sequences start before
vector<long long> getEnd() { return (getValues(endPosition)); } //returns vector of 8 locations. (min, 2.5, 25, 50, 75, 97.5, max, mean)
long long getEnd(double value) { return (getValue(endPosition, value)); } //2.5 = 2.5% of sequences of sequences end after, 25 = location 25% of sequences end after
vector<long long> getAmbig() { return (getValues(ambigBases)); } //returns vector of 8 locations. (min, 2.5, 25, 50, 75, 97.5, max, mean)
long long getAmbig(double value) { return (getValue(ambigBases, value)); } //25 = max abigous bases 25% of sequences contain
vector<long long> getLength() { return (getValues(seqLength)); } //returns vector of 8 locations. (min, 2.5, 25, 50, 75, 97.5, max, mean)
long long getLength(double value) { return (getValue(seqLength, value)); } // 25 = min length of 25% of sequences
vector<long long> getHomop() { return (getValues(longHomoPolymer)); } //returns vector of 8 locations. (min, 2.5, 25, 50, 75, 97.5, max, mean)
long long getHomop(double value) { return (getValue(longHomoPolymer, value)); }
//contigs
vector<long long> getOStart() { return (getValues(ostartPosition)); } //contigs overlap start - returns vector of 8 locations. (min, 2.5, 25, 50, 75, 97.5, max, mean)
long long getOStart(double value) { return (getValue(ostartPosition, value)); } //contigs overlap start - 2.5 = 2.5% of sequences of sequences start before, 25 = location 25% of sequences start before
vector<long long> getOEnd() { return (getValues(oendPosition)); } //contigs overlap end -returns vector of 8 locations. (min, 2.5, 25, 50, 75, 97.5, max, mean)
long long getOEnd(double value) { return (getValue(oendPosition, value)); } //contigs overlap end -2.5 = 2.5% of sequences of sequences end after, 25 = location 25% of sequences end after
vector<long long> getOLength() { return (getValues(oseqLength)); } //contigs overlap length - returns vector of 8 locations. (min, 2.5, 25, 50, 75, 97.5, max, mean)
long long getOLength(double value) { return (getValue(oseqLength, value)); } //contigs overlap length - 25 = min length of 25% of sequences
vector<long long> getMisMatches() { return (getValues(misMatches)); } //returns vector of 8 locations. (min, 2.5, 25, 50, 75, 97.5, max, mean)
long long getMisMatches(double value) { return (getValue(misMatches, value)); }
vector<long long> getNumNs() { return (getValues(numNs)); } //returns vector of 8 locations. (min, 2.5, 25, 50, 75, 97.5, max, mean)
long long getNumNs(double value) { return (getValue(numNs, value)); } //25 = max abigous bases 25% of sequences contain
vector<long long> getSims() { return (getValues(sims)); } //contigs overlap length - returns vector of 8 locations. (min, 2.5, 25, 50, 75, 97.5, max, mean)
long long getSims(double value) { return (getValue(sims, value)); } //contigs overlap length - 25 = min length of 25% of sequences
vector<long long> getScores() { return (getValues(scores)); } //returns vector of 8 locations. (min, 2.5, 25, 50, 75, 97.5, max, mean)
long long getScores(double value) { return (getValue(scores, value)); }
vector<long long> getNumInserts() { return (getValues(inserts)); } //returns vector of 8 locations. (min, 2.5, 25, 50, 75, 97.5, max, mean)
long long getNumInserts(double value) { return (getValue(inserts, value)); } //25 = max abigous bases 25% of sequences contain
int getMaxAbundance();
long long getTotalSeqs() { return total; }
long long getUniqueSeqs() { return numUniques; }
private:
MothurOut* m;
Utils util;
int processors;
long long total, numUniques, nameCountNumUniques;
bool hasNameOrCount;
string type;
map<int, long long> startPosition;
map<int, long long> endPosition;
map<int, long long> seqLength;
map<int, long long> ambigBases;
map<int, long long> longHomoPolymer;
map<int, long long> ostartPosition;
map<int, long long> oendPosition;
map<int, long long> oseqLength;
map<int, long long> misMatches;
map<int, long long> numNs;
map<float, long long> sims;
map<float, long long> scores;
map<int, long long> inserts;
map<string, int> nameMap;
map<int, long long>::iterator it;
void processNameCount(string n); //determines whether name or count and fills nameMap, ignored if n = ""
vector<long long> getValues(map<int, long long>& positions);
long long getValue(map<int, long long>& positions, double);
vector<long long> getValues(map<float, long long>& positions);
long long getValue(map<float, long long>& positions, double);
bool isCountFile(string);
};
/**************************************************************************************************/
struct seqSumData {
map<int, long long> startPosition;
map<int, long long> endPosition;
map<int, long long> seqLength;
map<int, long long> ambigBases;
map<int, long long> longHomoPolymer;
map<int, long long> ostartPosition;
map<int, long long> oendPosition;
map<int, long long> oseqLength;
map<int, long long> misMatches;
map<int, long long> numNs;
map<float, long long> sims;
map<float, long long> scores;
map<int, long long> inserts;
string filename, summaryFile, contigsfile, output;
double start;
double end;
long long count;
long long total;
MothurOut* m;
bool hasNameMap;
map<string, int> nameMap;
Utils util;
seqSumData(){}
//FastaSummarize - output file created
seqSumData(string f, string sum, double st, double en, bool na, map<string, int> nam) {
filename = f;
m = MothurOut::getInstance();
start = st;
end = en;
hasNameMap = na;
nameMap = nam;
count = 0;
total = 0;
summaryFile = sum;
}
//FastaSummarySummarize - no output files
seqSumData(string f, double st, double en, bool na, map<string, int> nam) {
filename = f;
m = MothurOut::getInstance();
start = st;
end = en;
hasNameMap = na;
nameMap = nam;
count = 0;
total = 0;
}
};
/**************************************************************************************************/
#endif /* summary_hpp */
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