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Changeset 28:2a3fdec156e0 (2013-04-29)

Previous changeset 27:4e7ee5683ef1 (2013-04-29) Next changeset 29:c78966712a57 (2013-04-29)

Commit message:
Deleted selected files

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/.RData

Binary file SMART/Java/Python/.RData has changed

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/.Rhistory
--- a/SMART/Java/Python/.Rhistory Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-install.packages("ggplot2")

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/.gitignore
--- a/SMART/Java/Python/.gitignore Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-/CleanTranscriptFile.py

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/CompareOverlapping.pyc

Binary file SMART/Java/Python/CompareOverlapping.pyc has changed

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/CompareOverlappingSmallQuery.pyc

Binary file SMART/Java/Python/CompareOverlappingSmallQuery.pyc has changed

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/CompareOverlappingSmallRef.pyc

Binary file SMART/Java/Python/CompareOverlappingSmallRef.pyc has changed

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/Cpp/Makefile
--- a/SMART/Java/Python/Cpp/Makefile Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,18 +0,0 @@
-#------------------------------------------------------------------------------
-OBJS=inputFileParser.o ncListCreator.o findOverlaps.o
-PROGRAM=findOverlaps
-CC=g++
-CFLAGS = -Wall -g
-#------------------------------------------------------------------------------
-
-
-all: $(PROGRAM)
-
-$(PROGRAM): $(OBJS)
- $(CC) $(OBJS) -o $(PROGRAM)
-
-%.o: %.cpp
- $(CC) $(CFLAGS) -c $<
-
-clean:
- rm -rf $(OBJS) $(PROGRAM)

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/Cpp/findOverlaps.cpp
--- a/SMART/Java/Python/Cpp/findOverlaps.cpp Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,19 +0,0 @@
-#include <string>
-#include "inputFileParser.hpp"
-#include "ncListCreator.hpp"
-using namespace std;
-
-int main (int argc, char* argv[]) {
-    if (argc < 4) {
-        cout << "Usage: findOverlaps input1 output\n";
-        exit(0);
-    }
-    string inputFileName1 = string(argv[1]);
-    string inputFileName2 = string(argv[2]);
-    string outputFileName = string(argv[3]);
-    NCListCreator creator = NCListCreator(inputFileName1);
-//  InputFileParser ifp(inputFileName1, outputFileName);
-//  ifp.parse();
-    return 0;
-}
-

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/Cpp/genomicInterval.hpp
--- a/SMART/Java/Python/Cpp/genomicInterval.hpp Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,47 +0,0 @@
-#ifndef GENOMIC_INTERVAL_HPP
-#define GENOMIC_INTERVAL_HPP
-
-#include "interval.hpp"
-#include <stdio.h>
-#include <stdlib.h>
-#include <string>
-#include <sstream>
-
-class GenomicInterval: public Interval {
-
-    public:
-        string chromosome;
-
-        GenomicInterval(string chromosome = "", unsigned int start = 0, unsigned int end = 0): Interval(start, end), chromosome(chromosome) { }
-
-        bool onSameChromosome(const GenomicInterval &i) const {
-            return (chromosome == i.chromosome);
-        }
-
-//      friend bool operator==(const GenomicInterval &i1, const GenomicInterval &i2) {
-//          return ((i1.onSameChromosome(i2)) && (Interval::i1 == Interval::i2));
-//      }
-
-//      friend bool operator<(const GenomicInterval &i1, const GenomicInterval &i2) {
-//          return ((i1.onSameChromosome(i2)) && (Interval::i1 < Interval::i2));
-//      }
-
-        friend ofstream& operator<<(ofstream &stream, const GenomicInterval &i) {
-            stream << i.chromosome << '\t' << i.start << '\t' << i.end << '\n';
-            return stream;
-        }
-
-        void parseFromLine(string &line) {
-            string strStart, strEnd;
-            istringstream iss(line);
-            getline(iss, chromosome, '\t');
-            getline(iss, strStart,   '\t');
-            getline(iss, strEnd,     '\t');
-            start = atoi(strStart.c_str());
-            end   = atoi(strEnd.c_str());
-            //cout << "read " << chromosome << ":" << start << ".." << end << endl;
-        }
-
-};
-
-#endif

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/Cpp/inputFileParser.cpp
--- a/SMART/Java/Python/Cpp/inputFileParser.cpp Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,134 +0,0 @@
-#include <algorithm>
-#include <set>
-#include <vector>
-#include <sstream>
-#include "inputFileParser.hpp"
-
-static const unsigned int MAX_SIZE = 10000;
-
-InputFileParser::InputFileParser(string inputFileName, string outputFileName): inputFileName(inputFileName), outputFileName(outputFileName) {
-    outputFilePrefix = outputFileName.substr(0, outputFileName.find_last_of('.'));
-}
-
-
-void InputFileParser::parse() {
-    ifstream file;
-    string line;
-    file.open(inputFileName.c_str());
-    if (file.is_open()) {
-        GenomicInterval genomicInterval;
-        while (file.good()) {
-            getline(file, line);
-            if (line.size() > 0) {
-                genomicInterval.parseFromLine(line);
-                addToList(genomicInterval);
-            }
-        }
-        syncFiles();
-        file.close();
-    }
-    else {
-        cout << "Unable to open file" << inputFileName;
-    }
-    merge();
-}
-
-
-void InputFileParser::addToList(GenomicInterval &genomicInterval) {
-    Interval interval (genomicInterval);
-    IntervalsType *intervals;
-    SortedIntervalsTypes::iterator iter = sortedIntervals.find(genomicInterval.chromosome);
-    if (iter == sortedIntervals.end()) {
-        intervals = new IntervalsType;
-        sortedIntervals[genomicInterval.chromosome] = intervals;
-    }
-    else {
-        intervals = iter->second;
-    }
-    //cout << "pushing " << interval.start << "-" << interval.end << endl;
-    intervals->push_back(&interval);
-    if (intervals->size() >= MAX_SIZE) {
-        writeTmpFile(genomicInterval.chromosome);
-    }
-}
-
-
-void InputFileParser::writeTmpFile(string &chromosome) {
-    SortedIntervalsTypes::iterator iter = sortedIntervals.find(chromosome);
-    IntervalsType *intervals = iter->second;
-
-    sort(intervals->begin(), intervals->end());
-    string fileName = getTmpName(chromosome);
-    ofstream file(fileName.c_str(), ios::out | ios::binary);
-    for (unsigned i = 0; i < intervals->size(); i++) {
-        cout << "writing " << (*intervals)[i]->start << "-" << (*intervals)[i]->end << endl;
-        (*intervals)[i]->writeBinary(file);
-    }
-    file.close();
-    ++counter[chromosome];
-
-    sortedIntervals[chromosome] = NULL;
-    delete intervals;
-}
-
-
-void InputFileParser::syncFiles() {
-    for (SortedIntervalsTypes::iterator iter = sortedIntervals.begin(); iter != sortedIntervals.end(); iter++) {
-        string chromosome = iter->first;
-        writeTmpFile(chromosome);
-    }
-}
-
-
-string InputFileParser::getTmpName(const string &chromosome, unsigned int i) {
-    stringstream s;
-    s << outputFilePrefix << outputFilePrefix << "_tmp_" << chromosome << "_" << i << ".tmp";
-    return s.str();
-}
-
-
-string InputFileParser::getTmpName(const string &chromosome) {
-    return getTmpName(chromosome, counter[chromosome]);
-}
-
-
-void InputFileParser::merge() {
-    ofstream outputFile(outputFileName.c_str());
-    for (SortedIntervalsTypes::iterator iter = sortedIntervals.begin(); iter != sortedIntervals.end(); iter++) {
-        merge(iter->first, outputFile);
-    }
-}
-
-
-void InputFileParser::merge(const string &chromosome, ofstream &outputFile) {
-    ifstream *files = new ifstream[counter[chromosome]];
-    set<NumberIntervalType *> intervals;
-    for (unsigned int i = 0; i < counter[chromosome]; i++) {
-        string fileName = getTmpName(chromosome, i);
-        files[i].open(fileName.c_str());
-    }
-    for (unsigned int i = 0; i < counter[chromosome]; i++) {
-        if (files[i].good()) {
-            Interval interval;
-            interval.parseBinary(files[i]);
-            NumberIntervalType ni = NumberIntervalType(&interval, i);
-            intervals.insert(&ni);
-        }
-    }
-    while (! intervals.empty()) {
-        NumberIntervalType *ni = *intervals.begin();
-        GenomicInterval gi(chromosome, ni->first->start, ni->first->end);
-        outputFile << gi;
-        intervals.erase(intervals.begin());
-        if (files[ni->second].good()) {
-            Interval interval;
-            interval.parseBinary(files[ni->second]);
-            NumberIntervalType nni = NumberIntervalType(&interval, ni->second);
-            intervals.insert(&nni);
-        }
-    }
-    for (unsigned int i = 0; i < counter[chromosome]; i++) {
-        files[i].close();
-    }
-    delete[] files;
-}

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/Cpp/inputFileParser.hpp
--- a/SMART/Java/Python/Cpp/inputFileParser.hpp Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,45 +0,0 @@
-#ifndef INPUT_FILE_PARSER_HPP
-#define INPUT_FILE_PARSER_HPP
-
-#include <string>
-#include <vector>
-#include <map>
-#include "genomicInterval.hpp"
-
-typedef vector<Interval *> IntervalsType;
-typedef map<string, IntervalsType *> SortedIntervalsTypes;
-typedef map<string, unsigned int> CounterType;
-typedef pair<Interval *, unsigned int> NumberIntervalType;
-
-static bool operator<(const NumberIntervalType &i1, const NumberIntervalType &i2) {
-    if (i1.first < i2.first) return true;
-    return ((i1.first == i2.first) && (i1.second < i2.second));
-}
-
-class InputFileParser {
-
-    private:
-        SortedIntervalsTypes sortedIntervals;
-        CounterType counter;
-
-        void addToList(GenomicInterval &genomicInterval);
-        void writeTmpFile(string &chromosome);
-        void syncFiles();
-        string getTmpName(const string &chromosome, unsigned int i);
-        string getTmpName(const string &chromosome);
-        void merge();
-        void merge(const string &chromosome, ofstream &outputFile);
-
-    public:
-        string inputFileName;
-        string outputFileName;
-        string outputFilePrefix;
-
-        InputFileParser(string inputFileName, string outputFileName);
-
-        void parse();
-
-};
-
-#endif
-

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/Cpp/inputFileParser.o

Binary file SMART/Java/Python/Cpp/inputFileParser.o has changed

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/Cpp/interval.hpp
--- a/SMART/Java/Python/Cpp/interval.hpp Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,45 +0,0 @@
-#ifndef INTERVAL_HPP
-#define INTERVAL_HPP
-#include <iostream>
-#include <fstream>
-using namespace std;
-
-typedef unsigned int Position;
-
-class Interval {
-
-    public:
-        Position start;
-        Position end;
-
-        Interval(unsigned int start = 0, unsigned int end = 0): start(start), end(end) { }
-
-        Interval(Interval &i): start(i.start), end(i.end) { }
-
-        bool include(Interval &interval) {
-            return ((start <= interval.start) && (end >= interval.end));
-        }
-
-        void writeBinary(ofstream &stream) {
-            stream.write(reinterpret_cast<const char*>(&start), sizeof(Position));
-            stream.write(reinterpret_cast<const char*>(&end),   sizeof(Position));
-        }
-
-        bool parseBinary(ifstream &stream) {
-            stream.read(reinterpret_cast<char*>(&start), sizeof(Position));
-            stream.read(reinterpret_cast<char*>(&end),   sizeof(Position));
-            return (! stream.eof());
-        }
-
-        friend bool operator==(const Interval &i1, const Interval &i2) {
-            return ((i1.start == i2.start) && (i1.start == i2.end));
-        }
-
-        friend bool operator<(const Interval &i1, const Interval &i2) {
-            if (i1.start < i2.start) return true;
-            return ((i1.start == i2.start) && (i1.end > i2.end));
-        }
-
-};
-
-#endif

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/Cpp/ncList.hpp
--- a/SMART/Java/Python/Cpp/ncList.hpp Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,20 +0,0 @@
-#ifndef NC_LIST_HPP
-#define NC_LIST_HPP
-
-#include "table.hpp"
-
-class NCList {
-
-    private:
-        Table *h, *l;
-
-
-    public:
-
-        NCList (Table *h, Table *l): h(h), l(l) {}
-
-
-};
-
-#endif
-

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/Cpp/ncListCreator.cpp
--- a/SMART/Java/Python/Cpp/ncListCreator.cpp Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,179 +0,0 @@
-#include "ncListCreator.hpp"
-
-NCListCreator::NCListCreator(string inputFileName): inputFileName(inputFileName) {}
-
-string NCListCreator::getFileName(string chromosome) {
-    return inputFileName.substr(0, inputFileName.find_last_of('.')) + "_" + chromosome + ".bed";
-}
-
-void NCListCreator::splitFile () {
-    Chromosomes chromosomes;
-    GenomicInterval interval;
-    map <string, ofstream> splittedFiles;
-    map <string, ofstream>::iterator it;
-    ifstream file;
-    string line, fileName;
-    string chromosome;
-    file.open(inputFileName.c_str());
-    if (file.is_open()) {
-        while (file.good()) {
-            getline(file, line);
-            if (line.size() > 0) {
-                interval.parseFromLine(line);
-                chromosomes.insert(interval.chromosome);
-                fileName = getFileName(interval.chromosome);
-                it = splittedFiles.find(interval.chromosome);
-                if (it == splittedFiles.end()) {
-                    ofstream outputFile;
-                    outputFile.open(fileName.c_str(), ios::out | ios::binary);
-                    interval.writeBinary(outputFile);
-                    splittedFiles[chromosome] = outputFile;
-                }
-                else {
-                    it->second << line << "\n";
-                }
-            }
-        }
-        file.close();
-        for (it = splittedFiles.begin(); it != splittedFiles.end(); it++) {
-            it->second.close();
-        }
-    }
-    else {
-        cout << "Unable to open file" << inputFileName;
-    }
-}
-
-void NCListCreator::run() {
-    for (Chromosomes::iterator it = chromosomes.begin(); splittedFiles != chromosomes.end(); splittedFiles++) {
-        buildLists(*it);
-    }
-}
-
-void NCListCreator::buildLists(string chromosome) {
-    createTables(chromosome);
-    labelLists();
-    computeSubStart();
-    computeAbsPosition();
-    cleanFiles();
-    transfer(chromosome);
-}
-
-void NCListCreator::createTables(string chromosome) {
-    initLists(chromosome);
-    h = new Table(H_CELL_SIZE, nbLists);
-    t = new Table(T_CELL_SIZE, nbLines);
-    l = new Table(L_CELL_SIZE, nbLines);
-    fillTables(chromosome);
-}
-
-void NCListCreator::initLists (string chromosome) {
-    nbLists = 0;
-    nbLines = 0;
-    ifstream file;
-    file.open(getFileName(chromosome).c_str(), ios::in | ios::binary);
-    Interval currentInterval, previousInterval;
-    if (file.is_open()) {
-        while (file.good()) {
-            if (currentInterval.parseBinary(file)) {
-                nbLines++;
-                if (previousInterval.include(currentInterval)) {
-                    nbLists++;
-                }
-            }
-            previousInterval = currentInterval;
-        }
-    }
-    file.close();
-}
-
-void NCListCreator::fillTables (string chromosome) {
-    ifstream file;
-    file.open(getFileName(chromosome).c_str(), ios::in | ios::binary);
-    Interval currentInterval, previousInterval;
-    unsigned int i = 0;
-    if (file.is_open()) {
-        while (file.good()) {
-            if (currentInterval.parseBinary(file)) {
-                t->write(currentInterval.start, i, 0);
-                t->writeHere(currentInterval.end);
-                t->writeHere(-1);
-                t->writeHere(-1);
-            }
-            i++;
-        }
-        file.close();
-    }
-    t->write(SENTINEL, LIST, -1);
-    l->write(SENTINEL, LIST,  0);
-    t->write(SENTINEL, NEW,  -1);
-}
-
-void NCListCreator::labelLists () {
-    unsigned int nextL = 0, thisL, length;
-    unsigned int p;
-    Interval current, parent;
-    for (unsigned int i = 0; i < nbLines; i++) {
-        p = i - 1;
-        t->moveTo(p, 0);
-        parent.readBinary(t->file);
-        t->moveTo(i, 0);
-        current.readBinary(t->file);
-        while ((p != SENTINEL) && (! parent.include(current))) {
-            p = t->read(p, PARENT);
-            t->moveTo(p, 0);
-            parent.readBinary(t->file);
-        }
-        thisL = t->read(p, LIST);
-        if (thisL == SENTINEL) {
-            thisL = nextL;
-            nextL++;
-            length = 0;
-            t->write(p, LIST, thisL);
-        }
-        else {
-            length = h->read(thisL, LENGTH);
-        }
-        t->write(i, PARENT, p);
-        h->write(thisL, LENGTH, length+1);
-    }
-}
-
-void NCListCreator::computeSubStart () {
-    unsigned int total = 0;
-    for (unsigned int i = 0; i < nbLists; i++) {
-        h->write(i, START, total);
-        total += h->read(i, LENGTH);
-        h->write(i, LENGTH, 0);
-    }
-}
-
-void NCListCreator::computeAbsPosition () {
-    Value s, e, pt, hp, pl, nb, lp;
-    for (unsigned int i = 0; i < nbLines; i++) {
-        s = t->read(i,   START);
-        e  = t->read(i,  END);
-        pt = t->read(i,  PARENT);
-        hp = t->read(pt, LIST);
-        pl = t->read(pt, NEW);
-        nb = h->read(hp, LENGTH);
-        lp = h->read(hp, START) + nb;
-        t->write(i,  NEW,    lp);
-        l->write(lp, START,  s);
-        l->write(lp, END,    e);
-        l->write(lp, LIST,   SENTINEL);
-        l->write(lp, PARENT, pl);
-        h->write(lp, LENGTH, nb+1);
-        if (nb == 0) {
-            l->write(pl, LIST, hp);
-        }
-    }
-}
-
-void NCListCreator::cleanFiles () {
-    t->destroy();
-}
-
-void NCListCreator::transfer (string chromosome) {
-    ncLists[chromosome] = NCList(h, l);
-}

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/Cpp/ncListCreator.hpp
--- a/SMART/Java/Python/Cpp/ncListCreator.hpp Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,57 +0,0 @@
-#ifndef NC_LIST_CREATOR_HPP
-#define NC_LIST_CREATOR_HPP
-
-#include "ncList.hpp"
-#include "table.hpp"
-#include "genomicInterval.hpp"
-#include <set>
-#include <map>
-
-typedef set<string> Chromosomes;
-typedef map<string, NCList *> NCLists;
-
-static const unsigned int H_CELL_SIZE = 2;
-static const unsigned int L_CELL_SIZE = 4;
-static const unsigned int T_CELL_SIZE = 5;
-
-static const unsigned int START   = 0;
-static const unsigned int END     = 1;
-static const unsigned int LIST    = 2;
-static const unsigned int PARENT  = 3;
-static const unsigned int NEW     = 4;
-static const unsigned int LENGTH  = 1;
-
-
-class NCListCreator {
-
-    private:
-        string inputFileName;
-        Table  *h, *l, *t;
-
-        string getFileName(string chromosome);
-        void buildLists(string chromosome);
-        void createTables(string chromosome);
-        void initLists(string chromosome);
-        void fillTables(string chromosome);
-        void labelLists();
-        void computeSubStart();
-        void computeAbsPosition();
-        void cleanFiles();
-        void transfer(string chromosome);
-        unsigned int nbLists, nbLines;
-
-
-    public:
-        Chromosomes chromosomes;
-        NCLists ncLists;
-
-        NCListCreator (string inputFileName);
-
-        void splitFile ();
-        void run ();
-
-};
-
-#endif
-
-

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/Cpp/table.hpp
--- a/SMART/Java/Python/Cpp/table.hpp Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,84 +0,0 @@
-#ifndef TABLE_HPP
-#define TABLE_HPP
-
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <stdio.h>
-using namespace std;
-
-typedef unsigned int Value;
-static const unsigned int SENTINEL = -1;
-
-class Table {
-    private:
-        int sentinel;
-        Value *values;
-
-    public:
-        string fileName;
-        unsigned int width;
-        unsigned int height;
-        fstream file;
-
-        Table (string fileName, unsigned int width, unsigned int height): sentinel(-1), fileName(fileName), width(width), height(height) {
-            file.open(fileName.c_str(), ios::out | ios::in | ios::binary);
-            Value v = 0;
-            for (unsigned int i = 0; i < width * height; i++) {
-                writeHere(v);
-            }
-            file.flush();
-            values = new Value[width];
-        }
-
-        ~Table () {
-            delete[] values;
-        }
-
-        void moveTo (unsigned int col, unsigned int line) {
-            if (col == SENTINEL) {
-                sentinel = line;
-            }
-            else {
-                sentinel = -1;
-                file.seekp((col * width + line) * sizeof(Value));
-            }
-        }
-
-        void write (Value v, unsigned int col, unsigned int line) {
-            moveTo(col, line);
-            writeHere(v);
-        }
-
-        void writeHere(Value v) {
-            if (sentinel >= 0)
-                values[sentinel] = v;
-            else
-                file.write(reinterpret_cast<const char*>(&v), sizeof(Value));
-        }
-
-
-        Value read (unsigned int col, unsigned int line) {
-            moveTo(col, line);
-            return readHere();
-        }
-
-        Value readHere () {
-            if (sentinel >= 0) {
-                return values[sentinel];
-            }
-            else {
-                Value v;
-                file.read(reinterpret_cast<char*>(&v), sizeof(Value));
-                return v;
-            }
-        }
-
-        void destroy () {
-            file.close();
-            remove(fileName.c_str());
-        }
-
-};
-
-#endif

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/Cpp/testIn.bed
--- a/SMART/Java/Python/Cpp/testIn.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,25 +0,0 @@
-arm_2R 15844993 15845110
-arm_2R 15845130 15845145
-arm_2R 15845456 15845471
-arm_2R 15845688 15845696
-arm_2R 15846253 15846278
-arm_2R 15847272 15847281
-arm_2R 15847296 15847324
-arm_2R 15847709 15847717
-arm_2R 15848021 15848030
-arm_2R 15848720 15848728
-arm_2R 15848918 15848963
-arm_2R 15849011 15849050
-arm_2R 15849065 15849104
-arm_2R 15849151 15849164
-arm_2R 15849748 15849756
-arm_2R 15849785 15849827
-arm_2R 15849861 15849978
-arm_2R 15849998 15850013
-arm_2R 15850181 15850209
-arm_2R 15850295 15850322
-arm_2R 15850357 15850376
-arm_2R 15850673 15850690
-arm_2R 15850717 15850760
-arm_2R 15850788 15850816
-arm_2R 15850961 15850974

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/Cpp/testOut.bed
--- a/SMART/Java/Python/Cpp/testOut.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,26 +0,0 @@
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 15850961 15850974
-arm_2R 0 0

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/GetUpDownStream.pyc

Binary file SMART/Java/Python/GetUpDownStream.pyc has changed

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/SR1.fastq
--- a/SMART/Java/Python/TestFiles/SR1.fastq Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,5000 +0,0 @@\n-@HWI-EAS337_3:7:1:415:1217/1\n-GATGTGCAGACTTTTCACGCAGGACTACATCACTGT\n-+HWI-EAS337_3:7:1:415:1217/1\n-WWWVVVWPWWWVWWWWVVVVKVPWWVVWVWUUQUTQ\n-@HWI-EAS337_3:7:1:208:1489/1\n-GGAAACATATGCACATAAACGTTGAAATCATGCTTA\n-+HWI-EAS337_3:7:1:208:1489/1\n-WWWWWWWWWWWWWWWWWVWWVWWVWWWWWWUUUUUU\n-@HWI-EAS337_3:7:1:278:1153/1\n-GAGAAAACCTGTAATAAATACTGAGAGAAAGTAGGG\n-+HWI-EAS337_3:7:1:278:1153/1\n-WWWWWWWWWWWWWWWWWWWWWWVWVVVWWVUUUUUR\n-@HWI-EAS337_3:7:1:1178:755/1\n-GGTGAGAGTGGTTGGTTGATGGTAAAACCATTGAAT\n-+HWI-EAS337_3:7:1:1178:755/1\n-WWWWWWWWWVWWWVVWWVVWVVVVWVWVVVUUUUUU\n-@HWI-EAS337_3:7:1:277:1259/1\n-GGGTGACAAAGAAAACAAAAGGGACATGGTACTTGG\n-+HWI-EAS337_3:7:1:277:1259/1\n-WWWWWWWWWWWWWWWWWWWWWWVWWWWWWVUUUUUU\n-@HWI-EAS337_3:7:1:447:1231/1\n-GACTTGTGGAAGAGTTGGAATGGAAAGCTGGAGCCT\n-+HWI-EAS337_3:7:1:447:1231/1\n-WWWWWWWWWWWVWVWWWVWWWVVVVVVVVVURUSUU\n-@HWI-EAS337_3:7:1:300:1199/1\n-GTTTTTGCATATAGATCTCTTTGTAAAGATATCCAT\n-+HWI-EAS337_3:7:1:300:1199/1\n-WVWWWWWWWWWWWVWWWWWWWWQWVVVTWWUUUURU\n-@HWI-EAS337_3:7:1:247:1210/1\n-GATAGCTTTGACTATAGGACTTTTATGTATGTGTTG\n-+HWI-EAS337_3:7:1:247:1210/1\n-WWWWWWWWWWWWVWWWVVWWWWWWWWTVVWRULUUR\n-@HWI-EAS337_3:7:1:1154:1517/1\n-GAATGTTGCAGACCTTACTCCTACCTATGAAGCACA\n-+HWI-EAS337_3:7:1:1154:1517/1\n-WWWWWWWVWWVWWWWWWWWWWWWWVWVWVWUSUUUU\n-@HWI-EAS337_3:7:1:164:1869/1\n-GTTTGATAGGAATTTATTTCTTCTTCGACATCCACC\n-+HWI-EAS337_3:7:1:164:1869/1\n-WWWWWWWWVVWWWWWWWWWWWWWWWWQWWWUUUUUU\n-@HWI-EAS337_3:7:1:415:1194/1\n-GATGGTTGACACATTAAGAACATTCTCACCGGTCTC\n-+HWI-EAS337_3:7:1:415:1194/1\n-WWWWWWWWWWWWWWWWWVWVWVWWWWWWWVSUUUUU\n-@HWI-EAS337_3:7:1:645:1892/1\n-GATAGTAAGCACCCCTCACTTCCAACCCAAAGATTG\n-+HWI-EAS337_3:7:1:645:1892/1\n-WWWWWWWWWWWWWWWWWVWWWWWVVWVWWVUUUUUU\n-@HWI-EAS337_3:7:1:33:1446/1\n-GTTATTCTTTCTTTCTCAAATGGATGCAGTAATGCA\n-+HWI-EAS337_3:7:1:33:1446/1\n-WWWWWWWWWWWWWWWWWWWWWUQWWVVWQWUUUSUU\n-@HWI-EAS337_3:7:1:1194:1427/1\n-GAAAAATCACATTTTTTTGTTTGATAAAAACCCAGA\n-+HWI-EAS337_3:7:1:1194:1427/1\n-WWWWWWWWVWVWWWWWWWVWWWUWWWWWWWUUUUSU\n-@HWI-EAS337_3:7:1:624:1913/1\n-GACATCTTCAACTCCGGAGTTTTGAGTAACATTATA\n-+HWI-EAS337_3:7:1:624:1913/1\n-WWWWWWWWWWVWWWWVVVVWWWWVVVWWVWUUUUUU\n-@HWI-EAS337_3:7:1:437:1202/1\n-GTACTTATGATGAAACTGAGATCAACTACCACCTCC\n-+HWI-EAS337_3:7:1:437:1202/1\n-WWWWWVWWWVWVWWWWWWWWVWWWWVWVVVUUUUUU\n-@HWI-EAS337_3:7:1:1386:1787/1\n-GTTTAGCTAGTATTAAGGCTAGAAATGGATATGATG\n-+HWI-EAS337_3:7:1:1386:1787/1\n-WWWWWWWWWWWWWWWWVVWWWVWVVWVVVWUUSUUO\n-@HWI-EAS337_3:7:1:227:1155/1\n-GATAGCAGCAAGGTTATTGGAATCTAAGCAATCTAC\n-+HWI-EAS337_3:7:1:227:1155/1\n-WWVWWVWWVVWVVIWVWVVUWVVVVWVTVVUUUUSU\n-@HWI-EAS337_3:7:1:472:1025/1\n-GAAGTGATACTCATAAAACTATTTAGAAAGTTAATT\n-+HWI-EAS337_3:7:1:472:1025/1\n-WWWWWWWWWWWWWWWVWVWWWWWWVVWWWVUUUUUU\n-@HWI-EAS337_3:7:1:220:1482/1\n-GCTATATGAGAATTCAGGCCACTTGTAGTTCGATAA\n-+HWI-EAS337_3:7:1:220:1482/1\n-WWWWWWWWWVWWWWWWWVWWWWWWWWVVWWURUUUU\n-@HWI-EAS337_3:7:1:1699:1966/1\n-GATGAAGGATACTACAAAAAAAAGGGTTATTTTGTG\n-+HWI-EAS337_3:7:1:1699:1966/1\n-WWWWWWWWWWWWWWWWVWVWWWWWWWVWWWUUUSUR\n-@HWI-EAS337_3:7:1:547:1084/1\n-GTGGTCAGGTCCTCTTCAAGTGATACAATGTTCCCC\n-+HWI-EAS337_3:7:1:547:1084/1\n-WWWWWWWWWWWWWWWWWWVVWVWWWWWWWVUUUUSU\n-@HWI-EAS337_3:7:1:464:1097/1\n-GAAATTGAAGCTAGTTATTGACAGTTTACCAAGTTA\n-+HWI-EAS337_3:7:1:464:1097/1\n-WWWWWWWWWWWVWWVWWWWWWWWVVWWWWVUUUUUR\n-@HWI-EAS337_3:7:1:171:1480/1\n-GATAATACTATTAGCACATCAGCCTCTAGATGAGAC\n-+HWI-EAS337_3:7:1:171:1480/1\n-WWWWWWWWWWWWWVWWWWWWWVWWWWWWTVUUUUUU\n-@HWI-EAS337_3:7:1:293:1251/1\n-GTGGTAGTGAGCTCCGTGGTGAACAAGATGACGGAA\n-+HWI-EAS337_3:7:1:293:1251/1\n-WWWWWWWVWVWWWWVVWWVVVVVVWVVVVVRPUURR\n-@HWI-EAS337_3:7:1:647:1863/1\n-GGGTTTCAGATTAGTAAGTTATAGTGAAAAAATATA\n-+HWI-EAS337_3:7:1:647:1863/1\n-WWVWWWWWVWWWWVWWVVWWWWWWWVWVVWUUUUUU\n-@HWI-EAS337_3:7:1:263:1275/1\n-GCTACGTCTGCTCTAACTCCTAATATGATCCTGTAT\n-+HWI-EAS337_3:7:1:263:1275/1\n-WWWWWWWWWWWWWWWWWWWWWVWWWWQVWWUUOUUU\n-@HWI-EAS337_3:7:1:1112:215/1\n-GGTGTTGATTTCACAAGGAGGAATACTCATCTAAAA\n-+HWI-EAS337_3:7:1:1112:215/1\n-WWVWWVVWVVWWWVWWVUWVVVWWWVWTVWUUUUUU\n-@HWI-EAS337_3:7:1:319:1275/1\n-GTTATAGTTCTTGACAACAAAGTACAGAGGTGGTCC\n-+HWI-EAS337_3:7:1:319:1275/1\n-WWWWWWWWWWWWVWWWWWWWWWWWWWVWVWUUSUUU\n-@HWI-EAS337_3:7:1:1310:1480/1'..b'A\n-+HWI-EAS337_3:7:1:986:591/1\n-WWWWWWWWWVWWWWWWWWWWWWWVWVVWVVUUUUUR\n-@HWI-EAS337_3:7:1:181:1099/1\n-GGTCGACGTAAGAGATCTGCAGGGCTATTACTCATT\n-+HWI-EAS337_3:7:1:181:1099/1\n-WWWWWWWWWWWWWVWWWWWWWVVWWWVWWVUUUUUU\n-@HWI-EAS337_3:7:1:509:832/1\n-GTGAAGTATGGGTGGAAATGCTTGCGTATGCTGCTA\n-+HWI-EAS337_3:7:1:509:832/1\n-WWWWVWWWWVVWWWWWWVWVWWWVVVVVWVSUUUUR\n-@HWI-EAS337_3:7:1:510:597/1\n-GGGTCTGGAATAGTAATGCGCTGATTCTAGTAAAGT\n-+HWI-EAS337_3:7:1:510:597/1\n-VWWWVWWWWWWWWWWWWVWWWWWVWWWWVVUUUUUU\n-@HWI-EAS337_3:7:1:1765:1489/1\n-GTCAATTTTTTCTTTGTTTAAATCCGGGGAGGCTAG\n-+HWI-EAS337_3:7:1:1765:1489/1\n-WVWWVWWWWWWWWWWVWWWWWWWWWQQVTVUSUUUR\n-@HWI-EAS337_3:7:1:417:1560/1\n-GTAACCTTCCCAGTGTCTCCTTAAGAAAGACTTGGA\n-+HWI-EAS337_3:7:1:417:1560/1\n-WWWWVWWSWSVWVVVVWWWWWWWWVSWWWWUQUUQU\n-@HWI-EAS337_3:7:1:1047:854/1\n-GTTGAAATTCCTGATTTTCCATGTGCATCATAAGCC\n-+HWI-EAS337_3:7:1:1047:854/1\n-WWWWWVWWWWWWWWUWWWWWVWVWVVVWVVUUUUUU\n-@HWI-EAS337_3:7:1:1296:202/1\n-GGTGTTGGAGTTGGATTTGTTTCTGCTTTGATATCC\n-+HWI-EAS337_3:7:1:1296:202/1\n-WWWWWWWVWVWWWVVWWWWWWWWWVVWWWTUUUUUF\n-@HWI-EAS337_3:7:1:502:642/1\n-GATGATTCTTGCTGGTTAAGTTGAGATGGGTTATAA\n-+HWI-EAS337_3:7:1:502:642/1\n-WWWWWVPVVVWWWVVVWWWVWWSVVVWVVVUUUUUR\n-@HWI-EAS337_3:7:1:82:1651/1\n-GGCATCCTGTTCATCCTTCTCTTCATTTTTAGGCGT\n-+HWI-EAS337_3:7:1:82:1651/1\n-WWWWWWWWVWWWWWWWWVWWWWWWVWWWWWUKJUQU\n-@HWI-EAS337_3:7:1:1505:1274/1\n-GAAACTTTTCAAAAAAAAAGTTGCATGAGAAATAAG\n-+HWI-EAS337_3:7:1:1505:1274/1\n-WWWWWWWWWWWWVWWWWWWWVWWWWWWVWWSUUUUR\n-@HWI-EAS337_3:7:1:5:1770/1\n-GTGTGAAAAAGTATTTCATTCACATATTGAGTTGTT\n-+HWI-EAS337_3:7:1:5:1770/1\n-WWWWWWWWWWVWWWWWWWWWWWWWWWWWVVSUUQUU\n-@HWI-EAS337_3:7:1:115:1005/1\n-GATTTTACTGGAATGGGGAAGGGTGAGGCATGGGTG\n-+HWI-EAS337_3:7:1:115:1005/1\n-WWWWWWWWWVVWWWVVVVWWVVVWWWVVWVUUUUUU\n-@HWI-EAS337_3:7:1:354:1708/1\n-GCATCCGACAGTGACTTAGACGATGAGGAATACGAG\n-+HWI-EAS337_3:7:1:354:1708/1\n-WWWWWWWWWWWWVWWWWWVWWVWWVWWVWWUUUUUR\n-@HWI-EAS337_3:7:1:1639:1500/1\n-GTGATTATTATCTAACTCTGCAACAGCATCCAGGGA\n-+HWI-EAS337_3:7:1:1639:1500/1\n-WWWWWWVVWWWWWVVWVVWUVVVVVVVVWVUUUUUR\n-@HWI-EAS337_3:7:1:766:243/1\n-GTGGCATCTATGGAAGATAAATTGGAGATTGTTGCT\n-+HWI-EAS337_3:7:1:766:243/1\n-WWVWWWWWWWWVVWWVWWWWWWWVVVTVWWRUUJSU\n-@HWI-EAS337_3:7:1:920:144/1\n-GTGCGATCACACTGTTTATGTTGTTGTTGATCATTG\n-+HWI-EAS337_3:7:1:920:144/1\n-WWVVWWWWWVWPWVWWVWWSWVSWWHWWLVUCPUUH\n-@HWI-EAS337_3:7:1:389:268/1\n-GGTCAATTAGAGAGGGCAACCACCCTCAAAGAATTT\n-+HWI-EAS337_3:7:1:389:268/1\n-WWWWWWWWWVWWWWVVWWWWWWWWWWWWVVSUUUUU\n-@HWI-EAS337_3:7:1:294:1868/1\n-GAAAAAAAATTGTTTGTCTTGAATTAATGTTTCAAT\n-+HWI-EAS337_3:7:1:294:1868/1\n-VWVWWWWWWWWVQWWWWOWVVWWVWVVWQWUURULU\n-@HWI-EAS337_3:7:1:1147:62/1\n-GAATTCCCCTCAGGTTGGAGTTGTGCACTTGGCACT\n-+HWI-EAS337_3:7:1:1147:62/1\n-WWWWWWWWWWWWVWWWWWWVWWVWVVWVVWUUUUUU\n-@HWI-EAS337_3:7:1:787:1759/1\n-GGTTTTATTAGAATTGGTAGCTGTTCTGATTTTCTG\n-+HWI-EAS337_3:7:1:787:1759/1\n-WVVWWWWVWWWWWWWVUWWUWWUVWVVTVVUUUUUH\n-@HWI-EAS337_3:7:1:425:1939/1\n-GCTAATTGTGGTGTCTGGGTCTATGTGGCTAAACTT\n-+HWI-EAS337_3:7:1:425:1939/1\n-WWWWVWWVWWWWVWWWVVVVWWWVVWVVVWUUUUUU\n-@HWI-EAS337_3:7:1:187:1132/1\n-GTGGGAGAGGCAAGGGGCTTGGCTCATATCCTCTTC\n-+HWI-EAS337_3:7:1:187:1132/1\n-WVWWWWWWWWWWWWWWWWWWWTVWVWWWVVUUUUUU\n-@HWI-EAS337_3:7:1:1739:1840/1\n-GGAGGGGTGAAATCGTTTCTGAAAAATAATGAAATG\n-+HWI-EAS337_3:7:1:1739:1840/1\n-WWVWWWWWWWWWWWWWWVTWWWVVVWWWWWUUUUUU\n-@HWI-EAS337_3:7:1:1505:1876/1\n-GAAAGATCAAGTGTTGTCAAGTTCACTAGTTTAGAG\n-+HWI-EAS337_3:7:1:1505:1876/1\n-WWWWWWWWWWWWWWWWWWWWVWWVWWWVVVUUUSUR\n-@HWI-EAS337_3:7:1:447:192/1\n-GACTATGCCTAGCAGCTGAAATCACCACAACAAGTT\n-+HWI-EAS337_3:7:1:447:192/1\n-WWWWWWWWWWWWWWWTWWWVVWWVWWWWWVUUUUUU\n-@HWI-EAS337_3:7:1:21:2019/1\n-GTATGAGGTAAAAGATGATAACCTGTCTTCCAGCCC\n-+HWI-EAS337_3:7:1:21:2019/1\n-VWWVVWWVVWWWWWWWWWWWWWWWQVVWWWUURUUU\n-@HWI-EAS337_3:7:1:1593:652/1\n-GTGATGAGTAAAACATCATCATATGAACTTGAAGAG\n-+HWI-EAS337_3:7:1:1593:652/1\n-WWWVWVWWVWVWWVWWWWWWVVWWVWWVWWUUUSUU\n-@HWI-EAS337_3:7:1:1254:1660/1\n-GAAGTTTGTAATTCCTTTTAGGATTGTGGTTAACAT\n-+HWI-EAS337_3:7:1:1254:1660/1\n-WWWVVWWWWWWWWWWWVWVWVUWWWTWVQWUUUUMU\n-@HWI-EAS337_3:7:1:291:629/1\n-GTAGAGGAGGTAGGCTTGGTGGTCCCTCTATGGTAA\n-+HWI-EAS337_3:7:1:291:629/1\n-WWWWWWWWWWVVVWVWVVWTWWKOVVTRVSUSSMFR\n'

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/Wig/chr1.wig
--- a/SMART/Java/Python/TestFiles/Wig/chr1.wig Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,9 +0,0 @@
-fixedStep  chrom=chr1  start=11  step=1
-1.1
-1.2
-fixedStep  chrom=chr1  start=14  step=1
-1.4
-1.5
-variableStep chrom=chr1
-17  1.7
-19  1.9

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/adress.txt
--- a/SMART/Java/Python/TestFiles/adress.txt Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,7 +0,0 @@
-0
-58
-115
-173
-231
-289
-347

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/clusterize_default_expected.gff3
--- a/SMART/Java/Python/TestFiles/clusterize_default_expected.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1790 +0,0 @@\n-chr4\tS-MART\ttranscript\t1\t50000\t.\t+\t.\tnbElements=0;ID=region1;Name=region1\n-chr4\tS-MART\ttranscript\t49951\t99950\t.\t+\t.\tnbElements=0;ID=region2;Name=region2\n-chr4\tS-MART\ttranscript\t99901\t149900\t.\t+\t.\tnbElements=0;ID=region3;Name=region3\n-chr4\tS-MART\ttranscript\t149851\t199850\t.\t+\t.\tnbElements=0;ID=region4;Name=region4\n-chr4\tS-MART\ttranscript\t199801\t249800\t.\t+\t.\tnbElements=0;ID=region5;Name=region5\n-chr4\tS-MART\ttranscript\t249751\t299750\t.\t+\t.\tnbElements=0;ID=region6;Name=region6\n-chr4\tS-MART\ttranscript\t299701\t349700\t.\t+\t.\tnbElements=0;ID=region7;Name=region7\n-chr4\tS-MART\ttranscript\t349651\t399650\t.\t+\t.\tnbElements=0;ID=region8;Name=region8\n-chr4\tS-MART\ttranscript\t399601\t449600\t.\t+\t.\tnbElements=0;ID=region9;Name=region9\n-chr4\tS-MART\ttranscript\t449551\t499550\t.\t+\t.\tnbElements=0;ID=region10;Name=region10\n-chr4\tS-MART\ttranscript\t499501\t549500\t.\t+\t.\tnbElements=0;ID=region11;Name=region11\n-chr4\tS-MART\ttranscript\t549451\t599450\t.\t+\t.\tnbElements=0;ID=region12;Name=region12\n-chr4\tS-MART\ttranscript\t599401\t649400\t.\t+\t.\tnbElements=0;ID=region13;Name=region13\n-chr4\tS-MART\ttranscript\t649351\t699350\t.\t+\t.\tnbElements=0;ID=region14;Name=region14\n-chr4\tS-MART\ttranscript\t699301\t749300\t.\t+\t.\tnbElements=0;ID=region15;Name=region15\n-chr4\tS-MART\ttranscript\t749251\t799250\t.\t+\t.\tnbElements=0;ID=region16;Name=region16\n-chr4\tS-MART\ttranscript\t799201\t849200\t.\t+\t.\tnbElements=0;ID=region17;Name=region17\n-chr4\tS-MART\ttranscript\t849151\t899150\t.\t+\t.\tnbElements=0;ID=region18;Name=region18\n-chr4\tS-MART\ttranscript\t899101\t949100\t.\t+\t.\tnbElements=0;ID=region19;Name=region19\n-chr4\tS-MART\ttranscript\t949051\t999050\t.\t+\t.\tnbElements=0;ID=region20;Name=region20\n-chr4\tS-MART\ttranscript\t999001\t1049000\t.\t+\t.\tnbElements=0;ID=region21;Name=region21\n-chr4\tS-MART\ttranscript\t1048951\t1098950\t.\t+\t.\tnbElements=0;ID=region22;Name=region22\n-chr4\tS-MART\ttranscript\t1098901\t1148900\t.\t+\t.\tnbElements=0;ID=region23;Name=region23\n-chr4\tS-MART\ttranscript\t1148851\t1198850\t.\t+\t.\tnbElements=0;ID=region24;Name=region24\n-chr4\tS-MART\ttranscript\t1198801\t1248800\t.\t+\t.\tnbElements=0;ID=region25;Name=region25\n-chr4\tS-MART\ttranscript\t1248751\t1298750\t.\t+\t.\tnbElements=0;ID=region26;Name=region26\n-chr4\tS-MART\ttranscript\t1298701\t1348700\t.\t+\t.\tnbElements=0;ID=region27;Name=region27\n-chr4\tS-MART\ttranscript\t1348651\t1398650\t.\t+\t.\tnbElements=0;ID=region28;Name=region28\n-chr4\tS-MART\ttranscript\t1398601\t1448600\t.\t+\t.\tnbElements=0;ID=region29;Name=region29\n-chr4\tS-MART\ttranscript\t1448551\t1498550\t.\t+\t.\tnbElements=0;ID=region30;Name=region30\n-chr4\tS-MART\ttranscript\t1498501\t1548500\t.\t+\t.\tnbElements=0;ID=region31;Name=region31\n-chr4\tS-MART\ttranscript\t1548451\t1598450\t.\t+\t.\tnbElements=0;ID=region32;Name=region32\n-chr4\tS-MART\ttranscript\t1598401\t1648400\t.\t+\t.\tnbElements=0;ID=region33;Name=region33\n-chr4\tS-MART\ttranscript\t1648351\t1698350\t.\t+\t.\tnbElements=0;ID=region34;Name=region34\n-chr4\tS-MART\ttranscript\t1698301\t1748300\t.\t+\t.\tnbElements=0;ID=region35;Name=region35\n-chr4\tS-MART\ttranscript\t1748251\t1798250\t.\t+\t.\tnbElements=0;ID=region36;Name=region36\n-chr4\tS-MART\ttranscript\t1798201\t1848200\t.\t+\t.\tnbElements=0;ID=region37;Name=region37\n-chr4\tS-MART\ttranscript\t1848151\t1898150\t.\t+\t.\tnbElements=0;ID=region38;Name=region38\n-chr4\tS-MART\ttranscript\t1898101\t1948100\t.\t+\t.\tnbElements=0;ID=region39;Name=region39\n-chr4\tS-MART\ttranscript\t1948051\t1998050\t.\t+\t.\tnbElements=0;ID=region40;Name=region40\n-chr4\tS-MART\ttranscript\t1998001\t2048000\t.\t+\t.\tnbElements=0;ID=region41;Name=region41\n-chr4\tS-MART\ttranscript\t2047951\t2097950\t.\t+\t.\tnbElements=0;ID=region42;Name=region42\n-chr4\tS-MART\ttranscript\t2097901\t2147900\t.\t+\t.\tnbElements=0;ID=region43;Name=region43\n-chr4\tS-MART\ttranscript\t2147851\t2197850\t.\t+\t.\tnbElements=0;ID=region44;Name=region44\n-chr4\tS-MART\ttranscript\t2197801\t2247800\t.\t+\t.\tnbElements=0;ID=region45;Name=region45\n-chr4\tS-MART\ttranscript\t2247751\t2297750\t.\t+\t.\tnbElements=0;ID=region46;Name=region46\n-chr4\tS-MART\ttranscript\t2297701\t2347700\t.\t+\t.\tnbElements=0;ID=region47;Name=region47\n-chr4\tS-MART\ttranscript\t2347651\t2397650\t.\t+\t.\tnbEleme'..b'MART\ttranscript\t3946051\t3996050\t.\t+\t.\tnbElements=0;ID=region1746;Name=region1746\n-chr1\tS-MART\ttranscript\t3996001\t4046000\t.\t+\t.\tnbElements=0;ID=region1747;Name=region1747\n-chr1\tS-MART\ttranscript\t4045951\t4095950\t.\t+\t.\tnbElements=0;ID=region1748;Name=region1748\n-chr1\tS-MART\ttranscript\t4095901\t4145900\t.\t+\t.\tnbElements=0;ID=region1749;Name=region1749\n-chr1\tS-MART\ttranscript\t4145851\t4195850\t.\t+\t.\tnbElements=0;ID=region1750;Name=region1750\n-chr1\tS-MART\ttranscript\t4195801\t4245800\t.\t+\t.\tnbElements=0;ID=region1751;Name=region1751\n-chr1\tS-MART\ttranscript\t4245751\t4295750\t.\t+\t.\tnbElements=0;ID=region1752;Name=region1752\n-chr1\tS-MART\ttranscript\t4295701\t4345700\t.\t+\t.\tnbElements=0;ID=region1753;Name=region1753\n-chr1\tS-MART\ttranscript\t4345651\t4395650\t.\t+\t.\tnbElements=0;ID=region1754;Name=region1754\n-chr1\tS-MART\ttranscript\t4395601\t4445600\t.\t+\t.\tnbElements=0;ID=region1755;Name=region1755\n-chr1\tS-MART\ttranscript\t4445551\t4495550\t.\t+\t.\tnbElements=0;ID=region1756;Name=region1756\n-chr1\tS-MART\ttranscript\t4495501\t4545500\t.\t+\t.\tnbElements=0;ID=region1757;Name=region1757\n-chr1\tS-MART\ttranscript\t4545451\t4595450\t.\t+\t.\tnbElements=0;ID=region1758;Name=region1758\n-chr1\tS-MART\ttranscript\t4595401\t4645400\t.\t+\t.\tnbElements=0;ID=region1759;Name=region1759\n-chr1\tS-MART\ttranscript\t4645351\t4695350\t.\t+\t.\tnbElements=0;ID=region1760;Name=region1760\n-chr1\tS-MART\ttranscript\t4695301\t4745300\t.\t+\t.\tnbElements=0;ID=region1761;Name=region1761\n-chr1\tS-MART\ttranscript\t4745251\t4795250\t.\t+\t.\tnbElements=0;ID=region1762;Name=region1762\n-chr1\tS-MART\ttranscript\t4795201\t4845200\t.\t+\t.\tnbElements=0;ID=region1763;Name=region1763\n-chr1\tS-MART\ttranscript\t4845151\t4895150\t.\t+\t.\tnbElements=0;ID=region1764;Name=region1764\n-chr1\tS-MART\ttranscript\t4895101\t4945100\t.\t+\t.\tnbElements=0;ID=region1765;Name=region1765\n-chr1\tS-MART\ttranscript\t4945051\t4995050\t.\t+\t.\tnbElements=0;ID=region1766;Name=region1766\n-chr1\tS-MART\ttranscript\t4995001\t5045000\t.\t+\t.\tnbElements=0;ID=region1767;Name=region1767\n-chr1\tS-MART\ttranscript\t5044951\t5094950\t.\t+\t.\tnbElements=0;ID=region1768;Name=region1768\n-chr1\tS-MART\ttranscript\t5094901\t5144900\t.\t+\t.\tnbElements=0;ID=region1769;Name=region1769\n-chr1\tS-MART\ttranscript\t5144851\t5194850\t.\t+\t.\tnbElements=0;ID=region1770;Name=region1770\n-chr1\tS-MART\ttranscript\t5194801\t5244800\t.\t+\t.\tnbElements=0;ID=region1771;Name=region1771\n-chr1\tS-MART\ttranscript\t5244751\t5294750\t.\t+\t.\tnbElements=0;ID=region1772;Name=region1772\n-chr1\tS-MART\ttranscript\t5294701\t5344700\t.\t+\t.\tnbElements=0;ID=region1773;Name=region1773\n-chr1\tS-MART\ttranscript\t5344651\t5394650\t.\t+\t.\tnbElements=0;ID=region1774;Name=region1774\n-chr1\tS-MART\ttranscript\t5394601\t5444600\t.\t+\t.\tnbElements=0;ID=region1775;Name=region1775\n-chr1\tS-MART\ttranscript\t5444551\t5494550\t.\t+\t.\tnbElements=0;ID=region1776;Name=region1776\n-chr1\tS-MART\ttranscript\t5494501\t5544500\t.\t+\t.\tnbElements=0;ID=region1777;Name=region1777\n-chr1\tS-MART\ttranscript\t5544451\t5594450\t.\t+\t.\tnbElements=0;ID=region1778;Name=region1778\n-chr1\tS-MART\ttranscript\t5594401\t5644400\t.\t+\t.\tnbElements=0;ID=region1779;Name=region1779\n-chr1\tS-MART\ttranscript\t5644351\t5694350\t.\t+\t.\tnbElements=0;ID=region1780;Name=region1780\n-chr1\tS-MART\ttranscript\t5694301\t5744300\t.\t+\t.\tnbElements=0;ID=region1781;Name=region1781\n-chr1\tS-MART\ttranscript\t5744251\t5794250\t.\t+\t.\tnbElements=0;ID=region1782;Name=region1782\n-chr1\tS-MART\ttranscript\t5794201\t5844200\t.\t+\t.\tnbElements=0;ID=region1783;Name=region1783\n-chr1\tS-MART\ttranscript\t5844151\t5894150\t.\t+\t.\tnbElements=0;ID=region1784;Name=region1784\n-chr1\tS-MART\ttranscript\t5894101\t5944100\t.\t+\t.\tnbElements=0;ID=region1785;Name=region1785\n-chr1\tS-MART\ttranscript\t5944051\t5994050\t.\t+\t.\tnbElements=0;ID=region1786;Name=region1786\n-chr1\tS-MART\ttranscript\t5994001\t6044000\t.\t+\t.\tnbElements=0;ID=region1787;Name=region1787\n-chr1\tS-MART\ttranscript\t6043951\t6093950\t.\t+\t.\tnbElements=0;ID=region1788;Name=region1788\n-chr1\tS-MART\ttranscript\t6093901\t6143900\t.\t+\t.\tnbElements=0;ID=region1789;Name=region1789\n-chr1\tS-MART\ttranscript\t6143851\t6193850\t.\t+\t.\tnbElements=1.0;ID=region1790;Name=region1790\n'

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/clusterize_default_expected.map
--- a/SMART/Java/Python/TestFiles/clusterize_default_expected.map Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1790 +0,0 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diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/clusterize_normalize_expected.gff3
--- a/SMART/Java/Python/TestFiles/clusterize_normalize_expected.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/clusterize_output_tag_expected.gff3
--- a/SMART/Java/Python/TestFiles/clusterize_output_tag_expected.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/clusterize_strands_expected.gff3
--- a/SMART/Java/Python/TestFiles/clusterize_strands_expected.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/expOutputGff.gff3
--- a/SMART/Java/Python/TestFiles/expOutputGff.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,2292 +0,0 @@\n-C02HBa0185P07_LR40\tS-MART\ttranscript\t3889\t3924\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:415:1217;identity=100.000000;Name=HWI-EAS337_3:7:1:415:1217\n-C02HBa0185P07_LR40\tS-MART\ttranscript\t3830\t3865\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:415:1217;identity=100.000000;Name=HWI-EAS337_3:7:1:415:1217\n-C11SLe0053P22_LR298\tS-MART\ttranscript\t2130\t2165\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:1178:755;identity=100.000000;Name=HWI-EAS337_3:7:1:1178:755\n-C11SLe0053P22_LR298\tS-MART\ttranscript\t1980\t2015\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:1178:755;identity=100.000000;Name=HWI-EAS337_3:7:1:1178:755\n-C06HBa0144J05_LR355\tS-MART\ttranscript\t1\t36\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:277:1259;identity=100.000000;Name=HWI-EAS337_3:7:1:277:1259\n-C06HBa0144J05_LR355\tS-MART\ttranscript\t101\t136\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:277:1259;identity=100.000000;Name=HWI-EAS337_3:7:1:277:1259\n-C08HBa0165B06_LR218\tS-MART\ttranscript\t3619\t3654\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:447:1231;identity=100.000000;Name=HWI-EAS337_3:7:1:447:1231\n-C08HBa0165B06_LR218\tS-MART\ttranscript\t3575\t3610\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:447:1231;identity=100.000000;Name=HWI-EAS337_3:7:1:447:1231\n-C02HBa0329G05_LR52\tS-MART\ttranscript\t4746\t4781\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:1154:1517;identity=100.000000;Name=HWI-EAS337_3:7:1:1154:1517\n-C02HBa0329G05_LR52\tS-MART\ttranscript\t4680\t4715\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:1154:1517;identity=100.000000;Name=HWI-EAS337_3:7:1:1154:1517\n-C04HBa80D3_LR100\tS-MART\ttranscript\t423\t458\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:164:1869;identity=100.000000;Name=HWI-EAS337_3:7:1:164:1869\n-C04HBa80D3_LR100\tS-MART\ttranscript\t397\t432\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:164:1869;identity=100.000000;Name=HWI-EAS337_3:7:1:164:1869\n-C01HBa0216G16_LR11\tS-MART\ttranscript\t648\t683\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:415:1194;identity=100.000000;Name=HWI-EAS337_3:7:1:415:1194\n-C01HBa0216G16_LR11\tS-MART\ttranscript\t511\t546\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=1.000000;ID=HWI-EAS337_3:7:1:415:1194;identity=97.222222;Name=HWI-EAS337_3:7:1:415:1194\n-C05HBa0145P19_LR136\tS-MART\ttranscript\t3686\t3721\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=2.000000;ID=HWI-EAS337_3:7:1:645:1892;identity=94.444444;Name=HWI-EAS337_3:7:1:645:1892\n-C05HBa0145P19_LR136\tS-MART\ttranscript\t3573\t3608\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:645:1892;identity=100.000000;Name=HWI-EAS337_3:7:1:645:1892\n-C08HBa0012O06_LR211\tS-MART\ttranscript\t1768\t1803\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=1.000000;ID=HWI-EAS337_3:7:1:33:1446;identity=97.222222;Name=HWI-EAS337_3:7:1:33:1446\n-C08HBa0012O06_LR211\tS-MART\ttranscript\t1649\t1684\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:33:1446;identity=100.000000;Name=HWI-EAS337_3:7:1:33:1446\n-C09HBa0194K19_LR362\tS-MART\ttranscript\t9168\t9203\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:1194:1427;identity=100.000000;Name=HWI-EAS337_3:7:1:1194:1427'..b':1:1147:62\n-C02HBa0204D01_LR334\tS-MART\ttranscript\t6704\t6739\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:1147:62;identity=100.000000;Name=HWI-EAS337_3:7:1:1147:62\n-C02SLe0018B07_LR335\tS-MART\ttranscript\t8378\t8413\t.\t-\t.\tquality=0;bestRegion=(self);nbGaps=0;nbOccurrences=2;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:787:1759;identity=100.000000;Name=HWI-EAS337_3:7:1:787:1759\n-C02SLe0018B07_LR335\tS-MART\ttranscript\t8208\t8243\t.\t+\t.\tquality=0;bestRegion=(self);nbGaps=0;nbOccurrences=2;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:787:1759;identity=100.000000;Name=HWI-EAS337_3:7:1:787:1759\n-C09SLm0143I09_LR365\tS-MART\ttranscript\t1546\t1581\t.\t-\t.\tquality=0;bestRegion=(self);nbGaps=0;nbOccurrences=2;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:425:1939;identity=100.000000;Name=HWI-EAS337_3:7:1:425:1939\n-C09SLm0143I09_LR365\tS-MART\ttranscript\t1490\t1525\t.\t+\t.\tquality=0;bestRegion=(self);nbGaps=0;nbOccurrences=2;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:425:1939;identity=100.000000;Name=HWI-EAS337_3:7:1:425:1939\n-C02SLe0018B07_LR335\tS-MART\ttranscript\t9178\t9213\t.\t-\t.\tquality=0;bestRegion=(self);nbGaps=0;nbOccurrences=2;nbMismatches=1.000000;ID=HWI-EAS337_3:7:1:187:1132;identity=97.222222;Name=HWI-EAS337_3:7:1:187:1132\n-C02SLe0018B07_LR335\tS-MART\ttranscript\t9065\t9100\t.\t+\t.\tquality=0;bestRegion=(self);nbGaps=0;nbOccurrences=2;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:187:1132;identity=100.000000;Name=HWI-EAS337_3:7:1:187:1132\n-C02HBa0072A04_LR26\tS-MART\ttranscript\t2868\t2903\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:1739:1840;identity=100.000000;Name=HWI-EAS337_3:7:1:1739:1840\n-C02HBa0072A04_LR26\tS-MART\ttranscript\t3189\t3224\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=1.000000;ID=HWI-EAS337_3:7:1:1739:1840;identity=97.222222;Name=HWI-EAS337_3:7:1:1739:1840\n-C07SLe0111B06_LR194\tS-MART\ttranscript\t8673\t8708\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:1505:1876;identity=100.000000;Name=HWI-EAS337_3:7:1:1505:1876\n-C07SLe0111B06_LR194\tS-MART\ttranscript\t8677\t8712\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:1505:1876;identity=100.000000;Name=HWI-EAS337_3:7:1:1505:1876\n-C09SLm0143I09_LR365\tS-MART\ttranscript\t6957\t6992\t.\t+\t.\tquality=0;bestRegion=(self);nbGaps=0;nbOccurrences=2;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:447:192;identity=100.000000;Name=HWI-EAS337_3:7:1:447:192\n-C09SLm0143I09_LR365\tS-MART\ttranscript\t7039\t7074\t.\t-\t.\tquality=0;bestRegion=(self);nbGaps=0;nbOccurrences=2;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:447:192;identity=100.000000;Name=HWI-EAS337_3:7:1:447:192\n-C09SLm0037I08_LR367\tS-MART\ttranscript\t1298\t1333\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:21:2019;identity=100.000000;Name=HWI-EAS337_3:7:1:21:2019\n-C09SLm0037I08_LR367\tS-MART\ttranscript\t955\t990\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:21:2019;identity=100.000000;Name=HWI-EAS337_3:7:1:21:2019\n-C04HBa8K13_LR338\tS-MART\ttranscript\t2175\t2210\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=1.000000;ID=HWI-EAS337_3:7:1:1593:652;identity=97.222222;Name=HWI-EAS337_3:7:1:1593:652\n-C04HBa8K13_LR338\tS-MART\ttranscript\t2226\t2261\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:1593:652;identity=100.000000;Name=HWI-EAS337_3:7:1:1593:652\n-C12HBa326K10_LR306\tS-MART\ttranscript\t8100\t8135\t.\t+\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:1254:1660;identity=100.000000;Name=HWI-EAS337_3:7:1:1254:1660\n-C12HBa326K10_LR306\tS-MART\ttranscript\t8243\t8278\t.\t-\t.\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:1254:1660;identity=100.000000;Name=HWI-EAS337_3:7:1:1254:1660\n'

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/expRef.fasta
--- a/SMART/Java/Python/TestFiles/expRef.fasta Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,33148 +0,0 @@\n->C10HBa0111D09_LR276\n-GAACAAACAACCCCTTTTTGGAGGTGTTGGCGCGTCGTGCAGCTTACACTCAAAAGTTAA\n-AAAGTTGCCTTGCGATGCGGTCATGTTACAAACCTCTCTGCCTTAAATTAAATTCCATAA\n-CCAAGATTTGGAGGTGCCTCAACGATGCGCAGCCATGTCCCATATTTGGTCGCCTCGTTT\n-AAAAGTCAAGTTAGACTTAATTAAGAGGTCCAACTAGTGTAGGGGCGTTTTGAGTACTTG\n-TGGGATTTATTATAAACGGTTTTGAGTCACTTTAAACCCACTTCACCAATTAAAACAAAA\n-TCCTCAAGTTAAAACTCAATATCTTTCCATTCTCTCTCTCTAAAACCTTCATTGGAGATA\n-TTTGAAGCTCCACGGAAGAAGGTTAATTTTCCAAGGTTTCAATGAAAATTTCGTGTATAG\n-GTCTTCAATAAGGTATGGTGATTTCATCCTTGATTCTTCTATCATTCAAGGATCCAATTC\n-AAAGGTTTTTCAAAAGATCTCAAAAATCCTATTTCGAATTCTAAGTATGGGTTCTTCCAT\n-TTAAAGGTTTAAATGGATGAATTATGATGTTTTCAATGTTAGTTGATGTTTTTATGATAA\n-AAAAACTCCATGAACCCATGAGCATCCTAATTCTCTAATTTTGTCTTGTAAATTGAGTTT\n-GATAATTGTGATTGGTTATGGATGGAATTGTATTTAGATTGCTCTATATTGTTGATTCTT\n-ATTGTTAACCTATCTCTATATATGTAGAATTGAGATTGTAAGGATGAGTTAGTAATCTTG\n-GCTTTATGGGCTTTCGAATCCGGGTTTACCCCCTGGATGTAACCGGCATCCTCGCCCTTT\n-TTCAAGGACTAAGACCAACCTTTTAGTCTCATGTCATTACATTCATAGGTTGACAAATGC\n-GGAAAAATTTAAAACTTTCATTATCACTACTTGGAGGTTTACATAGACCTCTACATACAC\n-ATAAGATATATTCATATAGAGTATACATAGACCCTTCGTATAGGAAGGTTACATAGCCAT\n-CTACTTTTATTACACATACATATATATAAAATATAAAAATAGTCTAACGATTGTCTCATC\n-TCATACCCTCTAAACGATTATCACAATATGGGCATAACCCTTACATCAATCAAACAAGAG\n-CACATATAGGTCATACAAAAGTATAGTACTCAATTAAAAAGGAAAGAAATGAAAGAGTCT\n-TTAAGCTCATAACAAGTCCATAAGCTAGATTATGGCATTGACCTCAAAAGTTGAGGACCT\n-TATGTGCGTACACAAGCAAAACATGCTAAAAAGGGACTTTTTAGTCAAAACATGCCCATT\n-TATCCCTTTAAGAACCTACTACAAAGCCAACAAGTCATACCAACCAACCAAACATGCTTA\n-CTATCTCAACAAGTAATACTTATCCCAACATACTTGAAACCATGATTTACTACAACCCTA\n-TCACCAAGGAAAAATATCACAAGAATGAATAAGAGTCAATCATATCATGATAGAGAGACA\n-ACTATTCATGAATCCTTATCAACTCAACAAGTGCAATAACCAAGCAAAGCCTCATAACCT\n-TACTCAATCAAGTATCCTCAAAAAGAAACCATGACCAATGTCCAACTTTACCTAACATAG\n-CATTTAGGTTTACATTTTATCATATATTAACATTATGACCCAAGGCATACTCATTAGTAA\n-ACTAATTAATATATAATATCAACAATGTGCCATAGTAATCATATATACATAATATATCAT\n-CATAACATAAACATATATAAAAACCTCCTTCTAAGACTCCCCTCAAGGCTAACTAGTGAA\n-ATGTTTAGGTAGAGCCCCATACCCCTACCTAGATTAAGCTAGACCCCTTAGGTTATCCAA\n-GTTAGAGTTCAAGTCCTTTAATTCGTTTTACCTTTTGGGAACATCTTGCCCTAACCGACA\n-TAGACCACATGAGCTAGTGTGGGATACGGTTCCAAAAAACCCTACACAGAAAGAAGGCGG\n-ACTACTTGCCAAAGTATTACCAAAACATGAAACATAGCAACTACGTTGATCCACTAGCAA\n-GTATTTCTATAGGGGCAACATAGTTCAAGAACTCTGAGATATACTTGAGACCCTCTTTAT\n-GCGCCATGCATTATAGTCTCCAACCTCAAGAGTAATGTAGTGTTCCTACCTTCCCCATGT\n-GAGAAAGGACACTCCTCAATCTAGTTCACTCGGTGCTAAGCTAGAGACCCTTTTTGAAAT\n-GTCTTTAAGCCTTTAATTATCAATCATAGCTTAGCTTAGGTCATAGGGTATATCTCTTGT\n-ATAATCATCATCATCAATAGCTCAATAATAATTGTATGAGTATAAGTCCTTTCATCACAA\n-TTCATATAAGTGAGGTTAACATGTTAGCATTTCATTGCATATCAAGAAACATTGATGATT\n-CTTACCATCCTTGTATCACATACACCTTAATCAATCTCACAACATAGTCAGGACATATCA\n-ATTCAACATCATACCACCCTATAATCCTAATATAAGGCATACTCCAATATAACTTCACGT\n-CTTAACAAAAATTTATCACAATTGGAATTAAAGATAGAGATTCTAAGACTTAACAAGTCT\n-TCCTTGTAGTTCATCATCAAGGTCTTACCATCAACCCATAACTCAACCAAGTTTGGGGAG\n-TAACATCATCACACAATGATAATCAATAGGATAACAAGGCTAATTTCATCTCTATAACAC\n-AATTCAACACTAGATCATAACTTAAGACAAGATACATAGGCTAATTTCACACTATAATTC\n-ATAACCTAAATCACATCTCAAGAAATAGCATTATAGTCCTATAATTCATATTAATTTGTT\n-CATAATAACACAATAGGATAGTAATTTAATCAATAACCAAGTCAATTGAATGATCACAAT\n-ACAATATACATCAATATCACAAGCTAGGGTTAGGGATGAAGGATCATATTCTTCAATTTA\n-GACCAAACCACTAACAATTACCATAATAAAGTTTAAATTCATGTAAATGTATTCAATATA\n-ACCTAAATAAATCATTAACAACTCAATCCATAACTTCAATTTCGTAATTGAATGAAACCC\n-ATAAGAAAATTCACCTTTTGAAATCCATTTTAAAGAAACCCTTTGAGGAAAGAGCCTCAA\n-AGGTGAATTAGATCCCATATATTAATGTTTGATGATGAATTCGCCCCTTTCCATCCCCCA\n-AACCCTTATCCTTGCTAGTTTTTAATGGTGAGTTCAAGTAGAGAGAGAAATAAGAGAGAA\n-GGAAGAGAGTTTTTGTCTTAGAGTTCTAATTAATTTAATTGGGGTTGGGGATTTTATATG\n-CGTTTTAAGTTAGTTAATTAGTCACCCCTCAATACCTAACTAACCCCTGAACCACCTAAT\n-TAATTAAATGAATCAATATAAAAACATACAGGAAATTTGACCTTCACAGACGAGACCCCG\n-AACGACGGGCCATCTGTGAGTCAACGGTCCCTCACCCCTCCGTCCTGCACTCTATCGATC\n-AGTTCATAGACTGTGCAGGCAGATCAATTCTTCAACTTGTCTAAGTATGGGATGACGGTG\n-GTATCGACTCCCCGTCAGTCCACACACGGACCGTAGGTGGTCCCATCGATGCGCATTGTC\n-TAGTCCTTGTTTGTTCAAACACAAGGGCCTCAAGGGCCCTTGGTTGGTGCTTGGGGAGTC\n-GTACCCATACGTTTCAATCATGAAACAACTCAAAAACCTATAATCTATCCTTCCACCAAT\n-TTTTGTACCTTTCCGACTCTTAAAAGGTAGTCAAATAGGCTAAGGCACGCTAACACCCCT\n-TTGAACCAACTTCCTGGACGTTCTTATACATTTTGGTTCTTAAACTTCCT'..b'CAATATTCCATATTGATCGCCAGCTTCCATTGCTACAAAAGA\n-TGCATATAGTATCAGCTTCTTTAGACAAAGCTATAAGAAGTATCAGTTGACCCAATTGAC\n-AAGTCACACGTGCTATAACAAGATATCACTTGACGCAAGTGACAAGTGTGAAGCTGACAG\n-GAAAATAGGCAATAGAATCCCTCATTCTTTGTTTATATATAGCAACCTATTACTTCAGTA\n-TCTGTTTACAAGTTCTGCACCACGATAAGTATAACTATTTAGAAATTATGAAGGGAGTGT\n-TGCACAAATTAGTCAGGGTTAGAATTTTAATAATCCAACACACCAGAAATTCTGAGGACT\n-ATGCCTAGCAGCTGAAATCACCACAACAAGTTCAAAGTCAAATCCTGGCTCTTCCACATC\n-CTTTCCCTTCGTACAGTAAACTGAACAGATGCCTTTTGGATATGTTTCACTCACATACTT\n-CATAATTTCAGCATCCATGGCAGACCTACACAAGAATTACCATGAATAGGAGAATTTGGC\n-AAGCAACGGTAATCACAAAGTCAGTACTCATAAACCAAGCCTCTGATGAGAAGAACTAAC\n-CATGTTAAGAAGGGAACTACTCACATAAAACAAAAACATGATTTTTATAATCTGCATGCC\n-AAGCATTAGGAACTATTGAAGAATTCACTGCGATCTCAGAATATAATCCTTTCATACTCT\n-TAATGCCTCCCAATTATACCAAATTTAGGTGTCTTACTACCATTTTAGTATCTGACATTG\n-ATGTCATTACCCATTAATTTGGAGACACTGGTTCCTCACCGATAAAGATGAACAAAAAGG\n-TAAACCAGTGTATTATGAATCAGATCTCTTTATGGAATAAAAACACACATGAATCATGAT\n-GTAGGATCTTATTAACACTTGAGGACTGAGGCGAAGATTACTAAGAATATCCCGAAAGAT\n-AAGACATAGAATGTAATATAGAAGGACAGAGAACAAATGATACTGATTAAGAAGAAGAGC\n-ATCTATATAGGAGAGATTAGCCTAAACTATTTATTTTCAGACTGATTTCGGTGAGCGCAG\n-ACCAAAACATGCAGCTTTTTTTTCAATTAAGCCGGAAAGACAATTTCCACAAGAAATGCA\n-ACTGTTCTAGCATATCTTAAACTATAATCTGAGTGCTGTCTGAGAACTGAGGTTGAATTT\n-GCAAGTCTTGTTGAGCATGGTTAAAAAATAAGTCCAATTAGGCAAAATAATTGTGAATGT\n-CATAATATAGAAGAACTTCAACATCTCAATGGGAAAAACAGAAAGTGAGTAGCTAAAAAG\n-GGGAGCAATACCAAAGATATTAAACTGAGAAATATATCTCATACCCTACAGATGCATACC\n-TATACTCTTCCACGAAAGCAGATGGAAGTTCTTCATCTCTTGCTGGCCTAACGTCTTTAC\n-AAACCTAGAATGCAGACATACCATGAGCTTACAAGAAGGGAGCATAAATTATTACACGGC\n-AACAATAACTAGGAAAAAAAGAGAGAGAGGAAATACATTTAATTTCACAGCCCTTGAATT\n-ATGAATAAAACCATGCACTTGTTATATTAAGCAGAGACTACTTCCACTTTTCCAATCTAT\n-TTACATCTACTTCATCACATTAACAAGAATAGAAAAGAAATGCATGTTATGTGACATTCA\n-GCACTGTAGACTAATGAGGATTAATTTACAACCATGGACCAGCTATAGCAGAAGAGACCT\n-TATTTTACTTTTCCAAAATTGGTATTTACTCCATCACCATTAACAAGAATAAAAAATGCA\n-TCTTATGTGAAGTTCATAACTATTGAATAATGAGGTTAATCAAGAGCTTGCTATATCAAA\n-GCACATTTTTCAAGTTTACAATTTCTTCATTCTTGGTATCCACTTCTATCATGAAAACCA\n-ACCTAACAGTTAACACAATTCACTCTGGTGTTTTGTTCTTTATCCCTAATGCCTGAGTGT\n-GTTTAACTAATCAAGTTCCAATCAGCCAGAAGATGTCTAAACATACTAAACTATAGATAA\n-ACAACATGAGCATAAAACCAGTTTATGTAGAGATTTTTAATTGCACAGCATAAAAAGGAG\n-TACCCCCGGCACTATATGTGCTTCTCTTTCTTTTTTTCTTACTTCGTCCTGATCTTTTTA\n-CTTTTCTTTTCCTTTCTTTCAGAATAAGCACATTTTTGGATATAGTCCCACCATCTCTAC\n-CAGGTTTATGTCTGTCCATATTATTGCTTTTTTGAATTACCTTCTAAACAAAATACTCAT\n-CCTTACAAACCTGCTTCCTCTTCTATGGATCCCACCACTCCATGCCCCGAAAAAAAAGAA\n-AGAAAAAGATAAGTTTTTCATAGTCACTTTAGATTATCATTTATTAAATTCTGTCGGCTC\n-AACTGATAGGAACAGTGAAATGGACTTTTCAATCATAAAAAGATAATAGAAGTTATTAAA\n-TGATTCCCTTCAAGATTATGAGCTTTTAAACTTACATATCATGCAACTATTGGGGAATTA\n-AGGGACTGGGGATTTGATGATAAATTCCAGCACCATTTTTGGTGCTTTTGTGTTTTTGCA\n-AGGTAGTTTGTTAGTGGCACATGGAAGGAGGTGCCTCATCCAATGAAATTATTAATCTTA\n-TCAACAAGAAGAAAGTCAAAACACCAAACTGTAAAAAATCCAAAAATAGCATTTTGCATT\n-GTGTACTAACTGAACAACGTACTTGCTTGACATGGTCAACTCTGGCAACCTGCGCAGTCC\n-GGGGATCAAGATACTCATCCTTATGAACCTCACTAAATGATGTAATCAGTACCTACAAAT\n-TAGTGAACAGCAACTTTACACAGCTAGATCATGAAAAATAGCTTCCAAGTGTCCATTACT\n-ACATAAATGAAAAGCATTATACTTTCTTTTTAGAAGAGGGGAACAAAATCTTAGACTTCA\n-TAAGGAACAGTTCTCCGGAAAGTTTTCTTTTCTATATTGAAGAAGTAATCATTTATTGAA\n-GTGGTGGAAATTCCCTAAGCTTTAAACAGATGTAGAGAACTTGTCCATAAACATGGTGCT\n-CAACAAACAACACCCAACTCATTCATATATAGTAGCGCCAGCATCCAAGTACCATGAAGT\n-ATATCTCTATCCTAAAAGCTTTACTTGAAGACTTATTAGATTAATCTTACTTATTTCTCA\n-TGCAACTTTTTTTTTGAAAAGTTTCTCAAGCATAACTTTTATCCTTTGTTTTCATTCAGT\n-CTTTGAGCTCTAAAGGATGCCTAGAGAGGTCATGAACCAAGTAAGGAAATTGCAACATCA\n-TATTGCTTCCAATTTACCTCATTTTTTATCTTCAACTACCGAAAACTACCAAATCTGAAA\n-TTATCAACTAAGGAAAATTACAACATCAGTACAATAAGTATTGCTTACAGTTCACTTAAT\n-ATTTCAATCTTCGACTACGGAAAACTGTCAAATCTGAAATTATCAATTTGAATGACACGA\n-TTAGTCTAACTTACATTTTCAAAGATCTAACTTACCCAATGAAAAAAGAAAACAAGAGAG\n-AGACTTACATCGCCACTTCTGTTTGGGAATTCGAGACAAATCAAGTGAGATTTGTTGTAC\n-GAAGGAAATGACTCCTCGGCCGCTTTCTTATATATATTTTCGTCCTTTAAAATAGCTCTA\n-ACATCTGCAAATCCAACCAAATGACGCTCAAAACCAAAAATGTAAAAAATAAACTGCCGA\n-TCGCAAATGAACACCAATGCGGTCACATTTTCAAGCACGAAAAAAGCTTCAAAATACAAA\n-AAACTTTAGCGCAGAAAATAAACGAAAGAGAAGAAGAAGAAGACCTTTGGCGACGTACTG\n-AATTTCGCCGGCTGGGGCATTAAGAAGGAACCATTTGGCAATCTCAAT\n'

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/inputCR.gff3
--- a/SMART/Java/Python/TestFiles/inputCR.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
-chr1 test match 6155418 6155441 24 + . Name=test1/1;occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100
-chr2 test match 26303950 26303981 32 + . Name=test2/1;occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93
-chr3 test match 28320540 28320574 35 + . Name=test2/1;occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94
-chr4 test match 28565007 28565041 35 + . Name=test2/1;occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88
-chr1 test match 6155418 6155441 24 + . Name=test3/1;occurrence=2;rank=2;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=1;ID=test3/1;identity=50
-chr1 test match 6155418 6155441 24 - . Name=test3/1;occurrence=2;rank=2;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=1;ID=test3/1;identity=50

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/inputFileTest1.bed
--- a/SMART/Java/Python/TestFiles/inputFileTest1.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,5 +0,0 @@
-track name=reads description="Reads" useScore=0 visibility=full offset=0
-arm_X 1000 2000 test1.1 1000 + 1000 2000 0 1 1000, 0,
-arm_X 1000 2000 test1.2 1000 - 1000 2000 0 1 1000, 0,
-arm_X 100 200 test1.3 1000 + 100 200 0 1 100, 0,
-arm_X 100 3200 test1.4 1000 + 100 3200 0 1 3100, 0,

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/inputFileTest2.bed
--- a/SMART/Java/Python/TestFiles/inputFileTest2.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-track name=reads454Relaxed description="reads454Relaxed" useScore=0 visibility=full offset=0
-arm_X 1000 2000 test2.1 1000 + 1000 2000 0 1 1000, 0,

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/inputMSWC1.gff3
--- a/SMART/Java/Python/TestFiles/inputMSWC1.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,5 +0,0 @@
-chr1 test match 6155418 6155441 24 + . Name=test1/1;occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100
-chr2 test match 26303950 26303981 32 + . Name=test2/1;occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93
-chr3 test match 28320540 28320574 35 + . Name=test2/1;occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94
-chr4 test match 28565007 28565041 35 + . Name=test2/1;occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88
-chr6 test match 48565007 48565041 35 + . Name=test2/1;occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=3;ID=test2/1-4;identity=80

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/inputMSWC2.gff3
--- a/SMART/Java/Python/TestFiles/inputMSWC2.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,5 +0,0 @@
-chr1 test match 6155418 6155441 24 + . Name=test1/1;occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100
-chr2 test match 26303990 26304021 32 + . Name=test2/1;occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93
-chr3 test match 28320540 28320574 35 + . Name=test2/1;occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94
-chr4 test match 28565017 28565051 35 + . Name=test2/1;occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88
-chr5 test match 30000000 30000050 50 + . Name=test3/1;occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=1;ID=test3/1-4;identity=50

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/inputMTC.sam
--- a/SMART/Java/Python/TestFiles/inputMTC.sam Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,2698 +0,0 @@\n-@SQ\tSN:C10HBa0111D09_LR276\tLN:9300\n-@SQ\tSN:C11HBa0029C01_LR281\tLN:10969\n-@SQ\tSN:C11HBa0034I10_LR282\tLN:9056\n-@SQ\tSN:C11HBa0054I23_LR283\tLN:10301\n-@SQ\tSN:C11HBa0062I24_LR284\tLN:10050\n-@SQ\tSN:C11HBa0064J13_LR285\tLN:9385\n-@SQ\tSN:C11HBa0072I13_LR286\tLN:9556\n-@SQ\tSN:C11HBa0089M02_LR287\tLN:9244\n-@SQ\tSN:C11HBa0096D22_LR288\tLN:9184\n-@SQ\tSN:C11HBa0107K14_LR289\tLN:9115\n-@SQ\tSN:C11HBa0139J14_LR291\tLN:10002\n-@SQ\tSN:C11HBa0143O06_LR374\tLN:10785\n-@SQ\tSN:C11HBa0161D01_LR292\tLN:9057\n-@SQ\tSN:C11HBa0168B23_LR293\tLN:9826\n-@SQ\tSN:C11HBa0190J03_LR294\tLN:10992\n-@SQ\tSN:C11HBa0249E07_LR279\tLN:10008\n-@SQ\tSN:C11HBa0303G16_LR296\tLN:9430\n-@SQ\tSN:C11HBa0323E19_LR297\tLN:9657\n-@SQ\tSN:C11SLe0053P22_LR298\tLN:9827\n-@SQ\tSN:C11SLm0052K14_LR376\tLN:10013\n-@SQ\tSN:C12HBa115G22_LR301\tLN:10021\n-@SQ\tSN:C12HBa120K4_LR313\tLN:10271\n-@SQ\tSN:C12HBa144B17_LR302\tLN:9247\n-@SQ\tSN:C12HBa149G24_LR381\tLN:9271\n-@SQ\tSN:C12HBa165B12_LR303\tLN:9257\n-@SQ\tSN:C12HBa183M6_LR379\tLN:9473\n-@SQ\tSN:C12HBa221M9_LR377\tLN:10755\n-@SQ\tSN:C12HBa224N6_LR382\tLN:9130\n-@SQ\tSN:C12HBa26C13_LR299\tLN:9139\n-@SQ\tSN:C12HBa326K10_LR306\tLN:10414\n-@SQ\tSN:C12HBa90D9_LR311\tLN:9638\n-@SQ\tSN:C12HBa93P12_LR312\tLN:9510\n-@SQ\tSN:C12SLe124D18_LR385\tLN:10545\n-@SQ\tSN:C12SLeRI72J6_LR378\tLN:9337\n-@SQ\tSN:C12SLm103K8_LR380\tLN:10118\n-@SQ\tSN:C01HBa0003D15_LR7\tLN:10776\n-@SQ\tSN:C01HBa0163B20_LR10\tLN:9321\n-@SQ\tSN:C01HBa0216G16_LR11\tLN:10332\n-@SQ\tSN:C01HBa0256E08_LR13\tLN:9024\n-@SQ\tSN:C01HBa0329A12_LR14\tLN:9536\n-@SQ\tSN:BAC19_LR16\tLN:9760\n-@SQ\tSN:C02HBa0008G02_LR67\tLN:9205\n-@SQ\tSN:C02HBa0011O23_LR68\tLN:9399\n-@SQ\tSN:C02HBa0016A12_LR19\tLN:9822\n-@SQ\tSN:C02HBa0027B01_LR21\tLN:9222\n-@SQ\tSN:C02HBa0030A21_LR22\tLN:9147\n-@SQ\tSN:C02HBa0046M08_LR23\tLN:10763\n-@SQ\tSN:C02HBa0072A04_LR26\tLN:9766\n-@SQ\tSN:C02HBa0075D08_LR28\tLN:10744\n-@SQ\tSN:C02HBa0124N09_LR31\tLN:9335\n-@SQ\tSN:C02HBa0155D20_LR36\tLN:10743\n-@SQ\tSN:C02HBa0155E05_LR37\tLN:10417\n-@SQ\tSN:C02HBa0164H08_LR38\tLN:10279\n-@SQ\tSN:C02HBa0167J21_LR39\tLN:9925\n-@SQ\tSN:C02HBa0185P07_LR40\tLN:9818\n-@SQ\tSN:C02HBa0190N21_LR41\tLN:10835\n-@SQ\tSN:C02HBa0190P16_LR331\tLN:10808\n-@SQ\tSN:C02HBa0194L19_LR42\tLN:10280\n-@SQ\tSN:C02HBa0204A09_LR332\tLN:10029\n-@SQ\tSN:C02HBa0204D01_LR334\tLN:9746\n-@SQ\tSN:C02HBa0214B22_LR325\tLN:9581\n-@SQ\tSN:C02HBa0215M12_LR319\tLN:9918\n-@SQ\tSN:C02HBa0228I09_LR329\tLN:10933\n-@SQ\tSN:C02HBa0236E02_LR326\tLN:9822\n-@SQ\tSN:C02HBa0284G15_LR47\tLN:9034\n-@SQ\tSN:C02HBa0291P19_LR48\tLN:9826\n-@SQ\tSN:C02HBa0329G05_LR52\tLN:9637\n-@SQ\tSN:C02SLe0010H16_LR53\tLN:10744\n-@SQ\tSN:C02SLe0018B07_LR335\tLN:9222\n-@SQ\tSN:C02SLe0034H10_LR327\tLN:10833\n-@SQ\tSN:C02SLe0127J16_LR59\tLN:10965\n-@SQ\tSN:C02SLe0132D01_LR60\tLN:10524\n-@SQ\tSN:C02SLm0057H03_LR336\tLN:9514\n-@SQ\tSN:C02SLm0057H03_LR64\tLN:9170\n-@SQ\tSN:C02SLm0057H03_LR65\tLN:9532\n-@SQ\tSN:C03HBa0012D06_LR72\tLN:10645\n-@SQ\tSN:C03HBa0030O03_LR74\tLN:10569\n-@SQ\tSN:C03HBa0034B23_LR76\tLN:10005\n-@SQ\tSN:C03HBa0040F22_LR77\tLN:10227\n-@SQ\tSN:C03HBa0054O21_LR78\tLN:9044\n-@SQ\tSN:C03HBa0076J13_LR79\tLN:10097\n-@SQ\tSN:C03HBa0233O20_LR82\tLN:9753\n-@SQ\tSN:C03HBa0295I12_LR83\tLN:10258\n-@SQ\tSN:C03HBa0318C22_LR84\tLN:10004\n-@SQ\tSN:C03HBa0323D22_LR85\tLN:9222\n-@SQ\tSN:C04HBa127N12_LR346\tLN:10533\n-@SQ\tSN:C04HBa132O11_LR104\tLN:10306\n-@SQ\tSN:C04HBa164O3_LR344\tLN:9345\n-@SQ\tSN:C04HBa190C13_LR106\tLN:10719\n-@SQ\tSN:C04HBa198I15_LR107\tLN:10673\n-@SQ\tSN:C04HBa219H8_LR109\tLN:10174\n-@SQ\tSN:C04HBa239P14_LR111\tLN:10483\n-@SQ\tSN:C04HBa255I2_LR112\tLN:10650\n-@SQ\tSN:C04HBa27G19_LR337\tLN:9788\n-@SQ\tSN:C04HBa2G1_LR120\tLN:9322\n-@SQ\tSN:C04HBa331L22_LR115\tLN:10697\n-@SQ\tSN:C04HBa35C16_LR339\tLN:9494\n-@SQ\tSN:C04HBa36C23_LR91\tLN:10103\n-@SQ\tSN:C04HBa50I18_LR341\tLN:10825\n-@SQ\tSN:C04HBa58E11_LR93\tLN:9927\n-@SQ\tSN:C04HBa66O12_LR94\tLN:9355\n-@SQ\tSN:C04HBa68N5_LR343\tLN:9886\n-@SQ\tSN:C04HBa6E18_LR87\tLN:9265\n-@SQ\tSN:C04HBa6O16_LR123\tLN:10386\n-@SQ\tSN:C04HBa78E4_LR98\tLN:9994\n-@SQ\tSN:C04HBa78J4_LR99\tLN:9165\n-@SQ\tSN:C04HBa80D3_LR100\tLN:9781\n-@SQ\tSN:C04HBa8K13_LR338\tLN:9345\n-@SQ\tSN:C04HBa96I8_LR101\tLN:9693\n-@SQ\tSN:C04SLm14G22_LR116\tLN:10306\n-@SQ\tSN:C04SLm39E17_LR117\tLN:9105\n-@SQ\tSN:C05HBa0003C20_LR126\tLN:9460\n-@SQ\tSN:C05HBa0006N20_LR128\tLN:101'..b'018B07_LR335,+8208,36M,0;\n-HWI-EAS337_3:7:1:425:1939\t83\tC09SLm0143I09_LR365\t1546\t0\t36M\t=\t1490\t-92\tAAGTTTAGCCACATAGACCCAGACACCACAATTAGC\tUUUUUUWVVVWVVWWWVVVVWWWVWWWWVWWVWWWW\tXT:A:R\tNM:i:0\tSM:i:0\tAM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C09SLe0076N09_LR363,-1546,36M,0;\n-HWI-EAS337_3:7:1:425:1939\t163\tC09SLm0143I09_LR365\t1490\t0\t36M\t=\t1546\t92\tTAACTTTTCTATCTGGTTTCTATGTTTTCCAGCTCT\tWVWWWWWWWWWWWWVVVWWWWWWUVWVWVVTQTTTS\tXT:A:R\tNM:i:0\tSM:i:0\tAM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C09SLm0143I09_LR365,+1490,36M,0;\n-HWI-EAS337_3:7:1:187:1132\t83\tC02SLe0018B07_LR335\t9178\t0\t36M\t=\t9065\t-149\tGAAGAGGATATGAGCCAAGCCCCTTGCCTCTCCCAC\tUUUUUUVVWWWVWVTWWWWWWWWWWWWWWWWWWWVW\tXT:A:R\tNM:i:1\tSM:i:0\tAM:i:0\tX0:i:2\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:14A21\tXA:Z:C02SLe0018B07_LR335,-9178,36M,1;\n-HWI-EAS337_3:7:1:187:1132\t163\tC02SLe0018B07_LR335\t9065\t0\t36M\t=\t9178\t149\tGAATAAAAAAAGACAACAACATATCAAGATACAAAG\tWWWVWVWWWWWVWWVWWWVWWVWWWVWWVWTTTTTR\tXT:A:R\tNM:i:0\tSM:i:0\tAM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C02SLe0018B07_LR335,+9065,36M,0;\n-HWI-EAS337_3:7:1:1739:1840\t99\tC02HBa0072A04_LR26\t2868\t60\t36M\t=\t3189\t357\tGGAGGGGTGAAATCGTTTCTGAAAAATAATGAAATG\tWWVWWWWWWWWWWWWWWVTWWWVVVWWWWWUUUUUU\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1739:1840\t147\tC02HBa0072A04_LR26\t3189\t60\t36M\t=\t2868\t-357\tCTTTTGACCCAAAAGTTTGACGGGAAGGACAGTTTT\tRTTTTTVVVVWWCVWVVWWWVWWWWWWWWWWWWVWW\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:12T23\n-HWI-EAS337_3:7:1:1505:1876\t99\tC07SLe0111B06_LR194\t8673\t60\t36M\t=\t8677\t40\tGAAAGATCAAGTGTTGTCAAGTTCACTAGTTTAGAG\tWWWWWWWWWWWWWWWWWWWWVWWVWWWVVVUUUSUR\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1505:1876\t147\tC07SLe0111B06_LR194\t8677\t60\t36M\t=\t8673\t-40\tGATCAAGTGTTGTCAAGTTCACTAGTTTAGAGAATG\tSTTTTTVVVWVVWVWWWWWVWWWWWWWWWWWWWWWW\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:447:192\t99\tC09SLm0143I09_LR365\t6957\t0\t36M\t=\t7039\t118\tGACTATGCCTAGCAGCTGAAATCACCACAACAAGTT\tWWWWWWWWWWWWWWWTWWWVVWWVWWWWWVUUUUUU\tXT:A:R\tNM:i:0\tSM:i:0\tAM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C09SLm0143I09_LR365,+6957,36M,0;\n-HWI-EAS337_3:7:1:447:192\t147\tC09SLm0143I09_LR365\t7039\t0\t36M\t=\t6957\t-118\tAACTGAACAGATGCCTTTTGGATATGTTTCACTCAC\tSTTTTTWVVWVWWVVVVVWWWVVWVWWWWWVWWWVW\tXT:A:R\tNM:i:0\tSM:i:0\tAM:i:0\tX0:i:2\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\tXA:Z:C09SLe0076N09_LR363,-7039,36M,0;\n-HWI-EAS337_3:7:1:21:2019\t83\tC09SLm0037I08_LR367\t1298\t60\t36M\t=\t955\t-379\tGGGCTGGAAGACAGGTTATCATCTTTTACCTCATAC\tUUURUUWWWVVQWWWWWWWWWWWWWWWVVWWVVWWV\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:21:2019\t163\tC09SLm0037I08_LR367\t955\t60\t36M\t=\t1298\t379\tATTATGTTTACGGGACAATTGTATGTTCCATTATCT\tVWVWWWWWWWWWWWWWWWWWVWVWUWVVWWTTTTTR\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1593:652\t99\tC04HBa8K13_LR338\t2175\t60\t36M\t=\t2226\t87\tGTGATGAGTAAAACATCATCATATGAACTTGAAGAG\tWWWVWVWWVWVWWVWWWWWWVVWWVWWVWWUUUSUU\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:28A7\n-HWI-EAS337_3:7:1:1593:652\t147\tC04HBa8K13_LR338\t2226\t60\t36M\t=\t2175\t-87\tTATGCTTAAAACAAGAGGAATTATACAGCTAAATAA\tSTTTKTWWWWWVWWWWVWVVVWVWWWWWWWVWVVWW\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1254:1660\t99\tC12HBa326K10_LR306\t8100\t60\t36M\t=\t8243\t179\tGAAGTTTGTAATTCCTTTTAGGATTGTGGTTAACAT\tWWWVVWWWWWWWWWWWVWVWVUWWWTWVQWUUUUMU\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:1254:1660\t147\tC12HBa326K10_LR306\t8243\t60\t36M\t=\t8100\t-179\tTGTACATTTTTCCTACCCATATGTGATGCCATTACT\tSTTTTTWVVVVWWVVWWVWWWVWVVWVWVWVWWWVW\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:36\n-HWI-EAS337_3:7:1:291:629\t77\t*\t0\t0\t*\t*\t0\t0\tGTAGAGGAGGTAGGCTTGGTGGTCCCTCTATGGTAA\tWWWWWWWWWWVVVWVWVVWTWWKOVVTRVSUSSMFR\n-HWI-EAS337_3:7:1:291:629\t141\t*\t0\t0\t*\t*\t0\t0\tATGAAGGGTTTTTTTGTTCTCTAATGTCATCTTATT\tWWWWVVWWWWWWWWWVWWVWVWVVVQWVVWTTTTTS\n'

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/inputMapping.map
--- a/SMART/Java/Python/TestFiles/inputMapping.map Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,21 +0,0 @@
-BlastclustCluster1Mb1 dmel 44957 60589
-BlastclustCluster2Mb1 dmel 441296 453986
-BlastclustCluster3Mb1 dmel 1263264 1272001
-BlastclustCluster4Mb1 dmel 691910 700435
-BlastclustCluster5Mb1 dmel 4887 13246
-BlastclustCluster6Mb1 dmel 340294 348412
-BlastclustCluster7Mb1 dmel 802363 809343
-BlastclustCluster8Mb1 dmel 303029 309770
-BlastclustCluster9Mb1 dmel 34275 40713
-BlastclustCluster10Mb1 dmel 976199 981423
-BlastclustCluster11Mb1 dmel 231806 236301
-BlastclustCluster12Mb1 dmel 323712 327988
-BlastclustCluster13Mb1 dmel 1011279 1014955
-BlastclustCluster14Mb1 dmel 474293 477597
-BlastclustCluster15Mb1 dmel 930649 933730
-BlastclustCluster16Mb1 dmel 1241523 1244351
-BlastclustCluster17Mb1 dmel 532049 534729
-BlastclustCluster18Mb1 dmel 335473 337381
-BlastclustCluster19Mb1 dmel 686181 687792
-BlastclustCluster20Mb1 dmel 1239136 1240579
-BlastclustCluster21Mb1 dmel 1261233 1262370

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/mapperAnalyzerExpected.gff3
--- a/SMART/Java/Python/TestFiles/mapperAnalyzerExpected.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
-chr1 test match 6155418 6155441 24 + . Name=test1/1;occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100
-chr2 test match 26303950 26303981 32 + . Name=test2/1;occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93
-chr3 test match 28320540 28320574 35 + . Name=test2/1;occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94
-chr4 test match 28565007 28565041 35 + . Name=test2/1;occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/mapperAnalyzerMappings.axt
--- a/SMART/Java/Python/TestFiles/mapperAnalyzerMappings.axt Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,12 +0,0 @@
-1 chr1 6155418 6155441 test1/1 1 24 + 66
-GTAACAGATTCAGAACATTAGCAG
-GTAACAGATTCAGAACATTAGCAG
-2 chr2 26303950 26303981 test2/1 3 36 + 0
-AT-ATT-AAAAAAAAAAAAAAAAAAAAAAAAAAA
-ATGATTGAAAAAAAAAAAAAAAAAAAAAAAAAAA
-3 chr3 28320540 28320574 test2/1 3 36 + 0
-ATGTTTGACAAAAAAAAAAAAAAAAAAAAAAAAAA
-ATGATTGA-AAAAAAAAAAAAAAAAAAAAAAAAAA
-4 chr4 28565007 28565041 test2/1 1 36 + 0
-ATAAGATT-AAAAAAAAAAAAAAAAAAAAGGAAAAA
-ATATGATTGAAAAAAAAAAAAAAAAAAAAAAAAAAA

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/mapperAnalyzerOutput.gff3
--- a/SMART/Java/Python/TestFiles/mapperAnalyzerOutput.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/mapperAnalyzerSequences.mfq
--- a/SMART/Java/Python/TestFiles/mapperAnalyzerSequences.mfq Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,12 +0,0 @@
-@test1/1
-GTAACAGATTCAGAACATTAGCAG
-+test1/1
-bb`b_bbbbb_bbbbababbbbb^
-@test2/1
-ATATGATTGAAAAAAAAAAAAAAAAAAAAAAAAAAA
-+test2/1
-BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
-@test3/1
-TTTGAATAAAACGGGAGGATATA
-+test3/1
-X^_Y`_____\R^BBBBBBBBBB

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/sorted_file_oneline.gff3
--- a/SMART/Java/Python/TestFiles/sorted_file_oneline.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-chr1 test test2.1 0 1000 1001 + . ID=test2.1;Name=test2.1
\ No newline at end of file

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/sorted_query.gff3
--- a/SMART/Java/Python/TestFiles/sorted_query.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
-chr1 query test1.1 25 150 126 + . ID=query_1;Name=test1.1
-chr1 query test1.2 70 850 781 + . ID=query_2;Name=test1.2
-chr1 query test1.3 550 850 201 + . ID=query_3;Name=test1.3
-chr1 query test1.4 925 1025 101 + . ID=query_4;Name=test1.4
-chr1 query test1.5 1201 1210 10 + . ID=query_5;Name=test1.5
-chr1 query test1.6 1500 1600 101 + . ID=query_6;Name=test1.6

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/sorted_query_wig.wig
--- a/SMART/Java/Python/TestFiles/sorted_query_wig.wig Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1040 +0,0 @@
-track type=wiggle_0 name="SMART"
-variableStep chrom=chr1
-25 1
-26 1
-27 1
-28 1
-29 1
-30 1
-31 1
-32 1
-33 1
-34 1
-35 1
-36 1
-37 1
-38 1
-39 1
-40 1
-41 1
-42 1
-43 1
-44 1
-45 1
-46 1
-47 1
-48 1
-49 1
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diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/sorted_ref.gff3
--- a/SMART/Java/Python/TestFiles/sorted_ref.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,7 +0,0 @@
-chr1 test test2.1 9 1000 1001 + . ID=test2.1;Name=test2.1
-chr1 test test2.2 50 350 301 + . ID=test2.2;Name=test2.2
-chr1 test test2.3 100 600 501 + . ID=test2.3;Name=test2.3
-chr1 test test2.4 200 450 251 + . ID=test2.4;Name=test2.4
-chr1 test test2.5 700 950 251 + . ID=test2.5;Name=test2.5
-chr1 test test2.6 800 900 101 + . ID=test2.6;Name=test2.6
-chr1 test test2.7 1200 1300 101 + . ID=test2.7;Name=test2.7

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testBedParser1.bed
--- a/SMART/Java/Python/TestFiles/testBedParser1.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-track name=reads description="Reads" useScore=0 visibility=full offset=0
-arm_X 1000 3000 test1.1 1000 + 1000 3000 0 2 100,1000, 0,1000,

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testC2S.fa
--- a/SMART/Java/Python/TestFiles/testC2S.fa Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,100 +0,0 @@
->chr1
-CAACATTAGCGCCATGCCCACTGTGGGGAATTTACCAGCAGCCCGCACAC
-TTAGCCGGCCTGCTGCAAAGCGGGATTTATTTAATTCATCCTCCAAGAGC
-CCAAACGAGCATCCTATGAGTTTCTCGGAAGTGGTAGCTGGAGCAGGTCC
-AGTTTCTATGGCACCCCCTAATCCGGCACCACTGACGAAAACCCCAGGAA
-AGCGGACAAACGACGATCTGGATTGCTCAAATTTTAAGACGCCCAATAAA
-AAATTATGCGCGACATCCAATTTTGTAACTCCCTGCATTTTTCCCCCGCT
-CATCACACCAGTTTTCAAAAGCAAGGCAGCTCAATCTGTTTATGAGGAAT
-CAAAAGCCAGAAACGGACCCACCCGCCAGCCGTTACCCTGTAGCATCAAT
-GTCTCTGCTTGCAGCGCAGCGGCGCCACCCGTTATCGCCCCCCTACCCCC
-TCAAAATACAGATGCACAGCTGCCTCCATGGAAAATCGTGCCCCAGAGCC
-GTAGAGCACCCCCTATACTCGTCAATGATGTGAAGGAAATTGTCCCTCTC
-CTGGAAAAGCTAAATTATACAGCAGGAGTATCCAGCTACACCACCAGAGC
-AATAGAAGGAAACGGGGTCAGGATCCAGGCCAAGGATATGACCGCCTACA
-ACAAAATTAAAGAAGTCCTGGTGGCCAACGGATTTCCTTTATTCACCAAC
-CAGCCCAAGTCTGAGAGAGGCTTCCGAGTCATCATCAGACACCTCCATCA
-TTCCACACCATGCTCGTGGATAGTCGAGGAGCTGCTGAAGCTCGGTCTCC
-AAGCGCGCTTCGTCAGAAACATGACGAATCCAGCTACAGGTGGCCCCATG
-CGAATGTTTGAAGTGGAGATCGTCATGGCCAAAGATGGCAGCCACGATAA
-AATTCTCTCACTCAAACAAATCGGTGGGCAAAAGGTGGATATTGAAAGGA
-AAAATAGGACACAGGAGCCGGTTCAGTGCTACAGATGCCAGGGCTTCAGA
-CATGCCAAAAATTCATGCATGAGGACGCCTAAATGCATGAAATGCGCTGG
-CGATCACCTGTCATCCTGCTGCACCAAGCCAAAATCCACCCCCGCCACCT
-GCATCAACTGCTCTGGGGAACATATCAGCGCTTATAAAGGATGCCCCGCC
-TACAAGGCCGAAAAACGAAAGCTGGCGGCTAACATTATTGACACAAACAA
-AATAAGGACAATCAAAGACGCAACTAATCACTTTTATAAACGACAAGGCC
-CCCCTCCACGTAATAATACCCCTCGACTACCGCACAGCTCAGCAATCCTG
-ACCAAGTCAATCGCTGAAGCTCGCCAGGAAGCCGCCAAAAAGTCGATGCT
-AAATCCTTATTGGCAAAGCTCGAACGACAGAAGGCCACGTTTCTCCTCCC
-ATGACACTGCCATTCAAAAACGGCTAAACAAATGGCGCCGAAACTCTAAT
-AAGATACCCAAAAAGGGTAGGATATCCTCAAAGGACAATGCAAAGCCAAG
-ACCGGCATCCAAGACAAGCAACCCAGCGCAAAGACATCTGGAAAAATACC
-AGGACATGCTCCGAAACGAAAGGAGTGAAGAAATTGACCATGAACCTGAA
-AAAGGTACTCCTAATCCCAGCCGAGTCGGCAACGACAGCCCTCCGACCAC
-CAGCAGAGCCGCCAGAGCTAACTTTAAGCCAAGAATTATCGATGAAGCTA
-CGCCATCGCCAAGAAACTCCAATCCTTACCTACAGAAGAGCTTCTCGGAC
-GACCCCACCATTAATCTAGCTAATAGAGTCGATAATTTAGAAAAGAAAAT
-TGACATTTTAATGGCTTTAATCATACAAGGAACCAATAACAATAATCTTG
-ACATTGATACATCAATCTAAATTTACATTACACTTATTTATATTTATACC
-TATTATAAATATATATATCCGACACAAAAGCGCACGTCTGCCCACCCTTA
-TAATGTTCTAATTATTATCACCTTCCTCGACGCAAAGCTTAAACCTCTGT
-TGAAAAACAAATCAATTAGATGGATGACATAAAAACGTAAATAAATAATC
-TTCTCACCTCAAGCATCCGGATAAAAAAGGCAATACGCACTCCAACTCCT
-GATGAAGCTATGTGAAGAAAACTACACCAGGATTCAAAAGTCGAATCGGA
-GGATGGACATGAGAAGAATCTGTGCGGCAGAAGCATGATGAATAGAGGCG
-ACTCGCTGCAGCAAAATATGCACTACGCCACTTACCTGAATCTTCTGCGG
-CGCAGTCTTTTTATGTACCATCATCTCCGCCGCAACCGCTTCACACAGCT
-CCACAACATAAGATGCGCCACCAAAGCTGCCTCCGTACTGAACTGGACAT
-CATGCGTTGCGCTGCAAATCCTATCCTATTGACGAGCGCCAACAGCGGGT
-CTGCGCTAAAAACCTAAAAACAAAACAAAACAAAACAATTAATCAACAAC
-AAATTGAACATAACAATCAAACAATAACAATCACTTACCTCCTTGACTGC
-ATCCAATCGCTGACCCAAATCCAACACAACCGACAACAGGAGACGGGCTT
-CGCAAATGCAAAACAAAATCGCCAACTTTTGCGATTATAAATACAAAAAA
-TTGACAATTTTCTGATGCCATCTCCATCCTTTGATCCCACTGCCCAAATA
-AGGATCATTAGCGCGGAGCTGAAGCCACATTAATAAGCTGTAAAATTGAT
-CCCCAAAATGTATATTTCTCCTCAATACCGTATCTTCAACGAACTTTCCG
-CCAACCTGCAATGAAAGGGAAATTAATAATAATGCTATACAGAATTAATC
-AGCGACACATAGAAAATAGCAAACCAGACAGGCAAAGTAGTAGATGCAAA
-CAGGCGACTCCATCCCGCCGACGACAAGCATTCAAATCCTTCATACTGAA
-ACAAGGAAGCACAAGCCAATACTGGGAATTATTTACTCAAACAAAATACT
-TATCTAATTACCAACTCGACGACTCCAAATACGCGGCACACCGGCTGCGA
-TAGCTCTTAAATAAAGGGCCTCCTAATTAACTACAAAACGTACCTGAAAA
-ATAAAACAATTAACGCAATCGTAAATAATTACAATTATAATACTCACCTC
-CAGATTAGCCTAATGTACCTGAAAAACAAAAACAAAAATTAATGCAATAA
-TTATAAAAACAAATAAATACAAACACAATACTTACCTCCAAATTACCTCC
-CAGCCAAAGCACCTGAAATACAAAAACAAAGAATTAATGCAATAAATAAA
-TCAAATAAATACAAATACAATACTCACCCCAAATAACCTCCCAGCTAATT
-TACCTGAAAAAACAAAAATTAATACAATATTAAAAACGAATAACAAATGT
-AATACTTACCAAATTTTAACTTTGTATTCATTTCCATGGCCCAAATCGTT
-GCGACGGTCCTCGGCAACAAATCATGTTCCGGCGGCTCCTAGCTGCCAAT
-CCCGACGCATTGGCCACAAGACGCGGCGCTCCTGGCAACTCTCGATGAAT
-AACCGAGCTCCAATTTCCACGACGACTCTTCTGCCAAACGAGTCAGATTA
-CACCAACATAATGCCAGCAGCTCCCAAACAATGCAATGACGGCTGCGCGG
-GATCCATCTTCAGATTTTCTTCTTCCTGACGACCGGCTAAGCTGCCCTGC
-AATTTAAGAAATTTTATTAAACAATTGCAAATATCTACCACTGAGGGTGG
-TAGAGACAACCACCAAATGACAGCGGCGCGGGATACACCCACCACGAATA
-GGCTTTCTGCAGCGCTGGCCGGACATGCATGTTGCGACGCGCATTCAGCG
-TCCACAACAAGCCCCAGCCAGAATACAACAAACACTCACCTGCAATGTTT
-CCTGAGGCTTCCAGCGACTCGGTGCTTCCGTCCTTCTGGCGGGGGTACCT
-GAAAAGAATTAATTCAAATTATGTTAGTCTTAAATTCCAATGTTTCTTGT
-TAAATAATTCAAATTATCAAATGTAAACATAACATACAATGTGATAATGT
-TACCAGTCCATGTTACTGCCAAAAACCTAAGTTTACAAAAAAATACTTAC
-CTCTTAATATTAATACTAAATCTATGTCCAATCCCCAAACTCACCCCACG
-TAATGTACACCTCAAAAATTCAAATAATTGTACCTACATATTGCATTCTA
-TGTAATCAAAGGCAAAATAAATTGTGGATGCGGAACAGAATTCATTCTGT
-CTCCGTACCTCCACCAGCAAAGTTAAAAATGAAATATCCCTCATCACCGC
-TGCAATCTACATACATGGATACAGCGCAAAAGACGGTCAACCACGTCGTC
-TCCGAGTCGTTCAGGACACCTTGCTGCTCTCAATAACCTCCAGCCTGACG
-AGCGCCAACAGCGAGTTGACGCTAAAACCTAAAAACAAACAACAACAAAT
-TAAATACAAACAAATAAAATAAAATCAAACAAAACACTTACTTCACTGAC
-AACAGCCAATTGCTGATCCACATTCAACGCAACAGACAACAGGAGACGGG
-CCCCGCAAACGCAAAACAAAATCGCCAATTTTTGCGATTTTAAATACAAA
-AAATCGACAATTTTACTAAGCCCTCTCCATCTCCTGATGCCACCGCCACA
-ATAAGGATCACTAGCGCGGCGCTGATGCCACATCAATAAACCGCAATATT
-TGTCCTCAAAACGTATACTTCTTCTCAGTATCGCAACTTCTACGAATTTC
-CCGCTAACCTACAATGAAAGGAAAATCAATAAGAATGTGATACAAAAAAT
-TAATCAAGGGCAAATAGAAAATAGCTTACCGGACAGGCATACTAGCAGAT
-GCTAATATGCAACTCCATCCTTCTGAGACAAATACGCAACTCCTTTTTTC
-CAAGATTGCAAATACTGAAACAAGGAAGCACAAGCCAATACTGGGAATTA
-TTTAATTAAACAAAATACTTATCTAATTGCCAATTCGACGACTCCAAATC

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testC2S.gff3
--- a/SMART/Java/Python/TestFiles/testC2S.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,3 +0,0 @@
-chr1 S-MART SMART 1 10 . + . Name=region0
-chr1 S-MART SMART 51 60 . + . Name=region1
-chr1 S-MART SMART 51 60 . - . Name=region2

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testCompareTranscriptListDistanceAntisense1.gff3
--- a/SMART/Java/Python/TestFiles/testCompareTranscriptListDistanceAntisense1.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-chr1 test test1.1 1000 2000 1001 + . ID=test1.1;Name=test1.1

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testCompareTranscriptListDistanceAntisense2.gff3
--- a/SMART/Java/Python/TestFiles/testCompareTranscriptListDistanceAntisense2.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-chr1 test test2.1 1500 2500 1001 + . ID=test2.1;Name=test2.1
-chr1 test test2.2 3000 4000 1001 - . ID=test2.2;Name=test2.2

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testCompareTranscriptListDistanceSimple1.gff3
--- a/SMART/Java/Python/TestFiles/testCompareTranscriptListDistanceSimple1.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-chr1 test test1.1 1000 2000 1001 + . ID=test1.1;Name=test1.1

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testCompareTranscriptListDistanceSimple2.gff3
--- a/SMART/Java/Python/TestFiles/testCompareTranscriptListDistanceSimple2.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-chr1 test test2.1 1500 2500 1001 + . ID=test2.1;Name=test2.1
-chr1 test test2.2 3000 4000 1001 + . ID=test2.2;Name=test2.2

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testDifferentialExpressionExpected.gff3
--- a/SMART/Java/Python/TestFiles/testDifferentialExpressionExpected.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-chr1 S-MART S-MART_transcript 100 200 101 + . Name=test3.1;nbReadsCond1=15;regulation=equal;nbReadsCond2=15;pValue=1.0;ID=test3.1
-chr1 S-MART S-MART_transcript 200 300 101 + . Name=test3.2;nbReadsCond1=30;regulation=equal;nbReadsCond2=30;pValue=1.0;ID=test3.2

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testDifferentialExpressionOutput.gff3
--- a/SMART/Java/Python/TestFiles/testDifferentialExpressionOutput.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testDifferentialExpressionReference.gff3
--- a/SMART/Java/Python/TestFiles/testDifferentialExpressionReference.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-chr1 S-MART transcript 100 200 100 + . Name=test3.1
-chr1 S-MART transcript 200 300 100 + . Name=test3.2

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testDifferentialExpressionSample1.gff3
--- a/SMART/Java/Python/TestFiles/testDifferentialExpressionSample1.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-chr1 S-MART S-MART_transcript 100 200 100 + . Name=test1.1;nbElements=10
-chr1 S-MART S-MART_transcript 200 300 100 + . Name=test1.2;nbElements=20

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testDifferentialExpressionSample2.gff3
--- a/SMART/Java/Python/TestFiles/testDifferentialExpressionSample2.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-chr1 S-MART S-MART_transcript 100 200 100 + . Name=test2.1;nbElements=20
-chr1 S-MART S-MART_transcript 200 300 100 + . Name=test2.2;nbElements=40

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testGffParser1.gff3
--- a/SMART/Java/Python/TestFiles/testGffParser1.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,7 +0,0 @@
-arm_X test test_transcript 1000 2000 1 + . ID=id1-1;Name=test1;field=value1
-arm_X test test_exon 1000 2000 1 + . ID=id1-1-exon1;Name=test1-exon1;Parent=id1-1
-arm_X test test_transcript 10000 20000 1 - . ID=id2-1;Name=test2;field=value2
-arm_X test test_exon 10000 10100 1 - . ID=id2-1-exon1;Name=test2-exon1;Parent=id2-1
-arm_X test test_exon 10500 20000 1 - . ID=id2-1-exon2;Name=test2-exon2;Parent=id2-1
-arm_X test test_transcript 1000 2000 1 + . ID=test1.1-1;Name=test1.1
-arm_X test test_exon 1000 2000 1 + . ID=test1.1-1-exon1;Name=test1.1-exon1;Parent=test1.1-1

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testPlot.gff3
--- a/SMART/Java/Python/TestFiles/testPlot.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
-chr1 S-MART SMART 100 200 . + . value2=6;value3=1
-chr1 S-MART SMART 200 300 . + . value1=2;value2=5;value3=2
-chr1 S-MART SMART 300 400 . + . value1=3;value2=4;value3=3
-chr1 S-MART SMART 400 500 . + . value1=4;value2=3;value3=4
-chr1 S-MART SMART 500 600 . + . value1=5;value2=2;value3=5
-chr1 S-MART SMART 600 700 . + . value1=6;value3=6

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testSW.gff3
--- a/SMART/Java/Python/TestFiles/testSW.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
-chr1 S-MART SMART 101 111 . + . value1=1
-chr1 S-MART SMART 111 121 . + . value1=2
-chr1 S-MART SMART 201 211 . + . value1=10
-chr1 S-MART SMART 211 221 . + . value1=12

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptList1.bed
--- a/SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptList1.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
-arm_X 1000 2000 test1.1 1000 + 1000 2000 0 1 1000, 0,
-arm_X 1000 2000 test1.2 1000 - 1000 2000 0 1 1000, 0,
-arm_X 100 200 test1.3 1000 + 100 200 0 1 100, 0,
-arm_X 100 3200 test1.4 1000 + 100 3200 0 2 100,100, 0,3000,

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptList2.bed
--- a/SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptList2.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-arm_X 1000 2000 test2.1 1000 + 1000 2000 0 1 1000, 0,

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListGetDifference1.gff3
--- a/SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListGetDifference1.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-arm_X test test_transcript 1000 4000 1 + . ID=id1-1;Name=test1;field=value1;nbElements=2

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListGetDifference2.gff3
--- a/SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListGetDifference2.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-arm_X test test_transcript 2000 3000 1 + . ID=id2;Name=test2;field=value1

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeAggregation1.bed
--- a/SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeAggregation1.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-arm_X 10000100 10000200 test1.1 100 - 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.2 100 - 10000000 10000100 0 1 100, 0,

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeAggregation2.bed
--- a/SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeAggregation2.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-arm_X 10000050 10000150 test2.1 100 - 10000050 10000150 0 1 100, 0,

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeSenseAntiSenseAway1.bed
--- a/SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeSenseAntiSenseAway1.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,7 +0,0 @@
-arm_X 10000100 10000200 test1.1 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000100 10000200 test1.2 100 - 10000100 10000200 0 1 100, 0,
-arm_2R 10000100 10000200 test1.3 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.4 100 + 10000000 10000100 0 1 100, 0,
-arm_X 10000200 10000300 test1.5 100 + 10000200 10000300 0 1 100, 0,
-arm_X 9999900 9999950 test1.6 100 + 9999900 9999950 0 1 50, 0,
-arm_X 10000000 10000050 test1.7 100 - 10000000 10000050 0 1 50, 0,
\ No newline at end of file

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeSenseAntiSenseAway1_modif.bed
--- a/SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeSenseAntiSenseAway1_modif.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,112 +0,0 @@
-arm_X 10000100 10000200 test1.1 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000100 10000200 test1.2 100 - 10000100 10000200 0 1 100, 0,
-arm_2R 10000100 10000200 test1.3 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.4 100 + 10000000 10000100 0 1 100, 0,
-arm_X 10000200 10000300 test1.5 100 + 10000200 10000300 0 1 100, 0,
-arm_X 9999900 9999950 test1.6 100 + 9999900 9999950 0 1 50, 0,
-arm_X 10000000 10000050 test1.7 100 - 10000000 10000050 0 1 50, 0,
-arm_X 10000100 10000200 test1.1 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000100 10000200 test1.2 100 - 10000100 10000200 0 1 100, 0,
-arm_2R 10000100 10000200 test1.3 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.4 100 + 10000000 10000100 0 1 100, 0,
-arm_X 10000200 10000300 test1.5 100 + 10000200 10000300 0 1 100, 0,
-arm_X 9999900 9999950 test1.6 100 + 9999900 9999950 0 1 50, 0,
-arm_X 10000000 10000050 test1.7 100 - 10000000 10000050 0 1 50, 0,
-arm_X 10000100 10000200 test1.1 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000100 10000200 test1.2 100 - 10000100 10000200 0 1 100, 0,
-arm_2R 10000100 10000200 test1.3 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.4 100 + 10000000 10000100 0 1 100, 0,
-arm_X 10000200 10000300 test1.5 100 + 10000200 10000300 0 1 100, 0,
-arm_X 9999900 9999950 test1.6 100 + 9999900 9999950 0 1 50, 0,
-arm_X 10000000 10000050 test1.7 100 - 10000000 10000050 0 1 50, 0,
-arm_X 10000100 10000200 test1.1 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000100 10000200 test1.2 100 - 10000100 10000200 0 1 100, 0,
-arm_2R 10000100 10000200 test1.3 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.4 100 + 10000000 10000100 0 1 100, 0,
-arm_X 10000200 10000300 test1.5 100 + 10000200 10000300 0 1 100, 0,
-arm_X 9999900 9999950 test1.6 100 + 9999900 9999950 0 1 50, 0,
-arm_X 10000000 10000050 test1.7 100 - 10000000 10000050 0 1 50, 0,
-arm_X 10000100 10000200 test1.1 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000100 10000200 test1.2 100 - 10000100 10000200 0 1 100, 0,
-arm_2R 10000100 10000200 test1.3 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.4 100 + 10000000 10000100 0 1 100, 0,
-arm_X 10000200 10000300 test1.5 100 + 10000200 10000300 0 1 100, 0,
-arm_X 9999900 9999950 test1.6 100 + 9999900 9999950 0 1 50, 0,
-arm_X 10000000 10000050 test1.7 100 - 10000000 10000050 0 1 50, 0,
-arm_X 10000100 10000200 test1.1 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000100 10000200 test1.2 100 - 10000100 10000200 0 1 100, 0,
-arm_2R 10000100 10000200 test1.3 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.4 100 + 10000000 10000100 0 1 100, 0,
-arm_X 10000200 10000300 test1.5 100 + 10000200 10000300 0 1 100, 0,
-arm_X 9999900 9999950 test1.6 100 + 9999900 9999950 0 1 50, 0,
-arm_X 10000000 10000050 test1.7 100 - 10000000 10000050 0 1 50, 0,
-arm_X 10000100 10000200 test1.1 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000100 10000200 test1.2 100 - 10000100 10000200 0 1 100, 0,
-arm_2R 10000100 10000200 test1.3 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.4 100 + 10000000 10000100 0 1 100, 0,
-arm_X 10000200 10000300 test1.5 100 + 10000200 10000300 0 1 100, 0,
-arm_X 9999900 9999950 test1.6 100 + 9999900 9999950 0 1 50, 0,
-arm_X 10000000 10000050 test1.7 100 - 10000000 10000050 0 1 50, 0,
-arm_X 10000100 10000200 test1.1 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000100 10000200 test1.2 100 - 10000100 10000200 0 1 100, 0,
-arm_2R 10000100 10000200 test1.3 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.4 100 + 10000000 10000100 0 1 100, 0,
-arm_X 10000200 10000300 test1.5 100 + 10000200 10000300 0 1 100, 0,
-arm_X 9999900 9999950 test1.6 100 + 9999900 9999950 0 1 50, 0,
-arm_X 10000000 10000050 test1.7 100 - 10000000 10000050 0 1 50, 0,
-arm_X 10000100 10000200 test1.1 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000100 10000200 test1.2 100 - 10000100 10000200 0 1 100, 0,
-arm_2R 10000100 10000200 test1.3 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.4 100 + 10000000 10000100 0 1 100, 0,
-arm_X 10000200 10000300 test1.5 100 + 10000200 10000300 0 1 100, 0,
-arm_X 9999900 9999950 test1.6 100 + 9999900 9999950 0 1 50, 0,
-arm_X 10000000 10000050 test1.7 100 - 10000000 10000050 0 1 50, 0,
-arm_X 10000100 10000200 test1.1 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000100 10000200 test1.2 100 - 10000100 10000200 0 1 100, 0,
-arm_2R 10000100 10000200 test1.3 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.4 100 + 10000000 10000100 0 1 100, 0,
-arm_X 10000200 10000300 test1.5 100 + 10000200 10000300 0 1 100, 0,
-arm_X 9999900 9999950 test1.6 100 + 9999900 9999950 0 1 50, 0,
-arm_X 10000000 10000050 test1.7 100 - 10000000 10000050 0 1 50, 0,
-arm_X 10000100 10000200 test1.1 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000100 10000200 test1.2 100 - 10000100 10000200 0 1 100, 0,
-arm_2R 10000100 10000200 test1.3 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.4 100 + 10000000 10000100 0 1 100, 0,
-arm_X 10000200 10000300 test1.5 100 + 10000200 10000300 0 1 100, 0,
-arm_X 9999900 9999950 test1.6 100 + 9999900 9999950 0 1 50, 0,
-arm_X 10000000 10000050 test1.7 100 - 10000000 10000050 0 1 50, 0,
-arm_X 10000100 10000200 test1.1 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000100 10000200 test1.2 100 - 10000100 10000200 0 1 100, 0,
-arm_2R 10000100 10000200 test1.3 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.4 100 + 10000000 10000100 0 1 100, 0,
-arm_X 10000200 10000300 test1.5 100 + 10000200 10000300 0 1 100, 0,
-arm_X 9999900 9999950 test1.6 100 + 9999900 9999950 0 1 50, 0,
-arm_X 10000000 10000050 test1.7 100 - 10000000 10000050 0 1 50, 0,
-arm_X 10000100 10000200 test1.1 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000100 10000200 test1.2 100 - 10000100 10000200 0 1 100, 0,
-arm_2R 10000100 10000200 test1.3 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.4 100 + 10000000 10000100 0 1 100, 0,
-arm_X 10000200 10000300 test1.5 100 + 10000200 10000300 0 1 100, 0,
-arm_X 9999900 9999950 test1.6 100 + 9999900 9999950 0 1 50, 0,
-arm_X 10000000 10000050 test1.7 100 - 10000000 10000050 0 1 50, 0,
-arm_X 10000100 10000200 test1.1 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000100 10000200 test1.2 100 - 10000100 10000200 0 1 100, 0,
-arm_2R 10000100 10000200 test1.3 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.4 100 + 10000000 10000100 0 1 100, 0,
-arm_X 10000200 10000300 test1.5 100 + 10000200 10000300 0 1 100, 0,
-arm_X 9999900 9999950 test1.6 100 + 9999900 9999950 0 1 50, 0,
-arm_X 10000000 10000050 test1.7 100 - 10000000 10000050 0 1 50, 0,
-arm_X 10000100 10000200 test1.1 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000100 10000200 test1.2 100 - 10000100 10000200 0 1 100, 0,
-arm_2R 10000100 10000200 test1.3 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.4 100 + 10000000 10000100 0 1 100, 0,
-arm_X 10000200 10000300 test1.5 100 + 10000200 10000300 0 1 100, 0,
-arm_X 9999900 9999950 test1.6 100 + 9999900 9999950 0 1 50, 0,
-arm_X 10000000 10000050 test1.7 100 - 10000000 10000050 0 1 50, 0,
-arm_X 10000100 10000200 test1.1 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000100 10000200 test1.2 100 - 10000100 10000200 0 1 100, 0,
-arm_2R 10000100 10000200 test1.3 100 + 10000100 10000200 0 1 100, 0,
-arm_X 10000000 10000100 test1.4 100 + 10000000 10000100 0 1 100, 0,
-arm_X 10000200 10000300 test1.5 100 + 10000200 10000300 0 1 100, 0,
-arm_X 9999900 9999950 test1.6 100 + 9999900 9999950 0 1 50, 0,
-arm_X 10000000 10000050 test1.7 100 - 10000000 10000050 0 1 50, 0,

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeSenseAntiSenseAway2.bed
--- a/SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeSenseAntiSenseAway2.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-arm_X 10000000 10000050 test2.1 50 - 10000000 10000050 0 1 50, 0,
-arm_3R 10000000 10000050 test2.2 50 - 10000000 10000050 0 1 50, 0,
\ No newline at end of file

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeSimple1.bed
--- a/SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeSimple1.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-arm_X 1000 3000 test1.1 1000 + 1000 3000 0 1 2000, 0,

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeSimple2.bed
--- a/SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListMergeSimple2.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-arm_X 2000 4000 test1.2 1000 + 2000 4000 0 1 2000, 0,

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListSelfMerge1.gff3
--- a/SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListSelfMerge1.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
-arm_X test test_transcript 1000 2000 1 + . ID=id1-1;Name=test1;field=value1;nbElements=2
-arm_X test test_exon 1000 2000 1 + . ID=id1-1-exon1;Name=test1-exon1;Parent=id1-1
-arm_X test test_transcript 1000 2000 1 + . ID=id2-1;Name=test2;field=value2
-arm_X test test_exon 1000 2000 1 + . ID=id2-1-exon1;Name=test2-exon1;Parent=id2-1

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListSelfMergeDifferentClusters1.bed
--- a/SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListSelfMergeDifferentClusters1.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-arm_X 1010 1110 test1.1 1000 + 1010 1110 0 1 100, 0,
-arm_X 100 100100 test1.2 1000 + 100 100100 0 1 100000, 0,

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListSelfMergeSense1.bed
--- a/SMART/Java/Python/TestFiles/testTranscriptListsComparatorCompareTranscriptListSelfMergeSense1.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-arm_X 1000 6000 test1.1 1000 + 1000 6000 0 2 1000,1000, 0,4000,
-arm_X 1000 4000 test1.2 1000 + 1000 4000 0 2 1000,1000, 0,2000,

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/testTranscriptNormalize.gff3
--- a/SMART/Java/Python/TestFiles/testTranscriptNormalize.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-chr1 S-MART transcript 1000 2000 1000 + . Name=test1;nbOccurrences=2
-chr1 S-MART transcript 1500 2500 1000 + . Name=test2;nbOccurrences=2

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/test_distance.bed
--- a/SMART/Java/Python/TestFiles/test_distance.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,3 +0,0 @@
-arm_X 1000 2000 test2.1 1000 + 1000 2000 0 1 1000, 0,
-arm_X 250 350 test2.2 1000 + 250 350 0 1 100, 0,
-arm_X 150 250 test2.3 1000 + 150 250 0 1 100, 0,

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/TestFiles/test_minoverlapp.bed
--- a/SMART/Java/Python/TestFiles/test_minoverlapp.bed Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
-track name=reads description="Reads" useScore=0 visibility=full offset=0
-arm_X 1000 2000 test1.1 1000 + 1000 2000 0 1 1000, 0,
-arm_X 1000 2000 test1.2 1000 - 1000 2000 0 1 1000, 0,
-arm_X 100 200 test1.3 1000 + 100 200 0 1 100, 0,
-arm_X 100 3200 test1.4 1000 + 100 3200 0 2 100,100, 0,3000,
-arm_X 1500 2000 test1.5 1000 + 1500 2000 0 1 500, 0,

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/__init__.pyc

Binary file SMART/Java/Python/__init__.pyc has changed

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/cleanGff.pyc

Binary file SMART/Java/Python/cleanGff.pyc has changed

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/genes.gtf
--- a/SMART/Java/Python/genes.gtf Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,27989 +0,0 @@\n-I\tprotein_coding\tCDS\t335\t646\t.\t+\t0\tgene_id "YAL069W"; transcript_id "YAL069W"; exon_number "1"; gene_name "YAL069W"; p_id "P1273"; protein_id "YAL069W"; transcript_name "YAL069W"; tss_id "TSS1127";\n-I\tprotein_coding\texon\t335\t649\t.\t+\t.\tgene_id "YAL069W"; transcript_id "YAL069W"; exon_number "1"; gene_name "YAL069W"; p_id "P1273"; seqedit "false"; transcript_name "YAL069W"; tss_id "TSS1127";\n-I\tprotein_coding\tstart_codon\t335\t337\t.\t+\t0\tgene_id "YAL069W"; transcript_id "YAL069W"; exon_number "1"; gene_name "YAL069W"; p_id "P1273"; transcript_name "YAL069W"; tss_id "TSS1127";\n-I\tprotein_coding\tCDS\t538\t789\t.\t+\t0\tgene_id "YAL068W-A"; transcript_id "YAL068W-A"; exon_number "1"; gene_name "YAL068W-A"; p_id "P3278"; protein_id "YAL068W-A"; transcript_name "YAL068W-A"; tss_id "TSS5440";\n-I\tprotein_coding\texon\t538\t792\t.\t+\t.\tgene_id "YAL068W-A"; transcript_id "YAL068W-A"; exon_number "1"; gene_name "YAL068W-A"; p_id "P3278"; seqedit "false"; transcript_name "YAL068W-A"; tss_id "TSS5440";\n-I\tprotein_coding\tstart_codon\t538\t540\t.\t+\t0\tgene_id "YAL068W-A"; transcript_id "YAL068W-A"; exon_number "1"; gene_name "YAL068W-A"; p_id "P3278"; transcript_name "YAL068W-A"; tss_id "TSS5440";\n-I\tprotein_coding\tstop_codon\t647\t649\t.\t+\t0\tgene_id "YAL069W"; transcript_id "YAL069W"; exon_number "1"; gene_name "YAL069W"; p_id "P1273"; transcript_name "YAL069W"; tss_id "TSS1127";\n-I\tprotein_coding\tstop_codon\t790\t792\t.\t+\t0\tgene_id "YAL068W-A"; transcript_id "YAL068W-A"; exon_number "1"; gene_name "YAL068W-A"; p_id "P3278"; transcript_name "YAL068W-A"; tss_id "TSS5440";\n-I\tprotein_coding\texon\t1807\t2169\t.\t-\t.\tgene_id "YAL068C"; transcript_id "YAL068C"; exon_number "1"; gene_name "PAU8"; p_id "P3469"; seqedit "false"; transcript_name "PAU8"; tss_id "TSS248";\n-I\tprotein_coding\tstop_codon\t1807\t1809\t.\t-\t0\tgene_id "YAL068C"; transcript_id "YAL068C"; exon_number "1"; gene_name "PAU8"; p_id "P3469"; transcript_name "PAU8"; tss_id "TSS248";\n-I\tprotein_coding\tCDS\t1810\t2169\t.\t-\t0\tgene_id "YAL068C"; transcript_id "YAL068C"; exon_number "1"; gene_name "PAU8"; p_id "P3469"; protein_id "YAL068C"; transcript_name "PAU8"; tss_id "TSS248";\n-I\tprotein_coding\tstart_codon\t2167\t2169\t.\t-\t0\tgene_id "YAL068C"; transcript_id "YAL068C"; exon_number "1"; gene_name "PAU8"; p_id "P3469"; transcript_name "PAU8"; tss_id "TSS248";\n-I\tprotein_coding\tCDS\t2480\t2704\t.\t+\t0\tgene_id "YAL067W-A"; transcript_id "YAL067W-A"; exon_number "1"; gene_name "YAL067W-A"; p_id "P5000"; protein_id "YAL067W-A"; transcript_name "YAL067W-A"; tss_id "TSS1247";\n-I\tprotein_coding\texon\t2480\t2707\t.\t+\t.\tgene_id "YAL067W-A"; transcript_id "YAL067W-A"; exon_number "1"; gene_name "YAL067W-A"; p_id "P5000"; seqedit "false"; transcript_name "YAL067W-A"; tss_id "TSS1247";\n-I\tprotein_coding\tstart_codon\t2480\t2482\t.\t+\t0\tgene_id "YAL067W-A"; transcript_id "YAL067W-A"; exon_number "1"; gene_name "YAL067W-A"; p_id "P5000"; transcript_name "YAL067W-A"; tss_id "TSS1247";\n-I\tprotein_coding\tstop_codon\t2705\t2707\t.\t+\t0\tgene_id "YAL067W-A"; transcript_id "YAL067W-A"; exon_number "1"; gene_name "YAL067W-A"; p_id "P5000"; transcript_name "YAL067W-A"; tss_id "TSS1247";\n-I\tprotein_coding\texon\t7235\t9016\t.\t-\t.\tgene_id "YAL067C"; transcript_id "YAL067C"; exon_number "1"; gene_name "SEO1"; p_id "P6606"; seqedit "false"; transcript_name "SEO1"; tss_id "TSS5465";\n-I\tprotein_coding\tstop_codon\t7235\t7237\t.\t-\t0\tgene_id "YAL067C"; transcript_id "YAL067C"; exon_number "1"; gene_name "SEO1"; p_id "P6606"; transcript_name "SEO1"; tss_id "TSS5465";\n-I\tprotein_coding\tCDS\t7238\t9016\t.\t-\t0\tgene_id "YAL067C"; transcript_id "YAL067C"; exon_number "1"; gene_name "SEO1"; p_id "P6606"; protein_id "YAL067C"; transcript_name "SEO1"; tss_id "TSS5465";\n-I\tprotein_coding\tstart_codon\t9014\t9016\t.\t-\t0\tgene_id "YAL067C"; transcript_id "YAL067C"; exon_number "1"; gene_name "SEO1"; p_id "P6606"; transcript_name "SEO1"; tss_id "TSS5465";\n-I\tprotein_coding\tCDS\t10091\t10396\t.\t+\t0\tgene_id "YAL066W"; transcript_id "YAL066W"; exon_number "1"; gene_name "YAL066W"; p_'..b'203";\n-XVI\tprotein_coding\tstart_codon\t939922\t939924\t.\t+\t0\tgene_id "YPR201W"; transcript_id "YPR201W"; exon_number "1"; gene_name "ARR3"; p_id "P1664"; transcript_name "ARR3"; tss_id "TSS5203";\n-XVI\tprotein_coding\tstop_codon\t941134\t941136\t.\t+\t0\tgene_id "YPR201W"; transcript_id "YPR201W"; exon_number "1"; gene_name "ARR3"; p_id "P1664"; transcript_name "ARR3"; tss_id "TSS5203";\n-XVI\tprotein_coding\tCDS\t943032\t943050\t.\t+\t0\tgene_id "YPR202W"; transcript_id "YPR202W"; exon_number "1"; gene_name "YPR202W"; p_id "P3577"; protein_id "YPR202W"; transcript_name "YPR202W"; tss_id "TSS6873";\n-XVI\tprotein_coding\texon\t943032\t943050\t.\t+\t.\tgene_id "YPR202W"; transcript_id "YPR202W"; exon_number "1"; gene_name "YPR202W"; p_id "P3577"; seqedit "false"; transcript_name "YPR202W"; tss_id "TSS6873";\n-XVI\tprotein_coding\tstart_codon\t943032\t943034\t.\t+\t0\tgene_id "YPR202W"; transcript_id "YPR202W"; exon_number "1"; gene_name "YPR202W"; p_id "P3577"; transcript_name "YPR202W"; tss_id "TSS6873";\n-XVI\tprotein_coding\tCDS\t943199\t943893\t.\t+\t1\tgene_id "YPR202W"; transcript_id "YPR202W"; exon_number "2"; gene_name "YPR202W"; p_id "P3577"; protein_id "YPR202W"; transcript_name "YPR202W"; tss_id "TSS6873";\n-XVI\tprotein_coding\texon\t943199\t943896\t.\t+\t.\tgene_id "YPR202W"; transcript_id "YPR202W"; exon_number "2"; gene_name "YPR202W"; p_id "P3577"; seqedit "false"; transcript_name "YPR202W"; tss_id "TSS6873";\n-XVI\tprotein_coding\tCDS\t943880\t944185\t.\t+\t0\tgene_id "YPR203W"; transcript_id "YPR203W"; exon_number "1"; gene_name "YPR203W"; p_id "P4951"; protein_id "YPR203W"; transcript_name "YPR203W"; tss_id "TSS2481";\n-XVI\tprotein_coding\texon\t943880\t944188\t.\t+\t.\tgene_id "YPR203W"; transcript_id "YPR203W"; exon_number "1"; gene_name "YPR203W"; p_id "P4951"; seqedit "false"; transcript_name "YPR203W"; tss_id "TSS2481";\n-XVI\tprotein_coding\tstart_codon\t943880\t943882\t.\t+\t0\tgene_id "YPR203W"; transcript_id "YPR203W"; exon_number "1"; gene_name "YPR203W"; p_id "P4951"; transcript_name "YPR203W"; tss_id "TSS2481";\n-XVI\tprotein_coding\tstop_codon\t943894\t943896\t.\t+\t0\tgene_id "YPR202W"; transcript_id "YPR202W"; exon_number "2"; gene_name "YPR202W"; p_id "P3577"; transcript_name "YPR202W"; tss_id "TSS6873";\n-XVI\tprotein_coding\tstop_codon\t944186\t944188\t.\t+\t0\tgene_id "YPR203W"; transcript_id "YPR203W"; exon_number "1"; gene_name "YPR203W"; p_id "P4951"; transcript_name "YPR203W"; tss_id "TSS2481";\n-XVI\tprotein_coding\tCDS\t944603\t947698\t.\t+\t0\tgene_id "YPR204W"; transcript_id "YPR204W"; exon_number "1"; gene_name "YPR204W"; p_id "P2697"; protein_id "YPR204W"; transcript_name "YPR204W"; tss_id "TSS839";\n-XVI\tprotein_coding\texon\t944603\t947701\t.\t+\t.\tgene_id "YPR204W"; transcript_id "YPR204W"; exon_number "1"; gene_name "YPR204W"; p_id "P2697"; seqedit "false"; transcript_name "YPR204W"; tss_id "TSS839";\n-XVI\tprotein_coding\tstart_codon\t944603\t944605\t.\t+\t0\tgene_id "YPR204W"; transcript_id "YPR204W"; exon_number "1"; gene_name "YPR204W"; p_id "P2697"; transcript_name "YPR204W"; tss_id "TSS839";\n-XVI\tprotein_coding\texon\t946856\t947338\t.\t-\t.\tgene_id "YPR204C-A"; transcript_id "YPR204C-A"; exon_number "1"; gene_name "YPR204C-A"; p_id "P6072"; seqedit "false"; transcript_name "YPR204C-A"; tss_id "TSS5621";\n-XVI\tprotein_coding\tstop_codon\t946856\t946858\t.\t-\t0\tgene_id "YPR204C-A"; transcript_id "YPR204C-A"; exon_number "1"; gene_name "YPR204C-A"; p_id "P6072"; transcript_name "YPR204C-A"; tss_id "TSS5621";\n-XVI\tprotein_coding\tCDS\t946859\t947338\t.\t-\t0\tgene_id "YPR204C-A"; transcript_id "YPR204C-A"; exon_number "1"; gene_name "YPR204C-A"; p_id "P6072"; protein_id "YPR204C-A"; transcript_name "YPR204C-A"; tss_id "TSS5621";\n-XVI\tprotein_coding\tstart_codon\t947336\t947338\t.\t-\t0\tgene_id "YPR204C-A"; transcript_id "YPR204C-A"; exon_number "1"; gene_name "YPR204C-A"; p_id "P6072"; transcript_name "YPR204C-A"; tss_id "TSS5621";\n-XVI\tprotein_coding\tstop_codon\t947699\t947701\t.\t+\t0\tgene_id "YPR204W"; transcript_id "YPR204W"; exon_number "1"; gene_name "YPR204W"; p_id "P2697"; transcript_name "YPR204W"; tss_id "TSS839";\n'

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/getRandomRegions.pyc

Binary file SMART/Java/Python/getRandomRegions.pyc has changed

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/MockGetLetterDistribution.py
--- a/SMART/Java/Python/test/MockGetLetterDistribution.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,69 +0,0 @@
-class MockGetLetterDistributionFasta (object) :
- def write(self,inFileName):
- f = open(inFileName,'w')
- f.write('>HWI-EAS337_3:7:1:415:1217/1\n')
- f.write('GATGTGCAGACTTTTCACGCAGGACTACATCACTGT\n')
- f.write('>HWI-EAS337_3:7:1:208:1489/1\n')
- f.write('GGAAACATATGCACATAAACGTTGAAATCATGCTTA\n')
- f.write('>HWI-EAS337_3:7:1:278:1153\n')
- f.write('GAGAAAACCTGTAATAAATACTGAGAGAAAGTAGGG\n')
- f.close()
-
-class MockGetLetterDistributionFastq (object) :
- def write(self,inFileName):
- f = open(inFileName,'w')
- f.write('@HWI-EAS337_3:7:1:415:1217/1\n')
- f.write('GATGTGCAGACTTTTCACGCAGGACTACATCACTGT\n')
- f.write('+HWI-EAS337_3:7:1:415:1217/1\n')
- f.write('WWWVVVWPWWWVWWWWVVVVKVPWWVVWVWUUQUTQ\n')
- f.write('@HWI-EAS337_3:7:1:208:1489/1\n')
- f.write('GGAAACATATGCACATAAACGTTGAAATCATGCTTA\n')
- f.write('+HWI-EAS337_3:7:1:208:1489/1\n')
- f.write('WWWWWWWWWWWWWWWWWVWWVWWVWWWWWWUUUUUU\n')
- f.write('@HWI-EAS337_3:7:1:278:1153/1\n')
- f.write('GAGAAAACCTGTAATAAATACTGAGAGAAAGTAGGG\n')
- f.write('+HWI-EAS337_3:7:1:278:1153/1\n')
- f.write('WWWWWWWWWWWWWWWWWWWWWWVWVVVWWVUUUUUR\n')
- f.close()
-
-class MockGetLetterDistributionExpectedCSV (object) :
- def write(self,inFileName):
- f = open(inFileName,'w')
- f.write('1;A=0%;C=0%;T=0%;G=0%;\n')
- f.write('2;A=0%;C=0%;T=0%;G=100.00%;\n')
- f.write('3;A=66.67%;C=0%;T=0%;G=33.33%;\n')
- f.write('4;A=33.33%;C=0%;T=33.33%;G=33.33%;\n')
- f.write('5;A=66.67%;C=0%;T=0%;G=33.33%;\n')
- f.write('6;A=66.67%;C=0%;T=33.33%;G=0%;\n')
- f.write('7;A=33.33%;C=33.33%;T=0%;G=33.33%;\n')
- f.write('8;A=66.67%;C=33.33%;T=0%;G=0%;\n')
- f.write('9;A=33.33%;C=33.33%;T=33.33%;G=0%;\n')
- f.write('10;A=33.33%;C=33.33%;T=0%;G=33.33%;\n')
- f.write('11;A=33.33%;C=0%;T=66.67%;G=0%;\n')
- f.write('12;A=0%;C=33.33%;T=0%;G=66.67%;\n')
- f.write('13;A=0%;C=33.33%;T=66.67%;G=0%;\n')
- f.write('14;A=66.67%;C=0%;T=33.33%;G=0%;\n')
- f.write('15;A=33.33%;C=33.33%;T=33.33%;G=0%;\n')
- f.write('16;A=33.33%;C=0%;T=66.67%;G=0%;\n')
- f.write('17;A=33.33%;C=33.33%;T=33.33%;G=0%;\n')
- f.write('18;A=100.00%;C=0%;T=0%;G=0%;\n')
- f.write('19;A=66.67%;C=33.33%;T=0%;G=0%;\n')
- f.write('20;A=33.33%;C=0%;T=33.33%;G=33.33%;\n')
- f.write('21;A=33.33%;C=66.67%;T=0%;G=0%;\n')
- f.write('22;A=33.33%;C=33.33%;T=0%;G=33.33%;\n')
- f.write('23;A=0%;C=0%;T=66.67%;G=33.33%;\n')
- f.write('24;A=0%;C=0%;T=33.33%;G=66.67%;\n')
- f.write('25;A=66.67%;C=0%;T=0%;G=33.33%;\n')
- f.write('26;A=33.33%;C=33.33%;T=0%;G=33.33%;\n')
- f.write('27;A=66.67%;C=0%;T=33.33%;G=0%;\n')
- f.write('28;A=66.67%;C=0%;T=0%;G=33.33%;\n')
- f.write('29;A=33.33%;C=33.33%;T=33.33%;G=0%;\n')
- f.write('30;A=66.67%;C=33.33%;T=0%;G=0%;\n')
- f.write('31;A=66.67%;C=0%;T=33.33%;G=0%;\n')
- f.write('32;A=0%;C=33.33%;T=33.33%;G=33.33%;\n')
- f.write('33;A=33.33%;C=0%;T=33.33%;G=33.33%;\n')
- f.write('34;A=33.33%;C=66.67%;T=0%;G=0%;\n')
- f.write('35;A=0%;C=0%;T=66.67%;G=33.33%;\n')
- f.write('36;A=0%;C=0%;T=33.33%;G=66.67%;\n')
- f.close()
-

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_Clusterize.py
--- a/SMART/Java/Python/test/Test_F_Clusterize.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,119 +0,0 @@\n-import unittest\n-import os, os.path\n-from optparse import OptionParser\n-from SMART.Java.Python.misc import Utils\n-from SMART.Java.Python.clusterize import Clusterize\n-#TODO: test for n option when option corrected\n-\n-SMART_PATH = os.environ["REPET_PATH"] + "/SMART"\n-\n-class Test_F_Clusterize(unittest.TestCase):\n-\n- def setUp(self):\n- self._inputFileName = "inputFileTest.bed"\n- self._expOutputFileName = "expOutput.gff3"\n- self._outputFileName = "output.gff3"\n- self._writeInputFile()\n- \n- def tearDown(self):\n- for file in (self._inputFileName, self._expOutputFileName, self._outputFileName):\n- if os.path.exists(file):\n- os.remove(file)\n-\n- def test_run_2DifferentStrand(self):\n- self._writeOutputFile_2DiffStrand(self._expOutputFileName)\n- \n- args = ["-i", self._inputFileName, "-f", "bed", "-o", self._outputFileName, "-v", "0"]\n- parser = OptionParser()\n- parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")\n- parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [format: transcript file format]")\n- parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")\n- parser.add_option("-c", "--colinear", dest="colinear", action="store_true", default=False, help="merge colinear transcripts only [format: bool] [default: false]")\n- parser.add_option("-d", "--distance", dest="distance", action="store", default=0, type="int", help="max. distance between two transcripts to be merged [format: int] [default: 0]")\n- parser.add_option("-n", "--normalize", dest="normalize", action="store_true", default=False, help="normalize the number of reads per cluster by the number of mappings per read [format: bool] [default: false]")\n- parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]")\n- (options, args) = parser.parse_args(args)\n- iClusterize = Clusterize(options.verbosity)\n- iClusterize.setInputFile(options.inputFileName, options.format)\n- iClusterize.setOutputFileName(options.outputFileName)\n- iClusterize.setColinear(options.colinear)\n- iClusterize.setDistance(options.distance)\n- iClusterize.setNormalize(options.normalize)\n- iClusterize.run()\n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))\n-\n- def test_runAsScript_2DifferentStrand(self):\n- self._writeOutputFile_2DiffStrand(self._expOutputFileName)\n- os.system("python %s/Java/Python/clusterize.py -i %s -f bed -o %s -v 0" % (SMART_PATH, self._inputFileName, self._outputFileName))\n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))\n- \n- def test_runAsScript_2DifferentStrand_map_output(self):\n- self._expOutputFileName = "expOutput.map"\n- self._outputFileName = "output.map"\n- self._writeOutputFile_2DiffStrandMapFormat(self._expOutputFileName)\n- os.system("python %s/Java/Python/clusterize.py -i %s -f bed -o %s -u map -v 0" % (SMART_PATH, self._inputFileName, self._outputFileName))\n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))\n- \n- def test_runAsScript_2SameStrand(self):\n- self._writeOutputFile_2SameStrand(self._expOutputFileName)\n- os.system("python %s/Java/Python/clusterize.py -i %s -f bed -o %s -c -v 0" % (SMART_PATH, self._inputFileName, self._outputFileNam'..b'f.write("arm_X\\t10000100\\t10000200\\ttest1.1\\t100\\t+\\t10000100\\t10000200\\t0\\t1\\t100,\\t0,\\n")\n- f.write("arm_X\\t10000100\\t10000200\\ttest1.2\\t100\\t-\\t10000100\\t10000200\\t0\\t1\\t100,\\t0,\\n")\n- f.write("arm_2R\\t10000100\\t10000200\\ttest1.3\\t100\\t+\\t10000100\\t10000200\\t0\\t1\\t100,\\t0,\\n")\n- f.write("arm_X\\t10000000\\t10000100\\ttest1.4\\t100\\t+\\t10000000\\t10000100\\t0\\t1\\t100,\\t0,\\n")\n- f.write("arm_X\\t10000200\\t10000300\\ttest1.5\\t100\\t+\\t10000200\\t10000300\\t0\\t1\\t100,\\t0,\\n")\n- f.write("arm_X\\t9999900\\t9999950\\ttest1.6\\t100\\t+\\t9999900\\t9999950\\t0\\t1\\t50,\\t0,\\n")\n- f.write("arm_X\\t10000000\\t10000050\\ttest1.7\\t100\\t-\\t10000000\\t10000050\\t0\\t1\\t50,\\t0,\\n")\n- f.close()\n- \n- def _writeOutputFile_2DiffStrand(self, outputFileName):\n- f = open(outputFileName, "w")\n- f.write("arm_2R\\tS-MART\\ttranscript\\t10000100\\t10000199\\t.\\t+\\t.\\tID=test1.3;Name=test1.3\\n")\n- f.write("arm_X\\tS-MART\\ttranscript\\t9999900\\t9999949\\t.\\t+\\t.\\tID=test1.6;Name=test1.6\\n")\n- f.write("arm_X\\tS-MART\\ttranscript\\t10000000\\t10000099\\t.\\t-\\t.\\tnbElements=2.000000;ID=test1.7--test1.4;Name=test1.7--test1.4\\n")\n- f.write("arm_X\\tS-MART\\ttranscript\\t10000100\\t10000199\\t.\\t-\\t.\\tnbElements=2.000000;ID=test1.2--test1.1;Name=test1.2--test1.1\\n")\n- f.write("arm_X\\tS-MART\\ttranscript\\t10000200\\t10000299\\t.\\t+\\t.\\tID=test1.5;Name=test1.5\\n")\n- f.close()\n- \n- def _writeOutputFile_2SameStrand(self, outputFileName):\n- f = open(outputFileName, "w")\n- f.write("arm_2R\\tS-MART\\ttranscript\\t10000100\\t10000199\\t.\\t+\\t.\\tID=test1.3;Name=test1.3\\n") \n- f.write("arm_X\\tS-MART\\ttranscript\\t9999900\\t9999949\\t.\\t+\\t.\\tID=test1.6;Name=test1.6\\n") \n- f.write("arm_X\\tS-MART\\ttranscript\\t10000000\\t10000099\\t.\\t+\\t.\\tID=test1.4;Name=test1.4\\n") \n- f.write("arm_X\\tS-MART\\ttranscript\\t10000000\\t10000049\\t.\\t-\\t.\\tID=test1.7;Name=test1.7\\n") \n- f.write("arm_X\\tS-MART\\ttranscript\\t10000100\\t10000199\\t.\\t+\\t.\\tID=test1.1;Name=test1.1\\n") \n- f.write("arm_X\\tS-MART\\ttranscript\\t10000100\\t10000199\\t.\\t-\\t.\\tID=test1.2;Name=test1.2\\n") \n- f.write("arm_X\\tS-MART\\ttranscript\\t10000200\\t10000299\\t.\\t+\\t.\\tID=test1.5;Name=test1.5\\n")\n- f.close()\n- \n- def _writeOutputFile_distance(self, outputFileName):\n- f = open(outputFileName, "w")\n- f.write("arm_2R\\tS-MART\\ttranscript\\t10000100\\t10000199\\t.\\t+\\t.\\tID=test1.3;Name=test1.3\\n")\n- f.write("arm_X\\tS-MART\\ttranscript\\t9999900\\t9999949\\t.\\t+\\t.\\tID=test1.6;Name=test1.6\\n")\n- f.write("arm_X\\tS-MART\\ttranscript\\t10000000\\t10000299\\t.\\t+\\t.\\tnbElements=5.000000;ID=test1.5--test1.2--test1.1--test1.7--test1.4;Name=test1.5--test1.2--test1.1--test1.7--test1.4\\n")\n- f.write("arm_X\\tS-MART\\texon\\t10000000\\t10000099\\t.\\t+\\t.\\tID=test1.5--test1.2--test1.1--test1.7--test1.4-exon1;Name=test1.5--test1.2--test1.1--test1.7--test1.4-exon1;Parent=test1.5--test1.2--test1.1--test1.7--test1.4\\n")\n- f.write("arm_X\\tS-MART\\texon\\t10000100\\t10000199\\t.\\t+\\t.\\tID=test1.5--test1.2--test1.1--test1.7--test1.4-exon2;Name=test1.5--test1.2--test1.1--test1.7--test1.4-exon2;Parent=test1.5--test1.2--test1.1--test1.7--test1.4\\n")\n- f.write("arm_X\\tS-MART\\texon\\t10000200\\t10000299\\t.\\t+\\t.\\tID=test1.5--test1.2--test1.1--test1.7--test1.4-exon3;Name=test1.5--test1.2--test1.1--test1.7--test1.4-exon3;Parent=test1.5--test1.2--test1.1--test1.7--test1.4\\n")\n- f.close()\n- \n- def _writeOutputFile_2DiffStrandMapFormat(self, outputFileName):\n- f = open(outputFileName, "w")\n- f.write("test1.3\\tarm_2R\\t10000100\\t10000200\\n")\n- f.write("test1.6\\tarm_X\\t9999900\\t9999950\\n")\n- f.write("test1.7--test1.4\\tarm_X\\t10000000\\t10000100\\n")\n- f.write("test1.2--test1.1\\tarm_X\\t10000100\\t10000200\\n")\n- f.write("test1.5\\tarm_X\\t10000200\\t10000300\\n")\n- f.close()\n- \n-\n-if __name__ == "__main__":\n- unittest.main()\n'

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_ClusterizeByTags.py
--- a/SMART/Java/Python/test/Test_F_ClusterizeByTags.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,144 +0,0 @@\n-import unittest, os, os.path\n-from SMART.Java.Python.misc import Utils\n-from SMART.Java.Python.ClusterizeByTags import ClusterizeByTags\n-\n-class Test_F_ClusterizeByTags(unittest.TestCase):\n-\n- def setUp(self):\n- self._inputFileName = "inputFileTest.gff3"\n- self._expOutputFileName = "expOutput.gff3"\n- self._outputFileName = "output.gff3"\n- \n- def tearDown(self):\n- for file in (self._inputFileName, self._expOutputFileName, self._outputFileName):\n- if os.path.exists(file):\n- os.remove(file)\n-\n- def test_diff_simple(self):\n- handle = open(self._inputFileName, "w")\n- handle.write("""chr1\\tS-MART\\ttest1.1\\t100\\t200\\t.\\t+\\t.\\tName=test1.1;score=10;ID=test1.1\n-chr1\\tS-MART\\ttest1.2\\t300\\t400\\t.\\t+\\t.\\tName=test1.2;score=15;ID=test1.2\n-chr1\\tS-MART\\ttest1.3\\t500\\t600\\t.\\t+\\t.\\tName=test1.3;score=15;ID=test1.3\n-chr1\\tS-MART\\ttest1.4\\t700\\t800\\t.\\t+\\t.\\tName=test1.4;score=100;ID=test1.4\n-chr1\\tS-MART\\ttest1.5\\t900\\t1000\\t.\\t+\\t.\\tName=test1.5;score=110;ID=test1.5\n-chr1\\tS-MART\\ttest1.6\\t1100\\t1200\\t.\\t+\\t.\\tName=test1.6;score=105;ID=test1.6\n-""")\n- handle.close()\n- handle = open(self._expOutputFileName, "w")\n- handle.write("""chr1\tS-MART\ttest1.1\t100\t600\t40\t+\t.\tnbElements=3.000000;ID=test1.1;Name=test1.1--test1.2--test1.3\n-chr1\tS-MART\texon\t100\t200\t10\t+\t.\tID=test1.1-exon1;Name=test1.1--test1.2--test1.3-exon1;Parent=test1.1\n-chr1\tS-MART\texon\t300\t400\t15\t+\t.\tID=test1.1-exon2;Name=test1.1--test1.2--test1.3-exon2;Parent=test1.1\n-chr1\tS-MART\texon\t500\t600\t15\t+\t.\tID=test1.1-exon3;Name=test1.1--test1.2--test1.3-exon3;Parent=test1.1\n-chr1\tS-MART\ttest1.4\t700\t1200\t315\t+\t.\tnbElements=3.000000;ID=test1.4;Name=test1.4--test1.5--test1.6\n-chr1\tS-MART\texon\t700\t800\t100\t+\t.\tID=test1.4-exon1;Name=test1.4--test1.5--test1.6-exon1;Parent=test1.4\n-chr1\tS-MART\texon\t900\t1000\t110\t+\t.\tID=test1.4-exon2;Name=test1.4--test1.5--test1.6-exon2;Parent=test1.4\n-chr1\tS-MART\texon\t1100\t1200\t105\t+\t.\tID=test1.4-exon3;Name=test1.4--test1.5--test1.6-exon3;Parent=test1.4\n-""")\n- handle.close()\n- cbt = ClusterizeByTags(0)\n- cbt.setInputFile(self._inputFileName, "gff3")\n- cbt.setOutputFile(self._outputFileName)\n- cbt.setTag("score", None)\n- cbt.setThreshold(20)\n- cbt.setOperation("diff")\n- cbt.setMaxDistance(None)\n- cbt.run()\n- self.assertTrue(Utils.diff(self._outputFileName, self._expOutputFileName))\n-\n- def test_diff_two_strands(self):\n- handle = open(self._inputFileName, "w")\n- handle.write("""chr1\\tS-MART\\ttest1.1\\t100\\t200\\t.\\t+\\t.\\tName=test1.1;score=10;ID=test1.1\n-chr1\\tS-MART\\ttest1.2\\t300\\t400\\t.\\t+\\t.\\tName=test1.2;score=15;ID=test1.2\n-chr1\\tS-MART\\ttest1.3\\t500\\t600\\t.\\t+\\t.\\tName=test1.3;score=15;ID=test1.3\n-chr1\\tS-MART\\ttest1.4\\t700\\t800\\t.\\t-\\t.\\tName=test1.4;score=10;ID=test1.4\n-chr1\\tS-MART\\ttest1.5\\t900\\t1000\\t.\\t-\\t.\\tName=test1.5;score=15;ID=test1.5\n-chr1\\tS-MART\\ttest1.6\\t1100\\t1200\\t.\\t-\\t.\\tName=test1.6;score=15;ID=test1.6\n-""")\n- handle.close()\n- handle = open(self._expOutputFileName, "w")\n- handle.write("""chr1\tS-MART\ttest1.4\t700\t1200\t40\t-\t.\tnbElements=3.000000;ID=test1.4;Name=test1.4--test1.5--test1.6\n-chr1\tS-MART\texon\t700\t800\t10\t-\t.\tID=test1.4-exon1;Name=test1.4--test1.5--test1.6-exon1;Parent=test1.4\n-chr1\tS-MART\texon\t900\t1000\t15\t-\t.\tID=test1.4-exon2;Name=test1.4--test1.5--test1.6-exon2;Parent=test1.4\n-chr1\tS-MART\texon\t1100\t1200\t15\t-\t.\tID=test1.4-exon3;Name=test1.4--test1.5--test1.6-exon3;Parent=test1.4\n-chr1\tS-MART\ttest1.1\t100\t600\t40\t+\t.\tnbElements=3.000000;ID=test1.1;Name=test1.1--test1.2--test1.3\n-chr1\tS-MART\texon\t100\t200\t10\t+\t.\tID=test1.1-exon1;Name=test1.1--test1.2--test1.3-exon1;Parent=test1.1\n-chr1\tS-MART\texon\t300\t400\t15\t+\t.\tID=test1.1-exon2;Name=test1.1--test1.2--test1.3-exon2;Parent=test1.1\n-chr1\tS-MART\texon\t500\t600\t15\t+\t.\tID=test1.1-exon3;Name=test1.1--test1.2--test1.3-exon3;Parent=test1.1\n-""")\n- handle.cl'..b'tance(None)\n- cbt.run()\n- self.assertTrue(Utils.diff(self._outputFileName, self._expOutputFileName))\n- \n- def test_diff_one_strands(self):\n- handle = open(self._inputFileName, "w")\n- handle.write("""chr1\\tS-MART\\ttest1.1\\t100\\t200\\t.\\t+\\t.\\tName=test1.1;score=10;ID=test1.1\n-chr1\\tS-MART\\ttest1.2\\t300\\t400\\t.\\t+\\t.\\tName=test1.2;score=15;ID=test1.2\n-chr1\\tS-MART\\ttest1.3\\t500\\t600\\t.\\t+\\t.\\tName=test1.3;score=15;ID=test1.3\n-chr1\\tS-MART\\ttest1.4\\t700\\t800\\t.\\t-\\t.\\tName=test1.4;score=10;ID=test1.4\n-chr1\\tS-MART\\ttest1.5\\t900\\t1000\\t.\\t-\\t.\\tName=test1.5;score=15;ID=test1.5\n-chr1\\tS-MART\\ttest1.6\\t1100\\t1200\\t.\\t-\\t.\\tName=test1.6;score=15;ID=test1.6\n-""")\n- handle.close()\n- handle = open(self._expOutputFileName, "w")\n- handle.write("""chr1\tS-MART\ttest1.1\t100\t600\t40\t+\t.\tnbElements=3.000000;ID=test1.1;Name=test1.1--test1.2--test1.3\n-chr1\tS-MART\texon\t100\t200\t10\t+\t.\tID=test1.1-exon1;Name=test1.1--test1.2--test1.3-exon1;Parent=test1.1\n-chr1\tS-MART\texon\t300\t400\t15\t+\t.\tID=test1.1-exon2;Name=test1.1--test1.2--test1.3-exon2;Parent=test1.1\n-chr1\tS-MART\texon\t500\t600\t15\t+\t.\tID=test1.1-exon3;Name=test1.1--test1.2--test1.3-exon3;Parent=test1.1\n-chr1\tS-MART\ttest1.4\t700\t1200\t40\t-\t.\tnbElements=3.000000;ID=test1.4;Name=test1.4--test1.5--test1.6\n-chr1\tS-MART\texon\t700\t800\t10\t-\t.\tID=test1.4-exon1;Name=test1.4--test1.5--test1.6-exon1;Parent=test1.4\n-chr1\tS-MART\texon\t900\t1000\t15\t-\t.\tID=test1.4-exon2;Name=test1.4--test1.5--test1.6-exon2;Parent=test1.4\n-chr1\tS-MART\texon\t1100\t1200\t15\t-\t.\tID=test1.4-exon3;Name=test1.4--test1.5--test1.6-exon3;Parent=test1.4\n-""")\n- handle.close()\n- cbt = ClusterizeByTags(0)\n- cbt.setInputFile(self._inputFileName, "gff3")\n- cbt.setOutputFile(self._outputFileName)\n- cbt.setTag("score", None)\n- cbt.setThreshold(20)\n- cbt.setOperation("diff")\n- cbt.setMaxDistance(None)\n- cbt.setOneStrand(True)\n- cbt.run()\n- self.assertTrue(Utils.diff(self._outputFileName, self._expOutputFileName))\n-\n- def test_diff_distance(self):\n- handle = open(self._inputFileName, "w")\n- handle.write("""chr1\\tS-MART\\ttest1.1\\t100\\t200\\t.\\t+\\t.\\tName=test1.1;score=10;ID=test1.1\n-chr1\\tS-MART\\ttest1.2\\t300\\t400\\t.\\t+\\t.\\tName=test1.2;score=15;ID=test1.2\n-chr1\\tS-MART\\ttest1.3\\t500\\t600\\t.\\t+\\t.\\tName=test1.3;score=15;ID=test1.3\n-chr1\\tS-MART\\ttest1.4\\t1000\\t1100\\t.\\t+\\t.\\tName=test1.4;score=10;ID=test1.4\n-chr1\\tS-MART\\ttest1.5\\t1200\\t1300\\t.\\t+\\t.\\tName=test1.5;score=15;ID=test1.5\n-chr1\\tS-MART\\ttest1.6\\t1400\\t1500\\t.\\t+\\t.\\tName=test1.6;score=15;ID=test1.6\n-""")\n- handle.close()\n- handle = open(self._expOutputFileName, "w")\n- handle.write("""chr1\tS-MART\ttest1.1\t100\t600\t40\t+\t.\tnbElements=3.000000;ID=test1.1;Name=test1.1--test1.2--test1.3\n-chr1\tS-MART\texon\t100\t200\t10\t+\t.\tID=test1.1-exon1;Name=test1.1--test1.2--test1.3-exon1;Parent=test1.1\n-chr1\tS-MART\texon\t300\t400\t15\t+\t.\tID=test1.1-exon2;Name=test1.1--test1.2--test1.3-exon2;Parent=test1.1\n-chr1\tS-MART\texon\t500\t600\t15\t+\t.\tID=test1.1-exon3;Name=test1.1--test1.2--test1.3-exon3;Parent=test1.1\n-chr1\tS-MART\ttest1.4\t1000\t1500\t40\t+\t.\tnbElements=3.000000;ID=test1.4;Name=test1.4--test1.5--test1.6\n-chr1\tS-MART\texon\t1000\t1100\t10\t+\t.\tID=test1.4-exon1;Name=test1.4--test1.5--test1.6-exon1;Parent=test1.4\n-chr1\tS-MART\texon\t1200\t1300\t15\t+\t.\tID=test1.4-exon2;Name=test1.4--test1.5--test1.6-exon2;Parent=test1.4\n-chr1\tS-MART\texon\t1400\t1500\t15\t+\t.\tID=test1.4-exon3;Name=test1.4--test1.5--test1.6-exon3;Parent=test1.4\n-""")\n- handle.close()\n- cbt = ClusterizeByTags(0)\n- cbt.setInputFile(self._inputFileName, "gff3")\n- cbt.setOutputFile(self._outputFileName)\n- cbt.setTag("score", None)\n- cbt.setThreshold(20)\n- cbt.setOperation("diff")\n- cbt.setMaxDistance(200)\n- cbt.run()\n- self.assertTrue(Utils.diff(self._outputFileName, self._expOutputFileName))\n-\n-\n-if __name__ == "__main__":\n- unittest.main()\n'

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_CollapseReads.py
--- a/SMART/Java/Python/test/Test_F_CollapseReads.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,92 +0,0 @@
-import unittest
-import os
-from SMART.Java.Python.CollapseReads import CollapseReads
-from SMART.Java.Python.misc import Utils
-from commons.core.utils.FileUtils import FileUtils
-from SMART.Java.Python.ncList.test.MockFindOverlaps_randomExample import MockFindOverlaps_randomExample_NonOrder
-
-class Test_F_CollapseReads(unittest.TestCase):
-
-    def setUp(self):
-        self._inputFileName = 'inputCR.gff3'
-        self._writeInput(self._inputFileName)
-        self._outputFileName = 'outputCR.gff3'
-        self._expOutputFileName = 'expOutputCR.gff3'
-
-    def tearDown(self):
-        return
-
-    def test_run_default_option(self):
-        iCR = CollapseReads(0)
-        iCR.setInputFile(self._inputFileName, 'gff3')
-        iCR.setOutputFile(self._outputFileName)
-        iCR.strands = False
-        iCR.collapse()
-        self._writeExp_strand_False(self._expOutputFileName)
-        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
-
-    def test_run_strand_option(self):
-        iCR = CollapseReads(0)
-        iCR.setInputFile(self._inputFileName, 'gff3')
-        iCR.setOutputFile(self._outputFileName)
-        iCR.strands = True
-        iCR.collapse()
-        self._writeExp_strand_True(self._expOutputFileName)
-        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
-
-    def test_run_asScript_default_option(self):
-        cmd = 'python ../CollapseReads.py -i %s -f gff3 -o %s -v 0' % (self._inputFileName, self._outputFileName)
-        os.system(cmd)
-        self._writeExp_strand_True(self._expOutputFileName)
-        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
-
-    def test_run_asScript_strand_option(self):
-        cmd = 'python ../CollapseReads.py -i %s -f gff3 -o %s -s -v 0' % (self._inputFileName, self._outputFileName)
-        os.system(cmd)
-        self._writeExp_strand_False(self._expOutputFileName)
-        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
-
-    def test_run_toOrderGff(self):
-        iMRE = MockFindOverlaps_randomExample_NonOrder(self._inputFileName, 'chrom', 10, 1000)
-        iMRE.write()
-        iCR = CollapseReads(0)
-        iCR.setInputFile(self._inputFileName, 'gff3')
-        iCR.setOutputFile(self._outputFileName)
-        iCR.strands = False
-        iCR.collapse()
-        f = open(self._expOutputFileName, "w")
-        f.close()
-        cmd = 'sort -f -n -k4 -k5.4rn -o %s %s'%(self._expOutputFileName, self._inputFileName)
-        os.system(cmd)
-
-    def _writeInput(self, fileName):
-        f = open(fileName, 'w')
-        f.write("chr1\ttest\tmatch\t6155418\t6155441\t.\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
-        f.write("chr2\ttest\tmatch\t26303950\t26303981\t.\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
-        f.write("chr3\ttest\tmatch\t28320540\t28320574\t.\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
-        f.write("chr4\ttest\tmatch\t28565007\t28565041\t.\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
-        f.write("chr1\ttest\tmatch\t6155418\t6155441\t.\t+\t.\toccurrence=2;rank=2;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=1;ID=test3/1;identity=50;Name=test3/1\n")
-        f.write("chr1\ttest\tmatch\t6155418\t6155441\t.\t-\t.\toccurrence=2;rank=2;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=1;ID=test3/1;identity=50;Name=test3/1\n")
-        f.close()
-
-    def _writeExp_strand_False(self, fileName):
-        f = open(fileName, 'w')
-        f.write("""chr1 S-MART match 6155418 6155441 . - . nbElements=3.000000;ID=test3/1;Name=test3/1--test3/1--test1/1
-chr2 S-MART match 26303950 26303981 . + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1
-chr3 S-MART match 28320540 28320574 . + . occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1
-chr4 S-MART match 28565007 28565041 . + . occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1
-""")
-        f.close()
-
-    def _writeExp_strand_True(self, fileName):
-        f = open(fileName, 'w')
-        f.write("""chr1 S-MART match 6155418 6155441 . + . nbElements=2.000000;ID=test3/1;Name=test3/1--test1/1
-chr1 S-MART match 6155418 6155441 . - . occurrence=2;rank=2;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=1;ID=test3/1;identity=50;Name=test3/1
-chr2 S-MART match 26303950 26303981 . + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1
-chr3 S-MART match 28320540 28320574 . + . occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1
-chr4 S-MART match 28565007 28565041 . + . occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1
-""")
-        f.close()
-
-if __name__ == "__main__":
-    unittest.main()

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_CombineTags.py
--- a/SMART/Java/Python/test/Test_F_CombineTags.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,109 +0,0 @@
-import unittest
-import os
-from optparse import OptionParser
-from SMART.Java.Python.structure.Transcript import Transcript
-from commons.core.parsing.ParserChooser import ParserChooser
-from commons.core.parsing.GffParser import GffParser
-from commons.core.writer.Gff3Writer import Gff3Writer
-from SMART.Java.Python.CombineTags import CombineTags
-
-class Test_F_CombineTags(unittest.TestCase):
-
-    def setUp(self):
-        self._inputFileName  = "inputFileTest.gff3"
-        self._outputFileName = "outputFileTest.gff3"
-        self._tag1           = "tag1"
-        self._tag2           = "tag2"
-        self._outputTag      = "outputTag"
-
-    def tearDown(self):
-        os.remove(self._inputFileName)
-        os.remove(self._outputFileName)
-
-    def test_plus(self):
-        transcript = self._createDummyTranscript()
-        transcript.setTagValue(self._tag1, 1)
-        transcript.setTagValue(self._tag2, 2)
-        self._writeTranscript(transcript)
-        combiner = CombineTags(0)
-        combiner.setInputFile(self._inputFileName, "gff3")
-        combiner.setOutputFile(self._outputFileName)
-        combiner.setTags(self._tag1, self._tag2, self._outputTag, None)
-        combiner.setOperation("plus")
-        combiner.run()
-        self._testOutputTag(3)
-
-    def test_minus(self):
-        transcript = self._createDummyTranscript()
-        transcript.setTagValue(self._tag1, 2)
-        transcript.setTagValue(self._tag2, 1)
-        self._writeTranscript(transcript)
-        combiner = CombineTags(0)
-        combiner.setInputFile(self._inputFileName, "gff3")
-        combiner.setOutputFile(self._outputFileName)
-        combiner.setTags(self._tag1, self._tag2, self._outputTag, None)
-        combiner.setOperation("minus")
-        combiner.run()
-        self._testOutputTag(1)
-
-    def test_times(self):
-        transcript = self._createDummyTranscript()
-        transcript.setTagValue(self._tag1, 6)
-        transcript.setTagValue(self._tag2, 3)
-        self._writeTranscript(transcript)
-        combiner = CombineTags(0)
-        combiner.setInputFile(self._inputFileName, "gff3")
-        combiner.setOutputFile(self._outputFileName)
-        combiner.setTags(self._tag1, self._tag2, self._outputTag, None)
-        combiner.setOperation("times")
-        combiner.run()
-        self._testOutputTag(18)
-
-    def test_div(self):
-        transcript = self._createDummyTranscript()
-        transcript.setTagValue(self._tag1, 6)
-        transcript.setTagValue(self._tag2, 3)
-        self._writeTranscript(transcript)
-        combiner = CombineTags(0)
-        combiner.setInputFile(self._inputFileName, "gff3")
-        combiner.setOutputFile(self._outputFileName)
-        combiner.setTags(self._tag1, self._tag2, self._outputTag, None)
-        combiner.setOperation("div")
-        combiner.run()
-        self._testOutputTag(2)
-
-    def test_default(self):
-        transcript = self._createDummyTranscript()
-        transcript.setTagValue(self._tag1, 1)
-        self._writeTranscript(transcript)
-        combiner = CombineTags(0)
-        combiner.setInputFile(self._inputFileName, "gff3")
-        combiner.setOutputFile(self._outputFileName)
-        combiner.setTags(self._tag1, self._tag2, self._outputTag, 0)
-        combiner.setOperation("plus")
-        combiner.run()
-        self._testOutputTag(0)
-
-    def _createDummyTranscript(self):
-        transcript = Transcript()
-        transcript.setChromosome("chr1")
-        transcript.setName("test1")
-        transcript.setEnd(200)
-        transcript.setStart(100)
-        transcript.setDirection("+")
-        return transcript
-
-    def _testOutputTag(self, value):
-        parser = GffParser(self._outputFileName, 0)
-        for transcript in parser.getIterator():
-            self.assertEquals(float(transcript.getTagValue(self._outputTag)), value)
-        parser.close()
-
-    def _writeTranscript(self, transcript):
-        f = open(self._inputFileName, "w")
-        f.write(transcript.printGff3("test"))
-        f.close()
-
-
-if __name__ == "__main__":
-    unittest.main()

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_FindOverlapsOptim.py
--- a/SMART/Java/Python/test/Test_F_FindOverlapsOptim.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,500 +0,0 @@\n-import unittest\n-import os\n-from SMART.Java.Python.misc import Utils\n-from commons.core.utils.FileUtils import FileUtils\n-from SMART.Java.Python.FindOverlapsOptim import FindOverlapsOptim\n-from SMART.Java.Python.ncList.test.MockFindOverlapsWithSeveralIntervals import *\n-\n-class Test_F_FindOverlapsOptim(unittest.TestCase):\n-\n- def setUp(self):\n- self._inputRefGff3FileName = \'sorted_Ref.gff3\'\n- self._writeGFF3File(self._inputRefGff3FileName)\n- self._inputQueryGff3FileName = \'sorted_Query.gff3\'\n- self._writeQueryGff3File(self._inputQueryGff3FileName)\n- self._outputGff3FileName = \'output.gff3\'\n- self._expOutputFileName = \'expOutGff3.gff3\'\n- \n- def tearDown(self):\n- for fileName in (self._inputRefGff3FileName, self._inputQueryGff3FileName, self._outputGff3FileName, self._expOutputFileName):\n- if os.path.exists(fileName):\n- os.remove(fileName)\n- \n- def test_run_general_asScript(self):\n- cmd = \'python ../FindOverlapsOptim.py -i %s -f gff -j %s -g gff -o %s -v 0\' % (self._inputQueryGff3FileName, self._inputRefGff3FileName, self._outputGff3FileName) \n- os.system(cmd)\n- self._writeExpOutFile_general(self._expOutputFileName)\n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName)) \n-\n- def test_run_overlap_special_case(self):\n- inputQueryGff3FileName = \'query2.gff3\'\n- self._writeQueryGff3File2(inputQueryGff3FileName)\n- iFOO = FindOverlapsOptim(0)\n- iFOO.setRefFileName(self._inputRefGff3FileName, "gff")\n- iFOO.setQueryFileName(inputQueryGff3FileName, "gff")\n- iFOO.setOutputFileName(self._outputGff3FileName)\n- iFOO.run()\n- iFOO.close()\n- self._writeExpOutFile_special_case(self._expOutputFileName) \n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName)) \n- os.remove(inputQueryGff3FileName) \n- \n- def test_run_overlap_special_case_asScript(self):\n- inputQueryGff3FileName = \'query2.gff3\'\n- self._writeQueryGff3File2(inputQueryGff3FileName)\n- cmd = \'python ../FindOverlapsOptim.py -i %s -f gff -j %s -g gff -o %s -v 0\' % (inputQueryGff3FileName, self._inputRefGff3FileName, self._outputGff3FileName) \n- os.system(cmd) \n- self._writeExpOutFile_special_case(self._expOutputFileName) \n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName)) \n- os.remove(inputQueryGff3FileName) \n- \n- def test_case_2(self):\n- inputRefGff3FileName = \'ref_case2.gff3\'\n- iMock = MockFindOverlapsWithServeralIntervals_case2()\n- iMock.write(inputRefGff3FileName)\n- inputQueryGff3FileName = \'query_case2.gff3\'\n- self._writeQueryGff3File_case2(inputQueryGff3FileName) \n- iFOO = FindOverlapsOptim(0)\n- iFOO.setRefFileName(inputRefGff3FileName, "gff")\n- iFOO.setQueryFileName(inputQueryGff3FileName, "gff")\n- iFOO.setOutputFileName(self._outputGff3FileName)\n- iFOO.run()\n- iFOO.close()\n- self._writeExpOutFile_case2(self._expOutputFileName) \n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputGff3FileName)) \n- os.remove(inputQueryGff3FileName) \n- os.remove(inputRefGff3FileName) \n- \n- def test_case_3(self):\n- inputRefGff3FileName = \'ref_case3.gff3\'\n- iMock = MockFindOverlapsWithServeralIntervals_case3()\n- iMock.write(inputRefGff3FileName)\n- inputQueryGff3FileName = \'query_case3.gff3\'\n- self._writeQueryGff3File_case3(inputQueryGff3FileName) \n- iFOO = FindOverlapsOptim(0)\n- iFOO.setRefFileName(inputRefGff3FileName, "gff")\n- iFOO.setQueryFileName(inputQueryGff3FileName, "gff")\n- iFOO.setOutputFileName(self._outputGff3FileName)\n- iFOO.run()\n- iFOO.close()\n- self._writeExpOu'..b'ry_4;Name=test3.4\\n")\n- f.write("chr1\\tquery\\ttest3.5\\t900\\t950\\t51\\t+\\t.\\tID=query_5;Name=test3.5\\n")\n- f.close()\n- \n- def _writeQueryGff3File_case4(self, fileName):\n- f = open(fileName, \'w\')\n- f.write("chr1\\tquery\\ttest4.1\\t400\\t500\\t101\\t+\\t.\\tID=query_1;Name=test4.1\\n")\n- f.write("chr1\\tquery\\ttest4.2\\t450\\t600\\t151\\t+\\t.\\tID=query_2;Name=test4.2\\n")\n- f.write("chr1\\tquery\\ttest4.3\\t700\\t800\\t101\\t+\\t.\\tID=query_3;Name=test4.3\\n")\n- f.close()\n- \n- def _writeQueryGff3File_case5(self, fileName):\n- f = open(fileName, \'w\')\n- f.write("chr1\\tquery\\ttest5.1\\t850\\t950\\t101\\t+\\t.\\tID=query_1;Name=test5.1\\n")\n- f.close()\n- \n- def _writeQueryGff3File_case6(self, fileName):\n- f = open(fileName, \'w\')\n- f.write("chr1\\tquery\\ttest6.1\\t200\\t300\\t101\\t+\\t.\\tID=query_1;Name=test6.1\\n")\n- f.write("chr1\\tquery\\ttest6.2\\t800\\t900\\t101\\t+\\t.\\tID=query_2;Name=test6.2\\n")\n- f.close()\n- \n- def _writeQueryGff3File_case7(self, fileName):\n- f = open(fileName, \'w\')\n- f.write("chr1\\tquery\\ttest7.1\\t530\\t550\\t21\\t+\\t.\\tID=query_1;Name=test7.1\\n")\n- f.write("chr1\\tquery\\ttest7.2\\t600\\t700\\t101\\t+\\t.\\tID=query_2;Name=test7.2\\n")\n- f.write("chr1\\tquery\\ttest7.3\\t650\\t900\\t251\\t+\\t.\\tID=query_3;Name=test7.3\\n")\n- f.close()\n- \n- def _writeQueryGff3File_case8(self, fileName):\n- f = open(fileName, \'w\')\n- f.write("chr1\\tquery\\ttest8.1\\t500\\t600\\t101\\t+\\t.\\tID=query_1;Name=test8.1\\n")\n- f.write("chr1\\tquery\\ttest8.2\\t700\\t800\\t101\\t+\\t.\\tID=query_2;Name=test8.2\\n")\n- f.write("chr1\\tquery\\ttest8.3\\t900\\t1100\\t201\\t+\\t.\\tID=query_3;Name=test8.3\\n")\n- f.write("chr1\\tquery\\ttest8.4\\t1200\\t1300\\t101\\t+\\t.\\tID=query_4;Name=test8.4\\n")\n- f.close()\n- \n- def _writeQueryGff3File_case9(self, fileName):\n- f = open(fileName, \'w\')\n- f.write("chr1\\tquery\\ttest9.1\\t400\\t500\\t101\\t+\\t.\\tID=query_1;Name=test9.1\\n")\n- f.write("chr1\\tquery\\ttest9.2\\t550\\t650\\t101\\t+\\t.\\tID=query_2;Name=test9.2\\n")\n- f.close()\n- \n- def _writeQueryGff3File_case10(self, fileName):\n- f = open(fileName, \'w\')\n- f.write("chr1\\tquery\\ttest10.1\\t700\\t800\\t101\\t+\\t.\\tID=query_1;Name=test10.1\\n")\n- f.write("chr1\\tquery\\ttest10.2\\t900\\t1000\\t101\\t+\\t.\\tID=query_2;Name=test10.2\\n")\n- f.write("chr1\\tquery\\ttest10.3\\t1100\\t1300\\t201\\t+\\t.\\tID=query_3;Name=test10.3\\n")\n- f.close()\n- \n- def _writeQueryGff3File_case11(self, fileName):\n- f = open(fileName, \'w\')\n- f.write("chr1\\tquery\\ttest11.1\\t420\\t480\\t61\\t+\\t.\\tID=query_1;Name=test11.1\\n")\n- f.write("chr1\\tquery\\ttest11.2\\t450\\t715\\t266\\t+\\t.\\tID=query_2;Name=test11.2\\n")\n- f.close()\n- \n- def _writeQueryGff3File_case12(self, fileName):\n- f = open(fileName, \'w\')\n- f.write("chr1\\tquery\\ttest12.1\\t200\\t400\\t.\\t+\\t.\\tID=query_1;Name=test12.1\\n")\n- f.write("chr1\\tquery\\ttest12.2\\t600\\t900\\t.\\t+\\t.\\tID=query_2;Name=test12.2\\n")\n- f.write("chr1\\tquery\\ttest12.3\\t700\\t1000\\t.\\t+\\t.\\tID=query_3;Name=test12.3\\n")\n- f.close()\n- \n- def _writeGFF3File(self, fileName):\n- f = open(fileName, "w")\n- f.write("chr1\\ttest\\ttest2.1\\t9\\t1000\\t1001\\t+\\t.\\tID=test2.1;Name=test2.1\\n")\n- f.write("chr1\\ttest\\ttest2.2\\t50\\t350\\t301\\t+\\t.\\tID=test2.2;Name=test2.2\\n")\n- f.write("chr1\\ttest\\ttest2.3\\t100\\t600\\t501\\t+\\t.\\tID=test2.3;Name=test2.3\\n")\n- f.write("chr1\\ttest\\ttest2.4\\t200\\t450\\t251\\t+\\t.\\tID=test2.4;Name=test2.4\\n")\n- f.write("chr1\\ttest\\ttest2.5\\t700\\t950\\t251\\t+\\t.\\tID=test2.5;Name=test2.5\\n")\n- f.write("chr1\\ttest\\ttest2.6\\t800\\t900\\t101\\t+\\t.\\tID=test2.6;Name=test2.6\\n")\n- f.write("chr1\\ttest\\ttest2.7\\t1200\\t1300\\t101\\t+\\t.\\tID=test2.7;Name=test2.7\\n")\n- f.close()\n- \n-if __name__ == "__main__":\n- unittest.main()\n'

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_GetDifferentialExpression.py
--- a/SMART/Java/Python/test/Test_F_GetDifferentialExpression.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,50 +0,0 @@
-import unittest
-import os, os.path, glob
-from SMART.Java.Python.GetDifferentialExpression import GetDifferentialExpression
-
-
-class Test_F_GetDifferentialExpression(unittest.TestCase):
-
-    def setUp(self):
-        self.inputFileName1 = "inputFile1.gff3"
-        self.inputFileName2 = "inputFile2.gff3"
-        self.refFileName    = "refFile.gff3"
-        self.outputFileName = "outputFile.gff3"
-        self.plotFileName   = "outputFile.png"
-
-    def tearDown(self):
-        for fileRoot in (self.inputFileName1, self.inputFileName2, self.refFileName, self.outputFileName, self.plotFileName):
-            for file in glob.glob("%s*" % (fileRoot)):
-                os.remove(file)
-        os.remove(".RData")
-
-    def test_run_simple(self):
-        handle = open(self.inputFileName1, "w")
-        handle.write("chr1\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test1;Name=test1;nbElements=100\n")
-        handle.write("chr2\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test2;Name=test2;nbElements=1000\n")
-        handle.close()
-        handle = open(self.inputFileName2, "w")
-        handle.write("chr1\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test1;Name=test1;nbElements=200\n")
-        handle.write("chr2\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test2;Name=test2;nbElements=1000\n")
-        handle.close()
-        handle = open(self.refFileName, "w")
-        handle.write("chr1\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test1;Name=test1")
-        handle.close()
-        differentialExpression = GetDifferentialExpression(0)
-        differentialExpression.setInputFile(0, self.inputFileName1, "gff3")
-        differentialExpression.setInputFile(1, self.inputFileName2, "gff3")
-        differentialExpression.setReferenceFile(self.refFileName, "gff3")
-        differentialExpression.setOutputFile(self.outputFileName)
-        differentialExpression.setPlotterName(self.plotFileName)
-        differentialExpression.setPlotter()
-        differentialExpression.getDifferentialExpression()
-        differentialExpression.mySqlConnection.deleteDatabase()
-        handle = open(self.outputFileName)
-        lines = handle.readlines()
-        self.assertEquals(len(lines), 1)
-        self.assertEquals(lines[0], "chr1\tS-MART\ttranscript\t1000\t2000\t.\t+\t.\tnbReadsCond1=100;nbReadsCond2=200;ID=test1;regulation=up;nbUnnormalizedReadsCond2=200;nbUnnormalizedReadsCond1=100;pValue=6.010045e-08;Name=test1\n")
-        self.assertTrue(os.path.exists(self.plotFileName))
-
-if __name__ == "__main__":
-    unittest.main()
-

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_GetFlanking.py
--- a/SMART/Java/Python/test/Test_F_GetFlanking.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,238 +0,0 @@\n-import unittest\n-import os, os.path, glob\n-from SMART.Java.Python.structure.Transcript import Transcript\n-from SMART.Java.Python.GetFlanking import GetFlanking\n-from commons.core.writer.Gff3Writer import Gff3Writer\n-from commons.core.parsing.GffParser import GffParser\n-\n-class Test_F_GetFlanking(unittest.TestCase):\n-\n- def setUp(self):\n- self.queryFileName = "testQuery.gff3"\n- self.referenceFileName = "testReference.gff3"\n- self.outputFileName = "testOutput.gff3"\n- \n- def tearDown(self):\n- for fileRoot in (self.queryFileName, self.referenceFileName, self.outputFileName):\n- for file in glob.glob("%s*" % (fileRoot)):\n- os.remove(file)\n-\n- def test_run_simple(self):\n- #return\n- reference1 = self._createTranscript("chr1", 1000, 1100, "+", "ref1")\n- reference2 = self._createTranscript("chr1", 2000, 2100, "+", "ref2")\n- reference3 = self._createTranscript("chr1", 1000000, 1200000, "+", "ref3")\n- writer = Gff3Writer(self.referenceFileName, 0)\n- writer.addTranscript(reference1)\n- writer.addTranscript(reference2)\n- writer.addTranscript(reference3)\n- writer.close()\n- query1 = self._createTranscript("chr1", 100, 200, "+", "query1")\n- query2 = self._createTranscript("chr1", 10000, 10100, "+", "query2")\n- writer = Gff3Writer(self.queryFileName, 0)\n- writer.addTranscript(query1)\n- writer.addTranscript(query2)\n- writer.close()\n- gf = GetFlanking(0)\n- gf.setInputFile(self.queryFileName, \'gff3\', 0)\n- gf.setInputFile(self.referenceFileName, \'gff3\', 1)\n- gf.setOutputFile(self.outputFileName)\n- gf.run()\n- parser = GffParser(self.outputFileName)\n- self.assertEqual(parser.getNbTranscripts(), 2)\n- for i, transcript in enumerate(sorted(parser.getIterator(), key = lambda t: t.getStart())):\n- if i == 0:\n- self._checkTranscript(transcript, "chr1", 100, 200, "+", "query1")\n- self.assertEqual(transcript.getTagValue("flanking"), "ref1")\n- self.assertEqual(transcript.getTagValue("_region_flanking"), "downstream")\n- self.assertEqual(transcript.getTagValue("_sense_flanking"), "collinear")\n- else:\n- self._checkTranscript(transcript, "chr1", 10000, 10100, "+", "query2")\n- self.assertEqual(transcript.getTagValue("flanking"), "ref2")\n- self.assertEqual(transcript.getTagValue("_region_flanking"), "upstream")\n- self.assertEqual(transcript.getTagValue("_sense_flanking"), "collinear")\n-\n- def test_run_simple_downstream(self):\n- return\n- reference1 = self._createTranscript("chr1", 300, 400, "+", "ref1")\n- reference2 = self._createTranscript("chr1", 1000, 1100, "+", "ref2")\n- writer = Gff3Writer(self.referenceFileName, 0)\n- writer.addTranscript(reference1)\n- writer.addTranscript(reference2)\n- writer.close()\n- query1 = self._createTranscript("chr1", 100, 200, "+", "query1")\n- query2 = self._createTranscript("chr1", 1200, 1300, "+", "query2")\n- query3 = self._createTranscript("chr1", 1400, 1500, "+", "query3")\n- writer = Gff3Writer(self.queryFileName, 0)\n- writer.addTranscript(query1)\n- writer.addTranscript(query2)\n- writer.addTranscript(query3)\n- writer.close()\n- gf = GetFlanking(0)\n- gf.setInputFile(self.queryFileName, \'gff3\', 0)\n- gf.setInputFile(self.referenceFileName, \'gff3\', 1)\n- gf.setOutputFile(self.outputFileName)\n- gf.addDownstreamDirection(True)\n- gf.run()\n- parser = GffParser(self.outputFileName)\n- self.assertEqual(parser.getNbTranscripts(), 3)\n- for i, transcript in enumerate(sorted(parser.getIterator(), key = lambda t: t.getStart())):\n- if i == 0:\n- self._checkTranscript'..b' "chr1", 100, 200, "+", "query1")\n- self.assertIsNone(transcript.getTagValue("flanking_upstream"))\n- if i == 1:\n- self._checkTranscript(transcript, "chr1", 300, 400, "+", "query2")\n- self.assertIsNone(transcript.getTagValue("flanking_upstream"))\n- if i == 2:\n- self._checkTranscript(transcript, "chr1", 1200, 1300, "+", "query3")\n- self.assertEqual(transcript.getTagValue("flanking_upstream"), "ref2")\n-\n- def test_run_simple_colinear(self):\n- return\n- reference1 = self._createTranscript("chr1", 100, 200, "+", "ref1")\n- reference2 = self._createTranscript("chr1", 1000, 1100, "+", "ref2")\n- reference3 = self._createTranscript("chr1", 1600, 1700, "+", "ref3")\n- writer = Gff3Writer(self.referenceFileName, 0)\n- writer.addTranscript(reference1)\n- writer.addTranscript(reference2)\n- writer.addTranscript(reference3)\n- writer.close()\n- query1 = self._createTranscript("chr1", 1200, 1300, "-", "query1")\n- query2 = self._createTranscript("chr1", 1400, 1500, "+", "query2")\n- writer = Gff3Writer(self.queryFileName, 0)\n- writer.addTranscript(query1)\n- writer.addTranscript(query2)\n- writer.close()\n- gf = GetFlanking(0)\n- gf.setInputFile(self.queryFileName, \'gff3\', 0)\n- gf.setInputFile(self.referenceFileName, \'gff3\', 1)\n- gf.setOutputFile(self.outputFileName)\n- gf.addUpstreamDirection(True)\n- gf.setColinear(True)\n- gf.run()\n- parser = GffParser(self.outputFileName)\n- self.assertEqual(parser.getNbTranscripts(), 2)\n- for i, transcript in enumerate(sorted(parser.getIterator(), key = lambda t: t.getStart())):\n- if i == 0:\n- self._checkTranscript(transcript, "chr1", 1200, 1300, "-", "query1")\n- self.assertIsNone(transcript.getTagValue("flanking"))\n- if i == 1:\n- self._checkTranscript(transcript, "chr1", 1400, 1500, "+", "query2")\n- self.assertEqual(transcript.getTagValue("flanking_upstream"), "ref2")\n-\n- def test_run_simple_max_distance(self):\n- return\n- reference = self._createTranscript("chr1", 1000, 1100, "+", "ref")\n- writer = Gff3Writer(self.referenceFileName, 0)\n- writer.addTranscript(reference)\n- writer.close()\n- query1 = self._createTranscript("chr1", 2000, 2100, "-", "query1")\n- writer = Gff3Writer(self.queryFileName, 0)\n- writer.addTranscript(query1)\n- writer.close()\n- gf = GetFlanking(0)\n- gf.setInputFile(self.queryFileName, \'gff3\', 0)\n- gf.setInputFile(self.referenceFileName, \'gff3\', 1)\n- gf.setOutputFile(self.outputFileName)\n- gf.setMaxDistance(100)\n- gf.run()\n- parser = GffParser(self.outputFileName)\n- self.assertEqual(parser.getNbTranscripts(), 1)\n- for i, transcript in enumerate(sorted(parser.getIterator(), key = lambda t: t.getStart())):\n- if i == 0:\n- self._checkTranscript(transcript, "chr1", 2000, 2100, "-", "query1")\n- self.assertIsNone(transcript.getTagValue("flanking"))\n-\n- def _createTranscript(self, chromosome, start, end, strand, name):\n- transcript = Transcript()\n- transcript.setChromosome(chromosome)\n- transcript.setStart(start)\n- transcript.setEnd(end)\n- transcript.setDirection(strand)\n- transcript.setName(name)\n- return transcript\n-\n- def _checkTranscript(self, transcript, chromosome, start, end, strand, name):\n- self.assertEqual(transcript.getChromosome(), chromosome)\n- self.assertEqual(transcript.getStart(), start)\n- self.assertEqual(transcript.getEnd(), end)\n- self.assertEqual(transcript.getStrand(), strand)\n- self.assertEqual(transcript.getName(), name)\n-\n- \n-if __name__ == "__main__":\n- unittest.main()\n'

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_GetRandomSubset.py
--- a/SMART/Java/Python/test/Test_F_GetRandomSubset.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,55 +0,0 @@
-import unittest
-import os
-from SMART.Java.Python.GetRandomSubset import GetRandomSubset
-from commons.core.parsing.BedParser import BedParser
-from commons.core.parsing.GffParser import GffParser
-
-class Test_F_GetRandomSubset(unittest.TestCase):
-
-    def setUp(self):
-        self._inputFileName = "inputFileTest.bed"
-        self._writeInputFile()
-        self._outputFileName = "output.gff3"
-
-    def tearDown(self):
-        os.remove(self._inputFileName)
-        os.remove(self._outputFileName)
-
-    def test_run_simple(self):
-        nbElements = 2
-        inputTranscripts = []
-        parser = BedParser(self._inputFileName, 0)
-        for transcript in parser.getIterator():
-            inputTranscripts.append(transcript)
-        grs = GetRandomSubset(0)
-        grs.setInputFile(self._inputFileName, "bed")
-        grs.setNumber(nbElements, None)
-        grs.setOutputFile(self._outputFileName)
-        grs.run()
-        outputTranscripts = []
-        parser = GffParser(self._outputFileName, 0)
-        for transcript in parser.getIterator():
-            outputTranscripts.append(transcript)
-        self.assertEqual(len(outputTranscripts), nbElements)
-        for outputTranscript in outputTranscripts:
-            for inputTranscript in inputTranscripts:
-                if outputTranscript.getChromosome() == inputTranscript.getChromosome() and outputTranscript.getDirection() == inputTranscript.getDirection() and outputTranscript.getStart() == inputTranscript.getStart() and outputTranscript.getEnd() == inputTranscript.getEnd() and outputTranscript.getName() == inputTranscript.getName():
-                    break
-            else:
-                self.fail()
-
-    def _writeInputFile(self):
-        f = open(self._inputFileName, "w")
-        f.write("arm_X\t10000100\t10000200\ttest1.1\t100\t+\t10000100\t10000200\t0\t1\t100,\t0,\n")
-        f.write("arm_X\t10000100\t10000200\ttest1.2\t100\t-\t10000100\t10000200\t0\t1\t100,\t0,\n")
-        f.write("arm_2R\t10000100\t10000200\ttest1.3\t100\t+\t10000100\t10000200\t0\t1\t100,\t0,\n")
-        f.write("arm_X\t10000000\t10000100\ttest1.4\t100\t+\t10000000\t10000100\t0\t1\t100,\t0,\n")
-        f.write("arm_X\t10000200\t10000300\ttest1.5\t100\t+\t10000200\t10000300\t0\t1\t100,\t0,\n")
-        f.write("arm_X\t9999900\t9999950\ttest1.6\t100\t+\t9999900\t9999950\t0\t1\t50,\t0,\n")
-        f.write("arm_X\t10000000\t10000050\ttest1.7\t100\t-\t10000000\t10000050\t0\t1\t50,\t0,\n")
-        f.close()
-
-
-
-if __name__ == "__main__":
-    unittest.main()

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_GetSizes.py
--- a/SMART/Java/Python/test/Test_F_GetSizes.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,78 +0,0 @@
-import unittest
-import os, glob
-import subprocess
-from SMART.Java.Python.getSizes import GetSizes
-
-class Test_F_GetSizes(unittest.TestCase):
-
-    def setUp(self):
-        self._inputFastaFileName =  "inputFile.fa"
-        self._inputFastqFileName =  "inputFile.fq"
-
-    def tearDown(self):
-        try :
-            os.remove(self._inputFastaFileName)
-        except:pass
-
-    def test_run(self):
-        self.writeInputFasta(self._inputFastaFileName)
-        format = "fasta"
-        iGetSizes = GetSizes(inFileName = self._inputFastaFileName, inFormat=format)
-        iGetSizes.run()
-
-        self.assertEquals(iGetSizes.items, 3)
-        self.assertEquals(iGetSizes.subItems, 3)
-        self.assertEquals(iGetSizes.nucleotides, 108)
-        self.assertEquals(iGetSizes.minAvgMedMax, (36, 36.0, 36, 36))
-
-    def test_run_as_script(self):
-        self.writeInputFasta(self._inputFastaFileName)
-        format = "fasta"
-        cmd = "%s/SMART/Java/Python/getSizes.py -i %s -f %s -v 0" % (os.environ["REPET_PATH"], self._inputFastaFileName, format)
-        process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-        obsOutput = process.communicate()[0]
-        expOutput = """3 items\n3 sub-items\n108 nucleotides\nmin/avg/med/max transcripts: 36/36.00/36.0/36\n"""
-
-        self.assertEquals(expOutput, obsOutput)
-
-    def writeInputFile(self, fileName):
-        f = open(fileName, 'w')
-        f.write("chr1\tS-MART\ttest2.1\t9\t1000\t1001\t+\t.\tName=test2.1;overlapsWith=query_3;ID=test2.1\n")
-        f.write("chr1\tS-MART\ttest2.3\t100\t600\t501\t+\t.\tName=test2.3;overlapsWith=query_3;ID=test2.3\n")
-        f.write("chr1\tS-MART\ttest2.5\t700\t950\t251\t+\t.\tName=test2.5;overlapsWith=query_3;ID=test2.5\n")
-        f.write("chr1\tS-MART\ttest2.6\t800\t900\t101\t+\t.\tName=test2.6;overlapsWith=query_3;ID=test2.6\n")
-        f.close()
-
-
-    def writeInputFasta(self,inFileName):
-        f = open(inFileName,'w')
-        f.write('>HWI-EAS337_3:7:1:415:1217/1\n')
-        f.write('GATGTGCAGACTTTTCACGCAGGACTACATCACTGT\n')
-        f.write('>HWI-EAS337_3:7:1:208:1489/1\n')
-        f.write('GGAAACATATGCACATAAACGTTGAAATCATGCTTA\n')
-        f.write('>HWI-EAS337_3:7:1:278:1153\n')
-        f.write('GAGAAAACCTGTAATAAATACTGAGAGAAAGTAGGG\n')
-        f.close()
-
-
-    def writeInputFastq(self,inFileName):
-        f = open(inFileName,'w')
-        f.write('@HWI-EAS337_3:7:1:415:1217/1\n')
-        f.write('GATGTGCAGACTTTTCACGCAGGACTACATCACTGT\n')
-        f.write('+HWI-EAS337_3:7:1:415:1217/1\n')
-        f.write('WWWVVVWPWWWVWWWWVVVVKVPWWVVWVWUUQUTQ\n')
-        f.write('@HWI-EAS337_3:7:1:208:1489/1\n')
-        f.write('GGAAACATATGCACATAAACGTTGAAATCATGCTTA\n')
-        f.write('+HWI-EAS337_3:7:1:208:1489/1\n')
-        f.write('WWWWWWWWWWWWWWWWWVWWVWWVWWWWWWUUUUUU\n')
-        f.write('@HWI-EAS337_3:7:1:278:1153/1\n')
-        f.write('GAGAAAACCTGTAATAAATACTGAGAGAAAGTAGGG\n')
-        f.write('+HWI-EAS337_3:7:1:278:1153/1\n')
-        f.write('WWWWWWWWWWWWWWWWWWWWWWVWVVVWWVUUUUUR\n')
-        f.close()
-
-
-
-if __name__ == "__main__":
-    unittest.main()
-

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_RestrictFromCoverage.py
--- a/SMART/Java/Python/test/Test_F_RestrictFromCoverage.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,133 +0,0 @@
-import unittest
-import os, os.path
-from optparse import OptionParser
-from SMART.Java.Python.misc import Utils
-from SMART.Java.Python.structure.Transcript import Transcript
-from commons.core.writer.Gff3Writer import Gff3Writer
-from commons.core.parsing.GffParser import GffParser
-from SMART.Java.Python.RestrictFromCoverage import RestrictFromCoverage
-
-REFERENCE = 0
-QUERY     = 1
-
-class Test_F_Clusterize(unittest.TestCase):
-
-    def setUp(self):
-        self._queryFileName     = "testQuery.gff3"
-        self._refFileName       = "testRef.gff3"
-        self._outputFileName    = "output.gff3"
-        self._parsers           = {QUERY: Gff3Writer(self._queryFileName, 0), REFERENCE: Gff3Writer(self._refFileName, 0)}
-        self._writeQuery()
-
-    def tearDown(self):
-        for file in (self._queryFileName, self._refFileName, self._outputFileName):
-            if os.path.exists(file):
-                os.remove(file)
-
-    def _writeQuery(self):
-        self._addTranscript(QUERY, 1, 1000, 2000, "+")
-        self._parsers[QUERY].close()
-
-    def _writeReferences(self, values):
-        for value in values:
-            self._addTranscript(REFERENCE, value["cpt"], value["start"], value["end"], value["strand"])
-        self._parsers[REFERENCE].close()
-
-    def _addTranscript(self, type, cpt, start, end, strand):
-        t = Transcript()
-        t.setChromosome("chr1")
-        t.setName("test%d" % (cpt))
-        t.setStart(start)
-        t.setEnd(end)
-        t.setDirection(strand)
-        self._parsers[type].addTranscript(t)
-
-    def _checkTranscript(self, transcript, start, end, strand):
-        self.assertEquals(transcript.getStart(),     start)
-        self.assertEquals(transcript.getEnd(),       end)
-        self.assertEquals(transcript.getDirection(), strand)
-
-    def _startTool(self, minNucleotides = None, maxNucleotides = None, minPercent = None, maxPercent = None, minOverlap = None, maxOverlap = None, strands = False):
-        rfc = RestrictFromCoverage(0)
-        rfc.setInputFileName(self._queryFileName, "gff3", QUERY)
-        rfc.setInputFileName(self._refFileName,   "gff3", REFERENCE)
-        rfc.setOutputFileName(self._outputFileName)
-        rfc.setNbNucleotides(minNucleotides, maxNucleotides)
-        rfc.setPercent(minPercent, maxPercent)
-        rfc.setOverlap(minOverlap, maxOverlap)
-        rfc.setStrands(strands)
-        rfc.run()
-        return GffParser(self._outputFileName, 0)
-
-    def test_simple(self):
-        self._writeReferences([{"cpt": 1, "start": 1000, "end": 2000, "strand": "+"}])
-        parser = self._startTool()
-        self.assertEquals(parser.getNbTranscripts(), 1)
-        for transcript in parser.getIterator():
-            self._checkTranscript(transcript, 1000, 2000, 1)
-
-    def test_nbOverlapsMin_pos(self):
-        self._writeReferences([{"cpt": 1, "start": 1000, "end": 2000, "strand": "+"}, {"cpt": 2, "start": 1000, "end": 2000, "strand": "+"}])
-        parser = self._startTool(1, None, None, None, 2)
-        self.assertEquals(parser.getNbTranscripts(), 1)
-        for transcript in parser.getIterator():
-            self._checkTranscript(transcript, 1000, 2000, 1)
-
-    def test_nbOverlapsMin_neg(self):
-        self._writeReferences([{"cpt": 1, "start": 1000, "end": 2000, "strand": "+"}])
-        parser = self._startTool(1, None, None, None, 2)
-        self.assertEquals(parser.getNbTranscripts(), 0)
-
-    def test_nbOverlapsMax_pos(self):
-        self._writeReferences([{"cpt": 1, "start": 1000, "end": 2000, "strand": "+"}])
-        parser = self._startTool(1, None, None, None, None, 1)
-        self.assertEquals(parser.getNbTranscripts(), 1)
-        for transcript in parser.getIterator():
-            self._checkTranscript(transcript, 1000, 2000, 1)
-
-    def test_nbOverlapsMax_neg(self):
-        self._writeReferences([{"cpt": 1, "start": 1000, "end": 2000, "strand": "+"}, {"cpt": 2, "start": 1000, "end": 2000, "strand": "+"}])
-        parser = self._startTool(1, None, None, None, None, 1)
-        self.assertEquals(parser.getNbTranscripts(), 0)
-
-    def test_nbNucleotidesMin_pos(self):
-        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1100, "strand": "+"}])
-        parser = self._startTool(100, None, None, None, 1)
-        self.assertEquals(parser.getNbTranscripts(), 1)
-        for transcript in parser.getIterator():
-            self._checkTranscript(transcript, 1000, 2000, 1)
-
-    def test_nbNucleotidesMin_neg(self):
-        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1100, "strand": "+"}])
-        parser = self._startTool(200, None, None, None, 1)
-        self.assertEquals(parser.getNbTranscripts(), 0)
-
-    def test_PercentMin_pos(self):
-        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1500, "strand": "+"}])
-        parser = self._startTool(None, None, 50, None, 1)
-        self.assertEquals(parser.getNbTranscripts(), 1)
-        for transcript in parser.getIterator():
-            self._checkTranscript(transcript, 1000, 2000, 1)
-
-    def test_PercentMin_neg(self):
-        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1500, "strand": "+"}])
-        parser = self._startTool(None, None, 100, None, 1)
-        self.assertEquals(parser.getNbTranscripts(), 0)
-
-    def test_NoStrand_neg(self):
-        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1500, "strand": "-"}])
-        parser = self._startTool(1, None, None, None, 1)
-        self.assertEquals(parser.getNbTranscripts(), 1)
-
-    def test_strand_pos(self):
-        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1500, "strand": "+"}])
-        parser = self._startTool(1, None, None, None, 1, None, True)
-        self.assertEquals(parser.getNbTranscripts(), 1)
-
-    def test_strand_neg(self):
-        self._writeReferences([{"cpt": 1, "start": 1000, "end": 1500, "strand": "-"}])
-        parser = self._startTool(1, None, None, None, 1, None, True)
-        self.assertEquals(parser.getNbTranscripts(), 0)
-
-if __name__ == "__main__":
-    unittest.main()

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_clusterizeBySlidingWindows.py
--- a/SMART/Java/Python/test/Test_F_clusterizeBySlidingWindows.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,79 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-from SMART.Java.Python.misc import Utils
-
-
-class Test_F_clusterizeBySlidingWindows(unittest.TestCase):
-
-    def setUp(self):
-        self._outputFileName         = 'output.gff3'
-        self._outputCsvFileName      = 'output.csv'
-        self._outputPngFileName      = 'output.png'
-        self._expectedOutputFileName = 'expOut.png'
-
-    def tearDown(self):
-        for fileName in (self._outputFileName, self._outputCsvFileName, self._outputPngFileName, self._expectedOutputFileName):
-            if os.path.exists(fileName):
-                os.remove(fileName)
-
-    def test_run_default_option(self):
-        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerExpected.gff3 -f gff3 -o %s -s 50000 -e 50 -v 0" % (self._outputFileName)
-        os.system(cmd)
-        exp = '../TestFiles/clusterize_default_expected.gff3'
-        self.assertTrue(Utils.diff(exp, self._outputFileName))
-
-    def test_run_default_option_map_output(self):
-        self._outputFileName         = 'output.map'
-        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerExpected.gff3 -f gff3 -o %s -s 50000 -e 50 -u map -v 0" % (self._outputFileName)
-        os.system(cmd)
-        exp = '../TestFiles/clusterize_default_expected.map'
-        self.assertTrue(Utils.diff(exp, self._outputFileName))
-
-    def test_run_newTag_option(self):
-        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerExpected.gff3 -f gff3 -o %s -s 50000 -e 50 -w newTag -v 0" % (self._outputFileName)
-        os.system(cmd)
-        exp = '../TestFiles/clusterize_output_tag_expected.gff3'
-        self.assertTrue(Utils.diff(exp, self._outputFileName))
-
-    def test_run_normalize_option(self):
-        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerOutput.gff3 -f gff3 -o %s -s 50000 -e 50 -m -v 0" % (self._outputFileName)
-        os.system(cmd)
-        exp = '../TestFiles/clusterize_normalize_expected.gff3'
-        self.assertTrue(Utils.diff(exp, self._outputFileName))
-
-    def test_run_strand_option(self):
-        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerOutput.gff3 -f gff3 -o %s -s 50000 -e 50 -2 -v 0"  % (self._outputFileName)
-        os.system(cmd)
-        exp = '../TestFiles/clusterize_strands_expected.gff3'
-        self.assertTrue(Utils.diff(exp, self._outputFileName))
-
-    def test_run_excel_option(self):
-        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerOutput.gff3 -f gff3 -o %s -s 50000 -e 50 -x %s -v 0" % (self._outputFileName, self._outputCsvFileName)
-        os.system(cmd)
-        self.assertTrue(FileUtils.isRessourceExists(self._outputCsvFileName))
-
-
-    def test_run_normalize_strand_excel_option(self):
-        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/mapperAnalyzerOutput.gff3 -f gff3 -o %s -s 50000 -e 50 -m -2 -x %s -v 0" % (self._outputFileName, self._outputCsvFileName)
-        os.system(cmd)
-        self.assertTrue(FileUtils.isRessourceExists(self._outputCsvFileName))
-
-    def test_run_tag_operation_options(self):
-        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/testSW.gff3 -f gff -s 100 -e 0 -g value1 -r min -o %s -v 0" % (self._outputFileName)
-        os.system(cmd)
-        exp = open(self._expectedOutputFileName, 'w')
-        exp.write("chr1\tS-MART\ttranscript\t1\t100\t.\t+\t.\tnbElements=0;minValue1=0;ID=region1;Name=region1\n")
-        exp.write("chr1\tS-MART\ttranscript\t101\t200\t.\t+\t.\tnbElements=2.000000;minValue1=1.0;ID=region2;Name=region2\n")
-        exp.write("chr1\tS-MART\ttranscript\t201\t300\t.\t+\t.\tnbElements=2.000000;minValue1=10.0;ID=region3;Name=region3\n")
-        exp.close()
-        self.assertTrue(Utils.diff(self._outputFileName, self._expectedOutputFileName))
-
-    def test_run_plot_options(self):
-        cmd = "python ../clusterizeBySlidingWindows.py -i ../TestFiles/testSW.gff3 -f gff -s 100 -e 0 -g value1 -r min -o %s -p %s -v 0" % (self._outputFileName, self._outputPngFileName)
-        os.system(cmd)
-        self.assertTrue(FileUtils.isRessourceExists(self._outputPngFileName))
-
-
-if __name__ == "__main__":
-    unittest.main()

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_compareOverlapping.py
--- a/SMART/Java/Python/test/Test_F_compareOverlapping.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,199 +0,0 @@\n-import unittest\n-import os, os.path\n-from SMART.Java.Python.misc import Utils\n-\n-SMART_PATH = os.environ["REPET_PATH"] + "/SMART"\n-\n-class Test_F_compareOverlapping(unittest.TestCase):\n-\n- def setUp(self):\n- self._inputFileQuery = "inputFileTest1.bed"\n- self._inputFileReference = "inputFileTest2.bed"\n- self._inputFileName3 = "inputFileTest3.bed"\n- self._expOutputFileName = "expOutput.gff3" \n- self._outputFileName = "output.gff3" \n- self._writeInputFileQuery()\n- self._writeInputFileRefence()\n- self._writeInputFile3() \n- \n- def tearDown(self):\n- for fileName in (self._inputFileQuery, self._inputFileReference, self._inputFileName3, self._expOutputFileName, self._outputFileName):\n- if os.path.exists(fileName):\n- os.remove(fileName)\n-\n- def test_runAsScript_withoutOption(self):\n- self._writeOutputFile_withoutOption(self._expOutputFileName) \n- os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))\n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))\n- \n- def test_runAsScript_optionNFirstNucleotide(self):\n- self._writeOutputFile_NFirstNucleotide(self._expOutputFileName) \n- os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -S 200 -s 200 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))\n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))\n-\n- def test_runAsScript_optionNLastNucleotide(self):\n- self._writeOutputFile_NLastNucleotide(self._expOutputFileName) \n- os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -U 200 -u 200 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))\n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))\n-\n- def test_runAsScript_option_5PrimeExtension(self):\n- self._writeOutputFile_5PrimeExtension(self._expOutputFileName) \n- os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -E 110 -e 110 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))\n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))\n-\n- def test_runAsScript_option_3PrimeExtension(self):\n- self._writeOutputFile_3PrimeExtension(self._expOutputFileName) \n- os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -N 110 -n 110 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))\n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))\n- \n- def test_runAsScript_colinear(self):\n- self._writeOutputFile_colinear(self._expOutputFileName) \n- os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -c -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))\n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))\n-\n- def test_runAsScript_antisense(self):\n- self._writeOutputFile_antisense(self._expOutputFileName) \n- os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -a -v 0" % (SMART_PATH, self._inputFileQuery, self._inputFileReference, self._outputFileName))\n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))\n-\n- def test_runAsScript_minOverlap(self):\n- self._writeOutputFile_minOverlap(self._expOutputFileName) \n- os.system("python %s/Java/Python/CompareOverlapping.py -i %s -f bed -j %s -g bed -o %s -m 51 -v 0" % (SMART_PATH, self._inputFileQuery, self._inputF'..b'890\\t1999\\t.\\t-\\t.\\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\\n")\n- f.close() \n- \n- def _writeOutputFile_colinear(self, outputFileName):\n- f = open(outputFileName, "w")\n- f.write("arm_X\\tS-MART\\ttranscript\\t100\\t3199\\t.\\t+\\t.\\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\\n")\n- f.write("arm_X\\tS-MART\\ttranscript\\t1000\\t1999\\t.\\t+\\t.\\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\\n")\n- f.close() \n- \n- def _writeOutputFile_antisense(self, outputFileName):\n- f = open(outputFileName, "w")\n- f.write("arm_X\\tS-MART\\ttranscript\\t1000\\t1999\\t.\\t-\\t.\\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\\n")\n- f.close() \n- \n- def _writeOutputFile_minOverlap(self, outputFileName):\n- f = open(outputFileName, "w")\n- f.write("arm_X\\tS-MART\\ttranscript\\t100\\t3199\\t.\\t+\\t.\\toverlapWith=test2.3,test2.2,test2.1;nbOverlaps=3.000000;ID=test1.4;Name=test1.4\\n")\n- f.write("arm_X\\tS-MART\\ttranscript\\t1000\\t1999\\t.\\t+\\t.\\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\\n")\n- f.write("arm_X\\tS-MART\\ttranscript\\t1000\\t1999\\t.\\t-\\t.\\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\\n")\n- f.close() \n- \n- def _writeOutputFile_pcOverlap(self, outputFileName):\n- f = open(outputFileName, "w")\n- f.write("arm_X\\tS-MART\\ttranscript\\t1000\\t1999\\t.\\t+\\t.\\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\\n")\n- f.write("arm_X\\tS-MART\\ttranscript\\t1000\\t1999\\t.\\t-\\t.\\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\\n")\n- f.close() \n- \n- def _writeOutputFile_includeNotOverlap(self, outputFileName):\n- f = open(outputFileName, "w")\n- f.write("arm_X\\tS-MART\\ttranscript\\t100\\t3199\\t.\\t+\\t.\\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\\n")\n- f.write("arm_X\\tS-MART\\ttranscript\\t100\\t199\\t.\\t+\\t.\\tnbOverlaps=0;ID=test1.3;Name=test1.3\\n")\n- f.write("arm_X\\tS-MART\\ttranscript\\t1000\\t1999\\t.\\t+\\t.\\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\\n")\n- f.write("arm_X\\tS-MART\\ttranscript\\t1000\\t1999\\t.\\t-\\t.\\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\\n")\n- f.close()\n-\n- def _writeOutputFile_exclude(self, outputFileName):\n- f = open(outputFileName, "w")\n- f.write("arm_X\\tS-MART\\ttranscript\\t100\\t199\\t.\\t+\\t.\\tID=test1.3;Name=test1.3\\n")\n- f.close()\n- \n- def _writeOutputFile_included(self, outputFileName):\n- f = open(outputFileName, "w")\n- f.write("arm_X\\tS-MART\\ttranscript\\t1000\\t1999\\t.\\t+\\t.\\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\\n")\n- f.write("arm_X\\tS-MART\\ttranscript\\t1000\\t1999\\t.\\t-\\t.\\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\\n")\n- f.close()\n-\n- def _writeOutputFile_including(self, outputFileName):\n- f = open(outputFileName, "w")\n- f.write("arm_X\\tS-MART\\ttranscript\\t100\\t3199\\t.\\t+\\t.\\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.4;Name=test1.4\\n")\n- f.write("arm_X\\tS-MART\\ttranscript\\t1000\\t1999\\t.\\t+\\t.\\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.1;Name=test1.1\\n")\n- f.write("arm_X\\tS-MART\\ttranscript\\t1000\\t1999\\t.\\t-\\t.\\toverlapWith=test2.1;nbOverlaps=1.000000;ID=test1.2;Name=test1.2\\n")\n- f.close()\n-\n- def _writeInputFileQuery_withExon(self):\n- f = open(self._inputFileQuery, "w")\n- f.write("arm_X\\t1000\\t2000\\ttest1.1\\t1000\\t+\\t1000\\t2000\\t0\\t1\\t1000,\\t0,\\n")\n- f.write("arm_X\\t1000\\t2000\\ttest1.2\\t1000\\t-\\t1000\\t2000\\t0\\t1\\t1000,\\t0,\\n")\n- f.write("arm_X\\t100\\t200\\ttest1.3\\t1000\\t+\\t100\\t200\\t0\\t1\\t100,\\t0,\\n")\n- f.write("arm_X\\t100\\t3200\\ttest1.4\\t1000\\t+\\t100\\t3200\\t0\\t2\\t100,100,\\t0,3000,\\n")\n- f.close()\n- \n-if __name__ == "__main__":\n- unittest.main()\n'

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_convertTranscriptFile.py
--- a/SMART/Java/Python/test/Test_F_convertTranscriptFile.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,125 +0,0 @@\n-import unittest\n-import os\n-from SMART.Java.Python.misc import Utils\n-from commons.core.utils.FileUtils import FileUtils\n-\n-\n-class Test_F_convertTranscriptFile(unittest.TestCase):\n-\n- def setUp(self):\n- self._inputFileName = None\n- self._expOutputFileName = None\n- self._outputFileName = None\n-\n- def tearDown(self):\n- for fileName in (self._expOutputFileName, self._outputFileName):\n- if fileName != None and os.path.exists(fileName):\n- os.remove(fileName)\n-\n- def test_run_SAMtoGFF3(self):\n- self._inputFileName = "%s/SMART/Java/Python/test/input.sam" % (os.environ["REPET_PATH"])\n- self._writeInputSam(self._inputFileName)\n- self._outputFileName = \'%s/SMART/Java/Python/test/obsOutput.gff3\' % (os.environ["REPET_PATH"])\n- cmd = \'python %s/SMART/Java/Python/convertTranscriptFile.py -i %s -f sam -o %s -g gff3 -v 0\' % (os.environ["REPET_PATH"], self._inputFileName, self._outputFileName)\n- os.system(cmd)\n- self._expOutputFileName = \'%s/SMART/Java/Python/test/expOutput.gff3\' % (os.environ["REPET_PATH"])\n- self._writeExpGff3File_test1(self._expOutputFileName)\n- \n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))\n- os.remove(self._inputFileName)\n- \n- def test_run_BEDtoGFF3(self):\n- self._inputFileName = "%s/SMART/Java/Python/TestFiles/test_distance.bed" % (os.environ["REPET_PATH"])\n- self._outputFileName = \'%s/SMART/Java/Python/test/obsOutput.gff3\' % (os.environ["REPET_PATH"])\n- cmd = \'python %s/SMART/Java/Python/convertTranscriptFile.py -i %s -f bed -o %s -g gff3 -v 0\' % (os.environ["REPET_PATH"], self._inputFileName, self._outputFileName)\n- os.system(cmd)\n- self._expOutputFileName = \'%s/SMART/Java/Python/test/expOutput.gff3\' % (os.environ["REPET_PATH"])\n- self._writeExpGff3File_test2(self._expOutputFileName)\n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))\n- \n- def test_run_GFF3toCSV(self):\n- self._inputFileName = "%s/SMART/Java/Python/TestFiles/mapperAnalyzerExpected.gff3" % (os.environ["REPET_PATH"])\n- self._outputFileName = \'%s/SMART/Java/Python/test/obsOutput.csv\' % (os.environ["REPET_PATH"])\n- cmd = \'python %s/SMART/Java/Python/convertTranscriptFile.py -i %s -f gff3 -o %s -g csv -v 0\' % (os.environ["REPET_PATH"], self._inputFileName, self._outputFileName)\n- os.system(cmd)\n- self._expOutputFileName = \'%s/SMART/Java/Python/test/expOutput.csv\' % (os.environ["REPET_PATH"])\n- self._writeExpCsvFile(self._expOutputFileName)\n- \n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))\n- \n- def test_run_GFF3toSam(self):\n- self._inputFileName = "%s/SMART/Java/Python/TestFiles/mapperAnalyzerExpected.gff3" % (os.environ["REPET_PATH"])\n- self._outputFileName = \'%s/SMART/Java/Python/test/obsOutput.sam\' % (os.environ["REPET_PATH"])\n- cmd = \'python %s/SMART/Java/Python/convertTranscriptFile.py -i %s -f gff3 -o %s -g sam -v 0\' % (os.environ["REPET_PATH"], self._inputFileName, self._outputFileName)\n- os.system(cmd)\n- self._expOutputFileName = \'%s/SMART/Java/Python/test/expOutput.sam\' % (os.environ["REPET_PATH"])\n- self._writeExpSamFile(self._expOutputFileName)\n- self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))\n-\n- def test_run_Gff3toWig(self):\n- self._inputFileName = \'%s/SMART/Java/Python/TestFiles/sorted_query.gff3\' % (os.environ["REPET_PATH"])\n- self._outputFileName = \'%s/SMART/Java/Python/test/obsOutput.wig\' % (os.environ["REPET_PATH"])\n- cmd = \'python %s/SMART/Java/Python/convertTranscriptFile.py -i %s -f gff3 -o %s -g wig -v 0\' % (os.environ["REPET_PATH"], self._inputFileName, self._outputFileName)\n- os.system(cmd) \n- outputFile = \'%s/SMART/Java/Python/Test'..b'WWWWVWWWWVVWWWWWVVWWWWVVWWTTTTTR\\tXT:A:U\\tNM:i:0\\tSM:i:37\\tAM:i:37\\tX0:i:1\\tX1:i:0\\tXM:i:0\\tXO:i:0\\tXG:i:0\\tMD:Z:36\\n\' )\n- file.close()\n- \n- def _writeExpGff3File_test1(self, fileName):\n- file = open(fileName, \'w\')\n- file.write( \'C02HBa0185P07_LR40\\tSMART\\ttranscript\\t3889\\t3924\\t.\\t-\\t.\\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:415:1217;identity=100.000000;Name=HWI-EAS337_3:7:1:415:1217\\n\')\n- file.write( \'C02HBa0185P07_LR40\\tSMART\\ttranscript\\t3830\\t3865\\t.\\t+\\t.\\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:415:1217;identity=100.000000;Name=HWI-EAS337_3:7:1:415:1217\\n\')\n- file.write( \'C11SLe0053P22_LR298\\tSMART\\ttranscript\\t2130\\t2165\\t.\\t-\\t.\\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:1178:755;identity=100.000000;Name=HWI-EAS337_3:7:1:1178:755\\n\')\n- file.write( \'C11SLe0053P22_LR298\\tSMART\\ttranscript\\t1980\\t2015\\t.\\t+\\t.\\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:1178:755;identity=100.000000;Name=HWI-EAS337_3:7:1:1178:755\\n\')\n- file.write( \'C06HBa0144J05_LR355\\tSMART\\ttranscript\\t1\\t36\\t.\\t+\\t.\\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:277:1259;identity=100.000000;Name=HWI-EAS337_3:7:1:277:1259\\n\')\n- file.write( \'C06HBa0144J05_LR355\\tSMART\\ttranscript\\t101\\t136\\t.\\t-\\t.\\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:277:1259;identity=100.000000;Name=HWI-EAS337_3:7:1:277:1259\\n\')\n- file.write( \'C08HBa0165B06_LR218\\tSMART\\ttranscript\\t3619\\t3654\\t.\\t-\\t.\\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:447:1231;identity=100.000000;Name=HWI-EAS337_3:7:1:447:1231\\n\')\n- file.write( \'C08HBa0165B06_LR218\\tSMART\\ttranscript\\t3575\\t3610\\t.\\t+\\t.\\tquality=60;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0.000000;ID=HWI-EAS337_3:7:1:447:1231;identity=100.000000;Name=HWI-EAS337_3:7:1:447:1231\\n\')\n- file.close()\n- \n- def _writeExpGff3File_test2(self, fileName):\n- file = open(fileName, \'w\')\n- file.write( \'arm_X\\tSMART\\ttranscript\\t1000\\t1999\\t.\\t+\\t.\\tID=test2.1;Name=test2.1\\n\' )\n- file.write( \'arm_X\\tSMART\\ttranscript\\t250\\t349\\t.\\t+\\t.\\tID=test2.2;Name=test2.2\\n\' )\n- file.write( \'arm_X\\tSMART\\ttranscript\\t150\\t249\\t.\\t+\\t.\\tID=test2.3;Name=test2.3\\n\' )\n- file.close()\n- \n- def _writeExpCsvFile(self, fileName):\n- file = open(fileName, \'w\') \n- file.write( \'chromosome,start,end,strand,exons,ID,bestRegion,feature,identity,nbGaps,nbMismatches,nbOccurrences,occurrence,rank,score\\n\' )\n- file.write( \'chr1,6155418,6155441,"+",None,test1/1,(self),match,100,0,0,1,1,1,24\\n\' )\n- file.write( \'chr2,26303950,26303981,"+",None,test2/1-1,(self),match,93,0,2,3,1,1,32\\n\' )\n- file.write( \'chr3,28320540,28320574,"+",None,test2/1-2,chr2:26303950-26303981,match,94,0,2,3,2,None,35\\n\' )\n- file.write( \'chr4,28565007,28565041,"+",None,test2/1-3,chr2:26303950-26303981,match,88,0,4,3,3,3,35\\n\' )\n- file.close()\n- \n- def _writeExpSamFile(self, fileName):\n- file = open(fileName, \'w\')\n- file.write(\'@SQ\\tSN:chr4\\tLN:28565041\\n\')\n- file.write(\'@SQ\\tSN:chr3\\tLN:28320574\\n\')\n- file.write(\'@SQ\\tSN:chr2\\tLN:26303981\\n\')\n- file.write(\'@SQ\\tSN:chr1\\tLN:6155441\\n\')\n- file.write(\'test1/1\\t0\\tchr1\\t6155418\\t255\\t24M\\t*\\t0\\t0\\t*\\t*\\tNM:i:0\\n\')\n- file.write(\'test2/1\\t0\\tchr2\\t26303950\\t255\\t32M\\t*\\t0\\t0\\t*\\t*\\tNM:i:0\\n\')\n- file.write(\'test2/1\\t0\\tchr3\\t28320540\\t255\\t35M\\t*\\t0\\t0\\t*\\t*\\tNM:i:0\\n\')\n- file.write(\'test2/1\\t0\\tchr4\\t28565007\\t255\\t35M\\t*\\t0\\t0\\t*\\t*\\tNM:i:0\\n\')\n- file.close()\n-\n-\n-if __name__ == "__main__":\n- unittest.main()\n'

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_coordinatesToSequence.py
--- a/SMART/Java/Python/test/Test_F_coordinatesToSequence.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,31 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-
-TESTFILES_PATH = os.environ['REPET_PATH'] + '/SMART/Java/Python/TestFiles'
-
-class Test_F_coordinatesToSequence(unittest.TestCase):
-
-    def test_run(self):
-        cmd = "python ../coordinatesToSequence.py -i %s/testC2S.gff3 -f gff3 -s %s/testC2S.fa -o testOut.fa -v 10 " % (TESTFILES_PATH, TESTFILES_PATH)
-        os.system(cmd)
-        obs = 'testOut.fa'
-        exp = 'expOut.fa'
-        self._writeExpOut(exp)
-        self.assertTrue(FileUtils.isRessourceExists(obs))
-        self.assertTrue(FileUtils.are2FilesIdentical(obs, exp))
-        os.remove(obs)
-        os.remove(exp)
-
-    def _writeExpOut(self, outputFileName):
-        f = open(outputFileName, "w")
-        f.write(">region0\n")
-        f.write("CAACATTAGC\n")
-        f.write(">region1\n")
-        f.write("TTAGCCGGCC\n")
-        f.write(">region2\n")
-        f.write("GGCCGGCTAA\n")
-        f.close()
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_findTss.py
--- a/SMART/Java/Python/test/Test_F_findTss.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,93 +0,0 @@
-import unittest
-import os, os.path
-from SMART.Java.Python.misc import Utils
-
-
-TestF_PATH = os.environ['REPET_PATH'] + '/SMART/Java/Python/TestFiles'
-
-
-class Test_F_findTss(unittest.TestCase):
-
-    def setUp(self):
-        self._outputFileName = 'output.gff3'
-        self._expOutputFileName = 'expOutput.gff3'
-
-    def tearDown(self):
-        os.remove(self._outputFileName)
-        os.remove(self._expOutputFileName)
-
-    def test_run_default_option(self):
-        cmd = "python ../findTss.py -i %s/mapperAnalyzerExpected.gff3 -f gff3 -o output.gff3 -v 0" % TestF_PATH
-        os.system(cmd)
-        self._writeExpDefaultOption(self._expOutputFileName)
-        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
-
-    def test_run_normalize_option(self):
-        cmd = "python ../findTss.py -i %s/mapperAnalyzerExpected.gff3 -f gff3 -o output.gff3 -n -v 0" % TestF_PATH
-        os.system(cmd)
-        self._writeExpNormalizeOption(self._expOutputFileName)
-        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
-
-    def test_run_distance_option(self):
-        cmd = "python ../findTss.py -i %s/mapperAnalyzerExpected.gff3 -f gff3 -o output.gff3 -d 20 -v 0" % TestF_PATH
-        os.system(cmd)
-        self._writeExpDistance_option(self._expOutputFileName)
-        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
-
-    def test_run_colinear_option(self):
-        cmd = "python ../findTss.py -i %s/mapperAnalyzerExpected.gff3 -f gff3 -o output.gff3 -e -v 0" % TestF_PATH
-        os.system(cmd)
-        self._writeExpColinearOption(self._expOutputFileName)
-        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
-
-    def test_run_excel_option(self):
-        cmd = "python ../findTss.py -i %s/mapperAnalyzerExpected.gff3 -f gff3 -o output.gff3 -c output.csv -v 0" % TestF_PATH
-        os.system(cmd)
-        obsCsv = 'output.csv'
-        self.assertTrue(os.path.exists(obsCsv))
-        os.remove(obsCsv)
-        self._writeExpExcelOption(self._expOutputFileName)
-        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
-
-    def _writeExpDefaultOption(self, fileName):
-        f = open(fileName, 'w')
-        f.write("chr1\tS-MART\tmatch\t6155418\t6155418\t24\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
-        f.write("chr2\tS-MART\tmatch\t26303950\t26303950\t32\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
-        f.write("chr3\tS-MART\tmatch\t28320540\t28320540\t35\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
-        f.write("chr4\tS-MART\tmatch\t28565007\t28565007\t35\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
-        f.close()
-
-    def _writeExpNormalizeOption(self, fileName):
-        f = open(fileName, 'w')
-        f.write("chr1\tS-MART\tmatch\t6155418\t6155418\t24\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
-        f.write("chr2\tS-MART\tmatch\t26303950\t26303950\t32\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
-        f.write("chr3\tS-MART\tmatch\t28320540\t28320540\t35\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
-        f.write("chr4\tS-MART\tmatch\t28565007\t28565007\t35\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
-        f.close()
-
-    def _writeExpDistance_option(self, fileName):
-        f = open(fileName, 'w')
-        f.write("chr1\tS-MART\tmatch\t6155418\t6155418\t24\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
-        f.write("chr2\tS-MART\tmatch\t26303950\t26303950\t32\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
-        f.write("chr3\tS-MART\tmatch\t28320540\t28320540\t35\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
-        f.write("chr4\tS-MART\tmatch\t28565007\t28565007\t35\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
-        f.close()
-
-    def _writeExpColinearOption(self, fileName):
-        f = open(fileName, 'w')
-        f.write("chr1\tS-MART\tmatch\t6155418\t6155418\t24\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
-        f.write("chr2\tS-MART\tmatch\t26303950\t26303950\t32\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
-        f.write("chr3\tS-MART\tmatch\t28320540\t28320540\t35\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
-        f.write("chr4\tS-MART\tmatch\t28565007\t28565007\t35\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
-        f.close()
-
-    def _writeExpExcelOption(self, fileName):
-        f = open(fileName, 'w')
-        f.write("chr1\tS-MART\tmatch\t6155418\t6155418\t24\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1\n")
-        f.write("chr2\tS-MART\tmatch\t26303950\t26303950\t32\t+\t.\toccurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1\n")
-        f.write("chr3\tS-MART\tmatch\t28320540\t28320540\t35\t+\t.\toccurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1\n")
-        f.write("chr4\tS-MART\tmatch\t28565007\t28565007\t35\t+\t.\toccurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1\n")
-        f.close()
-
-if __name__ == "__main__":
-    unittest.main()

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_getExons.py
--- a/SMART/Java/Python/test/Test_F_getExons.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,145 +0,0 @@
-import unittest
-import os
-from SMART.Java.Python.getExons import GetExons
-from commons.core.parsing.GffParser import GffParser
-
-class Test_F_GetExons(unittest.TestCase):
-
-    def setUp(self):
-        self._inputFileName = "inputFileTest.bed"
-        self._writeInputFile()
-        self._outputFileName = "output.gff3"
-
-    def tearDown(self):
-        os.remove(self._inputFileName)
-        os.remove(self._outputFileName)
-
-    def test_run_simple(self):
-        ge = GetExons(0)
-        ge.setInputFile(self._inputFileName, "bed")
-        ge.setOutputFile(self._outputFileName)
-        ge.run()
-        parser = GffParser(self._outputFileName, 0)
-        self.assertEqual(parser.getNbTranscripts(), 5)
-        for cpt, transcript in enumerate(parser.getIterator()):
-            self.assertEqual(transcript.getChromosome(), "arm_X")
-            self.assertEqual(transcript.getDirection(), 1)
-            self.assertEqual(transcript.getNbExons(), 1)
-            if cpt == 0:
-                self.assertEqual(transcript.getStart(), 10000001)
-                self.assertEqual(transcript.getEnd(),   10000100)
-            elif cpt == 1:
-                self.assertEqual(transcript.getStart(), 10000201)
-                self.assertEqual(transcript.getEnd(),   10000300)
-            elif cpt == 2:
-                self.assertEqual(transcript.getStart(), 10000401)
-                self.assertEqual(transcript.getEnd(),   10000500)
-            elif cpt == 3:
-                self.assertEqual(transcript.getStart(), 10000601)
-                self.assertEqual(transcript.getEnd(),   10000700)
-            elif cpt == 4:
-                self.assertEqual(transcript.getStart(), 10000801)
-                self.assertEqual(transcript.getEnd(),   10000900)
-
-    def test_run_firstExon(self):
-        ge = GetExons(0)
-        ge.setInputFile(self._inputFileName, "bed")
-        ge.setOutputFile(self._outputFileName)
-        ge.setSelection("1")
-        ge.run()
-        parser = GffParser(self._outputFileName, 0)
-        self.assertEqual(parser.getNbTranscripts(), 1)
-        for cpt, transcript in enumerate(parser.getIterator()):
-            self.assertEqual(transcript.getChromosome(), "arm_X")
-            self.assertEqual(transcript.getDirection(), 1)
-            self.assertEqual(transcript.getNbExons(), 1)
-            self.assertEqual(transcript.getStart(), 10000001)
-            self.assertEqual(transcript.getEnd(),   10000100)
-
-    def test_run_lastExon(self):
-        ge = GetExons(0)
-        ge.setInputFile(self._inputFileName, "bed")
-        ge.setOutputFile(self._outputFileName)
-        ge.setSelection("-1")
-        ge.run()
-        parser = GffParser(self._outputFileName, 0)
-        self.assertEqual(parser.getNbTranscripts(), 1)
-        for cpt, transcript in enumerate(parser.getIterator()):
-            self.assertEqual(transcript.getChromosome(), "arm_X")
-            self.assertEqual(transcript.getDirection(), 1)
-            self.assertEqual(transcript.getNbExons(), 1)
-            self.assertEqual(transcript.getStart(), 10000801)
-            self.assertEqual(transcript.getEnd(),   10000900)
-
-    def test_run_first_lastExon(self):
-        ge = GetExons(0)
-        ge.setInputFile(self._inputFileName, "bed")
-        ge.setOutputFile(self._outputFileName)
-        ge.setSelection("1,-1")
-        ge.run()
-        parser = GffParser(self._outputFileName, 0)
-        self.assertEqual(parser.getNbTranscripts(), 2)
-        for cpt, transcript in enumerate(parser.getIterator()):
-            self.assertEqual(transcript.getChromosome(), "arm_X")
-            self.assertEqual(transcript.getDirection(), 1)
-            self.assertEqual(transcript.getNbExons(), 1)
-            if cpt == 0:
-                self.assertEqual(transcript.getStart(), 10000001)
-                self.assertEqual(transcript.getEnd(),   10000100)
-            elif cpt == 1:
-                self.assertEqual(transcript.getStart(), 10000801)
-                self.assertEqual(transcript.getEnd(),   10000900)
-
-    def test_run_interval(self):
-        ge = GetExons(0)
-        ge.setInputFile(self._inputFileName, "bed")
-        ge.setOutputFile(self._outputFileName)
-        ge.setSelection("2..3")
-        ge.run()
-        parser = GffParser(self._outputFileName, 0)
-        self.assertEqual(parser.getNbTranscripts(), 2)
-        for cpt, transcript in enumerate(parser.getIterator()):
-            self.assertEqual(transcript.getChromosome(), "arm_X")
-            self.assertEqual(transcript.getDirection(), 1)
-            self.assertEqual(transcript.getNbExons(), 1)
-            if cpt == 0:
-                self.assertEqual(transcript.getStart(), 10000201)
-                self.assertEqual(transcript.getEnd(),   10000300)
-            elif cpt == 1:
-                self.assertEqual(transcript.getStart(), 10000401)
-                self.assertEqual(transcript.getEnd(),   10000500)
-
-    def test_run_interval_element(self):
-        ge = GetExons(0)
-        ge.setInputFile(self._inputFileName, "bed")
-        ge.setOutputFile(self._outputFileName)
-        ge.setSelection("2..3,-1")
-        ge.run()
-        parser = GffParser(self._outputFileName, 0)
-        self.assertEqual(parser.getNbTranscripts(), 3)
-        for cpt, transcript in enumerate(parser.getIterator()):
-            self.assertEqual(transcript.getChromosome(), "arm_X")
-            self.assertEqual(transcript.getDirection(), 1)
-            self.assertEqual(transcript.getNbExons(), 1)
-            if cpt == 0:
-                self.assertEqual(transcript.getStart(), 10000201)
-                self.assertEqual(transcript.getEnd(),   10000300)
-            elif cpt == 1:
-                self.assertEqual(transcript.getStart(), 10000401)
-                self.assertEqual(transcript.getEnd(),   10000500)
-            elif cpt == 2:
-                self.assertEqual(transcript.getStart(), 10000801)
-                self.assertEqual(transcript.getEnd(),   10000900)
-
-
-
-    def _writeInputFile(self):
-        f = open(self._inputFileName, "w")
-        f.write("arm_X\t10000001\t10000900\ttest1.1\t100\t+\t10000100\t10000200\t0\t5\t100,100,100,100,100,\t0,200,400,600,800,\n")
-        f.close()
-
-
-
-if __name__ == "__main__":
-    unittest.main()
-

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_getLetterDistribution.py
--- a/SMART/Java/Python/test/Test_F_getLetterDistribution.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,118 +0,0 @@
-import os
-import sys
-import unittest
-from SMART.Java.Python.test.MockGetLetterDistribution import MockGetLetterDistributionFasta
-from SMART.Java.Python.test.MockGetLetterDistribution import MockGetLetterDistributionFastq
-from SMART.Java.Python.test.MockGetLetterDistribution import MockGetLetterDistributionExpectedCSV
-
-class Test_F_getLetterDistribution(unittest.TestCase):
-
- def tearDown(self):
- os.system("rm tmp*.*")
-
- def test_getLetterDistributionWithFasta(self):
- iFastaMock = MockGetLetterDistributionFasta()
- fastaFileName = "MockFasta_GetLetterDistribution.fa"
- iFastaMock.write(fastaFileName)
-
- outputName = "dummy_result_fasta"
- os.system("python %s/SMART/Java/Python/getLetterDistribution.py -i %s -f fasta -o %s" % (os.environ["REPET_PATH"], fastaFileName, outputName))
-
- self.assertTrue (os.path.exists(outputName + ".png"))
- self.assertTrue (os.path.exists(outputName + "PerNt.png"))
-
- os.remove(outputName + ".png")
- os.remove(outputName + "PerNt.png")
- os.remove(fastaFileName)
-
- def test_getLetterDistributionWithFastq(self):
- iFastqMock = MockGetLetterDistributionFastq()
- fastqFileName = "MockFastq_GetLetterDistribution.fastq"
- iFastqMock.write(fastqFileName)
-
- outputName = "dummy_result_fastq"
- os.system("python %s/SMART/Java/Python/getLetterDistribution.py -i %s -f fastq -o %s" % (os.environ["REPET_PATH"], fastqFileName, outputName))
-
- self.assertTrue (os.path.exists(outputName + ".png"))
- self.assertTrue (os.path.exists(outputName + "PerNt.png"))
-
- os.remove(fastqFileName)
- os.remove(outputName + ".png")
- os.remove(outputName + "PerNt.png")
-
- def test_getLetterDistributionWithFastaCSVOutput(self):
- iFastaMock = MockGetLetterDistributionFasta()
- fastaFileName = "MockFasta_GetLetterDistribution.fa"
- iFastaMock.write(fastaFileName)
-
- iCSVMock = MockGetLetterDistributionExpectedCSV()
- expCSVFileName = "expCSV.csv"
- iCSVMock.write(expCSVFileName)
-
- outputName = "dummy_result_fasta"
- os.system("python %s/SMART/Java/Python/getLetterDistribution.py -i %s -f fasta -o %s -c" % (os.environ["REPET_PATH"], fastaFileName, outputName))
-
- obsCSVFileName = outputName + ".csv"
-
- self.assertTrue (os.path.exists(outputName + ".png"))
- self.assertTrue (os.path.exists(outputName + "PerNt.png"))
- self.assertTrue (self._are2FilesIdentical(expCSVFileName, obsCSVFileName))
-
- os.remove(outputName + ".png")
- os.remove(outputName + "PerNt.png")
- os.remove(fastaFileName)
- os.remove(expCSVFileName)
- os.remove(obsCSVFileName)
-
- def test_getLetterDistributionWithFastqCVSOutput(self):
- iFastqMock = MockGetLetterDistributionFastq()
- fastqFileName = "MockFastq_GetLetterDistribution.fastq"
- iFastqMock.write(fastqFileName)
-
- iCSVMock = MockGetLetterDistributionExpectedCSV()
- expCSVFileName = "expCSV.csv"
- iCSVMock.write(expCSVFileName)
-
- outputName = "dummy_result_fastq"
- os.system("python %s/SMART/Java/Python/getLetterDistribution.py -i %s -f fastq -o %s -c" % (os.environ["REPET_PATH"], fastqFileName, outputName))
-
- obsCSVFileName = outputName + ".csv"
-
- self.assertTrue (os.path.exists(outputName + ".png"))
- self.assertTrue (os.path.exists(outputName + "PerNt.png"))
- self.assertTrue (self._are2FilesIdentical(expCSVFileName, obsCSVFileName))
-
- os.remove(fastqFileName)
- os.remove(outputName + ".png")
- os.remove(outputName + "PerNt.png")
- os.remove(expCSVFileName)
- os.remove(obsCSVFileName)
-
- def _are2FilesIdentical(self, file1, file2 ):
- tmpFile = "diff_%s_%s" % ( os.path.basename(file1), os.path.basename(file2) )
- cmd = "diff %s %s >> %s" % ( file1, file2, tmpFile )
- returnStatus = os.system( cmd )
- if returnStatus != 0:
- msg = "ERROR: 'diff' returned '%i'" % ( returnStatus )
- sys.stderr.write( "%s\n" % msg )
- sys.stderr.flush()
- os.remove( tmpFile )
- return False
- if self.isEmpty( tmpFile ):
- os.remove( tmpFile )
- return True
- else:
- os.remove( tmpFile )
- return False
-
- def getNbLinesInSingleFile(self, fileName):
- fileHandler = open(fileName, "r" )
- lines = fileHandler.readlines()
- fileHandler.close()
- return len(lines)
-
- def isEmpty(self, fileName):
- return 0 == self.getNbLinesInSingleFile( fileName )
-
-if __name__ == "__main__":
- unittest.main()

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_getRandomRegions.py
--- a/SMART/Java/Python/test/Test_F_getRandomRegions.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,66 +0,0 @@
-import unittest
-import os
-from commons.core.parsing.GffParser import GffParser
-from SMART.Java.Python.getRandomRegions import RandomRegionsGenerator
-
-MIN_SIZE = 36
-MAX_SIZE = 100
-CHR      = "chr1"
-CHR_SIZE = 1000000
-NB_READS = 1000
-
-class Test_F_getRandomRegions(unittest.TestCase):
-
-    def setUp(self):
-        self._outputFileName = 'output.gff3'
-
-    def tearDown(self):
-        for fileName in [self._outputFileName]:
-            if os.path.exists(fileName):
-                os.remove(fileName)
-
-    def test_simple(self):
-        iRR = RandomRegionsGenerator(0)
-        iRR.setMinSize(MIN_SIZE)
-        iRR.setMaxSize(MAX_SIZE)
-        iRR.setGenomeSize(CHR_SIZE)
-        iRR.setChromosomeName(CHR)
-        iRR.setStrands(False)
-        iRR.setNumber(NB_READS)
-        iRR.setOutputFile(self._outputFileName)
-        iRR.run()
-        parser = GffParser(self._outputFileName, 0)
-        starts = set()
-        self.assertTrue(parser.getNbTranscripts(), CHR_SIZE)
-        for transcript in parser.getIterator():
-            start      = transcript.getStart()
-            end        = transcript.getEnd()
-            size       = transcript.getSize()
-            chromosome = transcript.getChromosome()
-            strand     = transcript.getDirection()
-            self.assertTrue(start not in starts)
-            self.assertTrue(start >= 1)
-            self.assertTrue(end <= CHR_SIZE)
-            self.assertEquals(chromosome, CHR)
-            self.assertEquals(strand, 1)
-            starts.add(start)
-
-    def test_both_strands(self):
-        iRR = RandomRegionsGenerator(0)
-        iRR.setMinSize(MIN_SIZE)
-        iRR.setMaxSize(MAX_SIZE)
-        iRR.setGenomeSize(CHR_SIZE)
-        iRR.setChromosomeName(CHR)
-        iRR.setStrands(True)
-        iRR.setNumber(NB_READS)
-        iRR.setOutputFile(self._outputFileName)
-        iRR.run()
-        parser = GffParser(self._outputFileName, 0)
-        strands = set()
-        for transcript in parser.getIterator():
-            strands.add(transcript.getDirection())
-        self.assertTrue(1 in strands)
-        self.assertTrue(-1 in strands)
-
-if __name__ == "__main__":
-    unittest.main()

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_getReadDistribution.py
--- a/SMART/Java/Python/test/Test_F_getReadDistribution.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,37 +0,0 @@
-import unittest
-import os, glob
-
-
-class Test_F_getReadDistribution(unittest.TestCase):
-
-    def setUp(self):
-        self.inputFileName  = "inputFile.fasta"
-        self.outputFileName = "outputFile"
-
-    def tearDown(self):
-        for fileRoot in (self.inputFileName, self.outputFileName):
-            for file in glob.glob("%s*" % (fileRoot)):
-                os.remove(file)
-        os.system("rm .RData")
-
-    def test_run_simple(self):
-        handle = open(self.inputFileName, "w")
-        handle.write(">test1\n")
-        handle.write("AAAAAA\n")
-        handle.write(">test2\n")
-        handle.write("AAAAAA\n")
-        handle.write(">test3\n")
-        handle.write("CCCCCC\n")
-        handle.close()
-        handle.close()
-        os.system("python ../getReadDistribution.py -i %s -f fasta -n 1 -o %s -v 0" % (self.inputFileName, self.outputFileName))
-        self.assertTrue(os.path.exists("%s.png" % (self.outputFileName)))
-        handle = open("%s.txt" % (self.outputFileName))
-        lines = handle.readlines()
-        self.assertEquals(len(lines), 1)
-        self.assertEquals(lines[0], "AAAAAA\t2\n")
-
-
-if __name__ == "__main__":
-    unittest.main()
-

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_getWigData.py
--- a/SMART/Java/Python/test/Test_F_getWigData.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,71 +0,0 @@
-import unittest
-import os, os.path
-from SMART.Java.Python.misc import Utils
-from SMART.Java.Python.getWigData import *
-
-class Test_F_getWigData(unittest.TestCase):
-
-
-    def setUp(self):
-        self._inputGffFileName = 'inputGff.gff3'
-        self._writeInputGff(self._inputGffFileName)
-        self._inputWigFileName = '../TestFiles/sorted_query_wig.wig'
-        self._expOutFileName = 'expOut.gff3'
-        self._outFileName = 'outGffWig.gff3'
-
-
-    def tearDown(self):
-        os.remove(self._inputGffFileName)
-        os.remove(self._expOutFileName)
-        os.remove(self._outFileName)
-
-
-    def test_getWigData_DefaultOption_asScript(self):
-        cmd = 'python ../getWigData.py -i %s -f gff3 -w %s -t wigValue -o %s -v 0' % (self._inputGffFileName, self._inputWigFileName, self._outFileName)
-        os.system(cmd)
-        self._writeExpDefaultOption(self._expOutFileName)
-        self.assertTrue(Utils.diff(self._expOutFileName, self._outFileName))
-
-    def test_getWigData_strandsOption(self):
-        cmd = 'python ../getWigData.py -i %s -f gff3 -w %s -t wigValue -o %s -s -v 0' % (self._inputGffFileName, self._inputWigFileName, self._outFileName)
-        os.system(cmd)
-        self._writeExpStransOption(self._expOutFileName)
-        self.assertTrue(Utils.diff(self._expOutFileName, self._outFileName))
-
-
-    def _writeInputGff(self, fileName):
-        f = open(fileName, 'w')
-        f.write("chr1\tquery\ttest1.1\t25\t150\t126\t+\t.\tID=query_1;Name=test1.1\n")
-        f.write("chr1\tquery\ttest1.2\t70\t850\t781\t-\t.\tID=query_2;Name=test1.2\n")
-        f.write("chr1\tquery\ttest1.3\t550\t850\t201\t-\t.\tID=query_3;Name=test1.3\n")
-        f.write("chr1\tquery\ttest1.4\t925\t1025\t101\t+\t.\tID=query_4;Name=test1.4\n")
-        f.write("chr1\tquery\ttest1.5\t1201\t1210\t10\t+\t.\tID=query_5;Name=test1.5\n")
-        f.write("chr1\tquery\ttest1.6\t1500\t1600\t101\t+\t.\tID=query_6;Name=test1.6\n")
-        f.close()
-
-    def _writeExpDefaultOption(self, fileName):
-        f = open(fileName, 'w')
-        f.write("chr1\tS-MART\ttest1.1\t25\t150\t126\t+\t.\twigValue=1.64285714286;ID=query_1;Name=test1.1\n")
-        f.write("chr1\tS-MART\ttest1.2\t70\t850\t781\t-\t.\twigValue=1.48911651729;ID=query_2;Name=test1.2\n")
-        f.write("chr1\tS-MART\ttest1.3\t550\t850\t201\t-\t.\twigValue=2.0;ID=query_3;Name=test1.3\n")
-        f.write("chr1\tS-MART\ttest1.4\t925\t1025\t101\t+\t.\twigValue=1.0;ID=query_4;Name=test1.4\n")
-        f.write("chr1\tS-MART\ttest1.5\t1201\t1210\t10\t+\t.\twigValue=1.0;ID=query_5;Name=test1.5\n")
-        f.write("chr1\tS-MART\ttest1.6\t1500\t1600\t101\t+\t.\twigValue=1.0;ID=query_6;Name=test1.6\n")
-        f.close()
-
-    def _writeExpStransOption(self, fileName):
-        f = open(fileName, 'w')
-        f.write("chr1\tS-MART\ttest1.1\t25\t150\t126\t+\t.\twigValue=0.0;ID=query_1;Name=test1.1\n")
-        f.write("chr1\tS-MART\ttest1.2\t70\t850\t781\t-\t.\twigValue=0.0;ID=query_2;Name=test1.2\n")
-        f.write("chr1\tS-MART\ttest1.3\t550\t850\t201\t-\t.\twigValue=0.0;ID=query_3;Name=test1.3\n")
-        f.write("chr1\tS-MART\ttest1.4\t925\t1025\t101\t+\t.\twigValue=0.0;ID=query_4;Name=test1.4\n")
-        f.write("chr1\tS-MART\ttest1.5\t1201\t1210\t10\t+\t.\twigValue=0.0;ID=query_5;Name=test1.5\n")
-        f.write("chr1\tS-MART\ttest1.6\t1500\t1600\t101\t+\t.\twigValue=0.0;ID=query_6;Name=test1.6\n")
-        f.close()
-
-
-
-
-
-if __name__ == "__main__":
-    unittest.main()

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_getWigDistance.py
--- a/SMART/Java/Python/test/Test_F_getWigDistance.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,45 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-from SMART.Java.Python.getWigDistance import *
-
-class Test_F_getWigDistance(unittest.TestCase):
-
-
-    def setUp(self):
-        self._inputGffFileName = 'inputGff.gff3'
-        self._writeInputGff(self._inputGffFileName)
-        self._inputWigFileName = '../TestFiles/sorted_query_wig.wig'
-        self._outFileName = 'outGffWig.png'
-
-    def tearDown(self):
-        os.remove(self._inputGffFileName)
-        os.remove(self._outFileName)
-
-    def test_getWigDistance_defaultOption(self):
-        cmd = 'python ../getWigDistance.py -i %s -f gff3 -w %s -d 10 -o %s' % (self._inputGffFileName, self._inputWigFileName, self._outFileName)
-        os.system(cmd)
-
-    def test_getWigDistance_strandsOption(self):
-        cmd = 'python ../getWigDistance.py -i %s -f gff3 -w %s -d 10 -o %s -s' % (self._inputGffFileName, self._inputWigFileName, self._outFileName)
-        os.system(cmd)
-
-    def test_getWigDistance_logOption(self):
-        cmd = 'python ../getWigDistance.py -i %s -f gff3 -w %s -d 10 -o %s -l' % (self._inputGffFileName, self._inputWigFileName, self._outFileName)
-        os.system(cmd)
-
-    def _writeInputGff(self, fileName):
-        f = open(fileName, 'w')
-        f.write("chr1\tquery\ttest1.1\t25\t150\t126\t+\t.\tID=query_1;Name=test1.1\n")
-        f.write("chr1\tquery\ttest1.2\t70\t850\t781\t-\t.\tID=query_2;Name=test1.2\n")
-        f.write("chr1\tquery\ttest1.3\t550\t850\t201\t-\t.\tID=query_3;Name=test1.3\n")
-        f.write("chr1\tquery\ttest1.4\t925\t1025\t101\t+\t.\tID=query_4;Name=test1.4\n")
-        f.write("chr1\tquery\ttest1.5\t1201\t1210\t10\t+\t.\tID=query_5;Name=test1.5\n")
-        f.write("chr1\tquery\ttest1.6\t1500\t1600\t101\t+\t.\tID=query_6;Name=test1.6\n")
-        f.close()
-
-
-
-if __name__ == "__main__":
-    #import sys;sys.argv = ['', 'Test.testName']
-    unittest.main()
\ No newline at end of file

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_getWigProfile.py
--- a/SMART/Java/Python/test/Test_F_getWigProfile.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,65 +0,0 @@
-import unittest
-import os, glob
-from SMART.Java.Python.getWigProfile import GetWigProfile
-
-
-class Test_F_GetWigProfile(unittest.TestCase):
-
-    def setUp(self):
-        self.transcriptFileName = "transcriptFile.gff3"
-        self.wigFileName        = "file.wig"
-        self.outputFileName     = "outputFile.png"
-
-    def tearDown(self):
-        for fileRoot in (self.transcriptFileName, self.wigFileName, self.outputFileName):
-            for file in glob.glob("%s*" % (fileRoot)):
-                os.remove(file)
-        os.system("rm .RData .chr1.index ")
-
-    def test_run_simple(self):
-        handle = open(self.transcriptFileName, "w")
-        handle.write("chr1\tSMART\tmRNA\t10\t20\t.\t+\t.\tID=test1;Name=test1")
-        handle.close()
-        handle = open(self.wigFileName, "w")
-        handle.write("variableStep chrom=chr1\n")
-        handle.write("1 1\n")
-        handle.write("2 1\n")
-        handle.write("3 1\n")
-        handle.write("4 1\n")
-        handle.write("5 1\n")
-        handle.write("6 1\n")
-        handle.write("7 1\n")
-        handle.write("8 1\n")
-        handle.write("9 1\n")
-        handle.write("10 1\n")
-        handle.write("11 2\n")
-        handle.write("12 3\n")
-        handle.write("13 4\n")
-        handle.write("14 5\n")
-        handle.write("15 5\n")
-        handle.write("16 5\n")
-        handle.write("17 5\n")
-        handle.write("18 5\n")
-        handle.write("19 5\n")
-        handle.write("20 5\n")
-        handle.write("21 1\n")
-        handle.write("21 1\n")
-        handle.close()
-        wigProfile = GetWigProfile(0)
-        wigProfile.strands        = False
-        wigProfile.inputFileName  = self.transcriptFileName
-        wigProfile.inputFormat    = "gff3"
-        wigProfile.wig            = self.wigFileName
-        wigProfile.nbPoints       = 11
-        wigProfile.distance       = 1
-        wigProfile.smoothenForce  = None
-        wigProfile.log            = False
-        wigProfile.outputFileName = self.outputFileName
-        wigProfile.readTranscripts()
-        wigProfile.smoothen()
-        wigProfile.plot()
-        self.assertTrue(os.path.exists(self.outputFileName))
-
-if __name__ == "__main__":
-    unittest.main()
-

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_mapperAnalyzer.py
--- a/SMART/Java/Python/test/Test_F_mapperAnalyzer.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,55 +0,0 @@
-import unittest
-import os, glob
-from SMART.Java.Python.mapperAnalyzer import MapperAnalyzer
-from commons.core.parsing.GffParser import GffParser
-
-class Test_F_mapperAnalyzer(unittest.TestCase):
-
-    def setUp(self):
-        self.readsFileName   = "inputFile.fastq"
-        self.mappingFileName = "inputFile.sam"
-        self.outputFileName  = "outputFile.gff3"
-
-    def tearDown(self):
-        for fileRoot in (self.readsFileName, self.mappingFileName, self.outputFileName):
-            for file in glob.glob("%s*" % (fileRoot)):
-                os.remove(file)
-        os.system("rm tmpNames_* tmpSequences_* smartdb*")
-
-    def test_run_simple(self):
-        handle = open(self.readsFileName, "w")
-        handle.write("@read1\n")
-        handle.write("AAAAAAAAAAAAAAAAAAAA\n")
-        handle.write("+\n")
-        handle.write("AAAAAAAAAAAAAAAAAAAA\n")
-        handle.write("@read2\n")
-        handle.write("CCCCCCCCCCCCCCCCCCCC\n")
-        handle.write("+\n")
-        handle.write("AAAAAAAAAAAAAAAAAAAA\n")
-        handle.close()
-        handle = open(self.mappingFileName, "w")
-        handle.write("read1\t0\tchr1\t1\t30\t20M\t*\t0\t0\tAAAAAAAAAAAAAAAAAAAA\tAAAAAAAAAAAAAAAAAAAA\tNM:i:0\n")
-        handle.write("read2\t0\tchr2\t1\t30\t20M\t*\t0\t0\tCCCCCCCCCCCCCCCCCCCC\tAAAAAAAAAAAAAAAAAAAA\tNM:i:0\n")
-        handle.write("read2\t0\tchr3\t1\t30\t20M\t*\t0\t0\tCCCCCCCCCCCCCCCCCCCC\tAAAAAAAAAAAAAAAAAAAA\tNM:i:0\n")
-        handle.close()
-        analyzer = MapperAnalyzer(0)
-        analyzer.setMappingFile(self.mappingFileName, "sam")
-        analyzer.setSequenceFile(self.readsFileName, "fastq")
-        analyzer.setOutputFile(self.outputFileName, "S-MART")
-        analyzer.setMaxMappings(1)
-        analyzer.mergeExons(True)
-        analyzer.analyze()
-
-        parser = GffParser(self.outputFileName)
-        self.assertEqual(parser.getNbTranscripts(), 1)
-        for transcript in parser.getIterator():
-            self.assertEqual(transcript.getName(), "read1")
-            self.assertEqual(transcript.getChromosome(), "chr1")
-            self.assertEqual(transcript.getStart(), 1)
-            self.assertEqual(transcript.getEnd(), 20)
-            self.assertEqual(transcript.getDirection(), 1)
-
-
-if __name__ == "__main__":
-    unittest.main()
-

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_mappingToCoordinates.py
--- a/SMART/Java/Python/test/Test_F_mappingToCoordinates.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,22 +0,0 @@
-import unittest
-import os
-from SMART.Java.Python.misc import Utils
-
-class Test_F_mappingToCoordinates(unittest.TestCase):
-
-
-    def setUp(self):
-        self._inputFileName = 'inputMTC.sam'
-        self._outputFileName = 'outputGff.gff3'
-        self._expOutputFileName = '../TestFiles/expOutputGff.gff3'
-
-    def tearDown(self):
-        os.remove(self._outputFileName)
-
-    def test_run_default_option(self):
-        cmd = 'python ../mappingToCoordinates.py -i ../TestFiles/%s -f sam -o %s -v 0' % (self._inputFileName, self._outputFileName)
-        os.system(cmd)
-        self.assertTrue(Utils.diff(self._outputFileName, self._expOutputFileName))
-
-if __name__ == "__main__":
-    unittest.main()

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_mergeSlidingWindowsClusters.py
--- a/SMART/Java/Python/test/Test_F_mergeSlidingWindowsClusters.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,80 +0,0 @@
-import unittest
-import os
-from SMART.Java.Python.mergeSlidingWindowsClusters import MergeSlidingWindowsClusters
-from SMART.Java.Python.misc import Utils
-
-class Test_F_mergeSlidingWindowsClusters(unittest.TestCase):
-
-
-    def setUp(self):
-        self._outputFileName = 'outputMSWC'
-        self._inputFileName1 = 'inputMSWC1.gff3'
-        self._inputFileName2 = 'inputMSWC2.gff3'
-        self._writeInput1(self._inputFileName1)
-        self._writeInput2(self._inputFileName2)
-        self._expOutput = 'expOutputMSWC.gff3'
-        self._writeExpOutput(self._expOutput)
-
-    def tearDown(self):
-        os.remove(self._inputFileName1)
-        os.remove(self._inputFileName2)
-        os.remove(self._outputFileName+'.gff3')
-        os.remove(self._expOutput)
-
-
-    def test_run(self):
-        iMSWC = MergeSlidingWindowsClusters(0)
-        iMSWC.addInput(self._inputFileName1, 'gff3')
-        iMSWC.addInput(self._inputFileName2, 'gff3')
-        iMSWC.setOutput(self._outputFileName)
-        iMSWC.merge()
-        self.assertTrue(Utils.diff(self._outputFileName+'.gff3', self._expOutput))
-
-    def test_run_asScript(self):
-        cmd = 'python ../mergeSlidingWindowsClusters.py -i %s -f gff3 -j %s -g gff3 -o outputMSWC.gff3 --galaxy -v 0' % (self._inputFileName1, self._inputFileName2)
-        os.system(cmd)
-        self.assertTrue(Utils.diff(self._outputFileName+'.gff3', self._expOutput))
-
-    def _writeInput1(self, fileName):
-        f = open(fileName, 'w')
-        f.write("chr1\ttest\tmatch\t6155418\t6155441\t24\t+\t.\tName=test1/1;occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100\n")
-        f.write("chr2\ttest\tmatch\t26303950\t26303981\t32\t+\t.\tName=test2/1;occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93\n")
-        f.write("chr3\ttest\tmatch\t28320540\t28320574\t35\t+\t.\tName=test2/1;occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94\n")
-        f.write("chr4\ttest\tmatch\t28565007\t28565041\t35\t+\t.\tName=test2/1;occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88\n")
-        f.write("chr6\ttest\tmatch\t48565007\t48565041\t35\t+\t.\tName=test2/1;occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=3;ID=test2/1-4;identity=80\n")
-        f.close()
-
-    def _writeInput2(self, fileName):
-        f = open(fileName, 'w')
-        f.write("chr1\ttest\tmatch\t6155418\t6155441\t24\t+\t.\tName=test1/1;occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100\n")
-        f.write("chr2\ttest\tmatch\t26303990\t26304021\t32\t+\t.\tName=test2/1;occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93\n")
-        f.write("chr3\ttest\tmatch\t28320540\t28320574\t35\t+\t.\tName=test2/1;occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94\n")
-        f.write("chr4\ttest\tmatch\t28565017\t28565051\t35\t+\t.\tName=test2/1;occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88\n")
-        f.write("chr5\ttest\tmatch\t30000000\t30000050\t50\t+\t.\tName=test3/1;occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=1;ID=test3/1-4;identity=50\n")
-        f.close()
-
-    def _writeExpOutput(self, fileName):
-        f = open(fileName, 'w')
-        f.write("""chr6 S-MART match 48565007 48565041 35 + . occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=3;ID=test2/1-4;identity=80;Name=region_1
-chr5 S-MART match 30000000 30000050 50 + . occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=1;ID=test3/1-4;identity=50;Name=region_2
-chr4 S-MART match 28565017 28565051 35 + . occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=region_3
-chr4 S-MART match 28565007 28565041 35 + . occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=region_4
-chr3 S-MART match 28320540 28320574 35 + . occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=region_5
-chr2 S-MART match 26303990 26304021 32 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=region_6
-chr2 S-MART match 26303950 26303981 32 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=region_7
-chr1 S-MART match 6155418 6155441 24 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=region_8
-""")
-#       f.write("chr6\tS-MART\tmatch\t48565007\t48565041\t35\t+\t.\tName=region_1;occurrence=3;feature=match;rank=3;score=35;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=3;ID=test2/1-4;identity=80\n")
-#       f.write("chr5\tS-MART\tmatch\t30000000\t30000050\t50\t+\t.\tName=region_2;occurrence=3;feature=match;rank=3;score=50;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=1;ID=test3/1-4;identity=50\n")
-#       f.write("chr4\tS-MART\tmatch\t28565017\t28565051\t35\t+\t.\tName=region_3;occurrence=3;feature=match;rank=3;score=35;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88\n")
-#       f.write("chr4\tS-MART\tmatch\t28565007\t28565041\t35\t+\t.\tName=region_4;occurrence=3;feature=match;rank=3;score=35;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88\n")
-#       f.write("chr3\tS-MART\tmatch\t28320540\t28320574\t35\t+\t.\tName=region_5;occurrence=2;feature=match;score=35;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94\n")
-#       f.write("chr2\tS-MART\tmatch\t26303990\t26304021\t32\t+\t.\tName=region_6;occurrence=1;feature=match;rank=1;score=32;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93\n")
-#       f.write("chr2\tS-MART\tmatch\t26303950\t26303981\t32\t+\t.\tName=region_7;occurrence=1;feature=match;rank=1;score=32;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93\n")
-#       f.write("chr1\tS-MART\tmatch\t6155418\t6155441\t24\t+\t.\tName=region_8;occurrence=1;feature=match;rank=1;score=24;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100\n")
-        f.close()
-
-
-
-if __name__ == "__main__":
-    unittest.main()

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_mergeTranscriptLists.py
--- a/SMART/Java/Python/test/Test_F_mergeTranscriptLists.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,92 +0,0 @@
-import unittest
-import os, os.path, glob
-from SMART.Java.Python.structure.Transcript import Transcript
-from SMART.Java.Python.mergeTranscriptLists import MergeLists
-from commons.core.writer.Gff3Writer import Gff3Writer
-from commons.core.parsing.GffParser import GffParser
-
-class Test_F_mergeTranscriptLists(unittest.TestCase):
-
-    def setUp(self):
-        self.queryFileName     = "testQuery.gff3"
-        self.referenceFileName = "testReference.gff3"
-        self.outputFileName    = "testOutput.gff3"
-
-    def tearDown(self):
-        for fileRoot in (self.queryFileName, self.referenceFileName, self.outputFileName):
-            for file in glob.glob("%s*" % (fileRoot)):
-                os.remove(file)
-        for file in glob.glob("tmp_*.gff3"):
-            os.remove(file)
-
-    def test_run_simple(self):
-        reference1 = self._createTranscript("chr1", 1000, 2000, "+", "ref1")
-        reference2 = self._createTranscript("chr1", 3000, 4000, "+", "ref2")
-        reference3 = self._createTranscript("chr1", 5000, 6000, "+", "ref3")
-        writer = Gff3Writer(self.referenceFileName, 0)
-        writer.addTranscript(reference1)
-        writer.addTranscript(reference2)
-        writer.addTranscript(reference3)
-        writer.close()
-        query1 = self._createTranscript("chr1", 1500, 3500, "+", "query1")
-        writer = Gff3Writer(self.queryFileName, 0)
-        writer.addTranscript(query1)
-        writer.close()
-        ml = MergeLists(0)
-        ml.setInputFileName(self.queryFileName, 'gff3', 0)
-        ml.setInputFileName(self.referenceFileName, 'gff3', 1)
-        ml.setOutputFileName(self.outputFileName)
-        ml.run()
-        parser = GffParser(self.outputFileName)
-        self.assertEqual(parser.getNbTranscripts(), 1)
-        for transcript in parser.getIterator():
-            self._checkTranscript(transcript, "chr1", 1000, 4000, "+", None)
-
-    def test_run_simple_aggregate(self):
-        reference1 = self._createTranscript("chr1", 1000, 2000, "+", "ref1")
-        reference2 = self._createTranscript("chr1", 3000, 4000, "+", "ref2")
-        reference3 = self._createTranscript("chr1", 5000, 6000, "+", "ref3")
-        writer = Gff3Writer(self.referenceFileName, 0)
-        writer.addTranscript(reference1)
-        writer.addTranscript(reference2)
-        writer.addTranscript(reference3)
-        writer.close()
-        query1 = self._createTranscript("chr1", 1500, 3500, "+", "query1")
-        writer = Gff3Writer(self.queryFileName, 0)
-        writer.addTranscript(query1)
-        writer.close()
-        ml = MergeLists(0)
-        ml.setInputFileName(self.queryFileName, 'gff3', 0)
-        ml.setInputFileName(self.referenceFileName, 'gff3', 1)
-        ml.setOutputFileName(self.outputFileName)
-        ml.setAggregate(True)
-        ml.run()
-        parser = GffParser(self.outputFileName)
-        self.assertEqual(parser.getNbTranscripts(), 2)
-        for cpt, transcript in enumerate(parser.getIterator()):
-            if cpt == 0:
-                self._checkTranscript(transcript, "chr1", 1000, 4000, "+", None)
-            else:
-                self._checkTranscript(transcript, "chr1", 5000, 6000, "+", None)
-
-    def _createTranscript(self, chromosome, start, end, strand, name):
-        transcript = Transcript()
-        transcript.setChromosome(chromosome)
-        transcript.setStart(start)
-        transcript.setEnd(end)
-        transcript.setDirection(strand)
-        transcript.setName(name)
-        return transcript
-
-    def _checkTranscript(self, transcript, chromosome, start, end, strand, name):
-        self.assertEqual(transcript.getChromosome(), chromosome)
-        self.assertEqual(transcript.getStart(), start)
-        self.assertEqual(transcript.getEnd(), end)
-        self.assertEqual(transcript.getStrand(), strand)
-        if name != None:
-            self.assertEqual(transcript.getName(), name)
-
-
-if __name__ == "__main__":
-    unittest.main()
-

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_plot.py
--- a/SMART/Java/Python/test/Test_F_plot.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,42 +0,0 @@
-import unittest
-import os
-from commons.core.utils.FileUtils import FileUtils
-
-TestF_PATH = os.environ['REPET_PATH'] + '/SMART/Java/Python/TestFiles'
-
-
-class Test_F_plot(unittest.TestCase):
-
-    def setUp(self):
-        self.outputFileName = "testOut.png"
-
-    def tearDown(self):
-        os.remove(self.outputFileName)
-
-    def test_run_default_option(self):
-        cmd = "python ../plot.py -i %s/mapperAnalyzerOutput.gff3 -f gff3 -x identity -y nbMismatches -s line -o %s " % (TestF_PATH, self.outputFileName)
-        os.system(cmd)
-        self.assertTrue(FileUtils.isRessourceExists(self.outputFileName))
-
-    def test_run_log_option(self):
-        cmd = "python ../plot.py -i %s/mapperAnalyzerOutput.gff3 -f gff3 -x identity -y nbMismatches -s line -o %s -l xy" % (TestF_PATH, self.outputFileName)
-        os.system(cmd)
-        self.assertTrue(FileUtils.isRessourceExists(self.outputFileName))
-
-    def test_run_z_xDefault_yDefault_heatPoints_option(self):
-        cmd = "python ../plot.py -i %s/testPlot.gff3 -f gff3 -x value1 -X 1 -y value2 -Y 1 -z value3 -s heatPoints -o %s -v 10 " % (TestF_PATH, self.outputFileName)
-        os.system(cmd)
-        self.assertTrue(FileUtils.isRessourceExists(self.outputFileName))
-
-    def test_points_option(self):
-        cmd = "python ../plot.py -i %s/testPlot.gff3 -f gff3 -x value1 -X 1 -y value2 -Y 1 -s points -o %s -v 10 " % (TestF_PATH, self.outputFileName)
-        os.system(cmd)
-        self.assertTrue(FileUtils.isRessourceExists(self.outputFileName))
-
-    def test_xDefault_points_option(self):
-        cmd = "python ../plot.py -i %s/testPlot.gff3 -f gff3 -x value1 -X 1 -n 2 -s barplot -o %s -v 10 " % (TestF_PATH, self.outputFileName)
-        os.system(cmd)
-        self.assertTrue(FileUtils.isRessourceExists(self.outputFileName))
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_plotCoverage.py
--- a/SMART/Java/Python/test/Test_F_plotCoverage.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,39 +0,0 @@
-import unittest
-import os, glob
-from SMART.Java.Python.plotCoverage import PlotParser
-
-
-class Test_F_PlotCoverage(unittest.TestCase):
-
-    def setUp(self):
-        self.queryFileName  = "queryFile.gff3"
-        self.refFileName    = "refFile.gff3"
-        self.outputFileName = "outputFile"
-
-    def tearDown(self):
-        for fileRoot in (self.queryFileName, self.refFileName, self.outputFileName):
-            for file in glob.glob("%s*" % (fileRoot)):
-                os.remove(file)
-        os.remove(".RData")
-
-    def test_run_simple(self):
-        handle = open(self.refFileName, "w")
-        handle.write("chr1\tSMART\tmRNA\t1000\t2000\t.\t+\t.\tID=test1;Name=test1")
-        handle.close()
-        handle = open(self.queryFileName, "w")
-        handle.write("chr1\tSMART\tmRNA\t1100\t1200\t.\t+\t.\tID=test2.1;Name=test2.1\n")
-        handle.write("chr1\tSMART\tmRNA\t1300\t1400\t.\t+\t.\tID=test2.2;Name=test2.2\n")
-        handle.close()
-        pp = PlotParser(0)
-        pp.addInput(0, self.queryFileName, "gff3")
-        pp.addInput(1, self.refFileName, "gff3")
-        pp.setLabels("x", "y")
-        pp.setPlotSize(1000, 500)
-        pp.setOutput(self.outputFileName)
-        pp.start()
-        self.assertTrue(os.path.exists("%s_test1_overlap.png" % (self.outputFileName)))
-        self.assertTrue(os.path.exists("%s_test1_coverage.png" % (self.outputFileName)))
-
-if __name__ == "__main__":
-    unittest.main()
-

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_qualToFastq.py
--- a/SMART/Java/Python/test/Test_F_qualToFastq.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,38 +0,0 @@
-import unittest
-import os, glob
-
-
-class Test_F_qualToFastq(unittest.TestCase):
-
-    def setUp(self):
-        self.fastaFileName  = "file.fasta"
-        self.qualFileName   = "file.qual"
-        self.outputFileName = "outputFile.fastq"
-
-    def tearDown(self):
-        for fileRoot in (self.fastaFileName, self.qualFileName, self.outputFileName):
-            for file in glob.glob("%s*" % (fileRoot)):
-                os.remove(file)
-
-    def test_run_simple(self):
-        handle = open(self.fastaFileName, "w")
-        handle.write(">test1\n")
-        handle.write("AAAAAA")
-        handle.close()
-        handle = open(self.qualFileName, "w")
-        handle.write(">test1\n")
-        handle.write("32\t32\t32\t32\t32\t32")
-        handle.close()
-        os.system("python ../qualToFastq.py -f %s -q %s -o %s -v 0" % (self.fastaFileName, self.qualFileName, self.outputFileName))
-        handle = open(self.outputFileName)
-        lines = handle.readlines()
-        self.assertEquals(len(lines), 4)
-        self.assertEquals(lines[0], "@test1\n")
-        self.assertEquals(lines[1], "AAAAAA\n")
-        self.assertEquals(lines[2], "+\n")
-        self.assertEquals(lines[3], "AAAAAA\n")
-
-
-if __name__ == "__main__":
-    unittest.main()
-

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_restrictSequenceList.py
--- a/SMART/Java/Python/test/Test_F_restrictSequenceList.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,37 +0,0 @@
-import unittest
-import os, glob
-
-class Test_F_restrictSequenceList(unittest.TestCase):
-
-    def setUp(self):
-        self.sequencesFileName = "inputFile.fasta"
-        self.namesFileName     = "names.txt"
-        self.outputFileName    = "outputFile.fasta"
-
-    def tearDown(self):
-        for fileRoot in (self.sequencesFileName, self.namesFileName, self.outputFileName):
-            for file in glob.glob("%s*" % (fileRoot)):
-                os.remove(file)
-
-    def test_run_simple(self):
-        handle = open(self.sequencesFileName, "w")
-        handle.write(">sequence1\n")
-        handle.write("AAAAAAAAAAAAAAAAAAAA\n")
-        handle.write(">sequence2\n")
-        handle.write("CCCCCCCCCCCCCCCCCCCC\n")
-        handle.close()
-        handle = open(self.namesFileName, "w")
-        handle.write("""sequence1""")
-        handle.close()
-        os.system("python ../restrictSequenceList.py -i %s -f fasta -n %s -o %s -v 0" % (self.sequencesFileName, self.namesFileName, self.outputFileName))
-        handle = open(self.outputFileName)
-        lines = handle.readlines()
-        handle.close()
-        self.assertEqual(len(lines), 2)
-        self.assertEqual(lines[0], ">sequence1\n")
-        self.assertEqual(lines[1], "AAAAAAAAAAAAAAAAAAAA\n")
-
-
-if __name__ == "__main__":
-    unittest.main()
-

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_selectByTag.py
--- a/SMART/Java/Python/test/Test_F_selectByTag.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,86 +0,0 @@
-import unittest
-import os
-from SMART.Java.Python.misc import Utils
-
-class Test_F_selectByTag(unittest.TestCase):
-
-    def setUp(self):
-        self._inputFileName = "%s/SMART/Java/Python/TestFiles/inputMSWC1.gff3" % os.environ["REPET_PATH"]
-        self._outputFileName = "outputSBT.gff3"
-        self._expOutputFileName = "expSBT.gff3"
-
-    def tearDown(self):
-        os.remove(self._outputFileName)
-        os.remove(self._expOutputFileName)
-
-    def test_run_compulsory_option(self):
-        cmd = 'python ../SelectByTag.py -i %s -f gff3 -g occurrence -o %s -v 0' % (self._inputFileName, self._outputFileName)
-        os.system(cmd)
-        self._writeExpDefault(self._expOutputFileName)
-        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
-
-    def test_run_value_option(self):
-        cmd = 'python ../SelectByTag.py -i %s -f gff3 -a 1 -g occurrence -o %s -v 0' % (self._inputFileName, self._outputFileName)
-        os.system(cmd)
-        self._writeExpValueOption(self._expOutputFileName)
-        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
-
-    def test_run_min_option(self):
-        cmd = 'python ../SelectByTag.py -i %s -f gff3 -m 3 -g occurrence -o %s -v 0' % (self._inputFileName, self._outputFileName)
-        os.system(cmd)
-        self._writeExpMinOption(self._expOutputFileName)
-        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
-
-    def test_run_max_option(self):
-        cmd = 'python ../SelectByTag.py -i %s -f gff3 -M 1 -g occurrence -o %s -v 0' % (self._inputFileName, self._outputFileName)
-        os.system(cmd)
-        self._writeExpMaxOption(self._expOutputFileName)
-        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
-
-    def test_run_max_min_option(self):
-        cmd = 'python ../SelectByTag.py -i %s -f gff3 -M 2 -m 1 -g occurrence -o %s -v 0' % (self._inputFileName, self._outputFileName)
-        os.system(cmd)
-        self._writeExpMaxMinOption(self._expOutputFileName)
-        self.assertTrue(Utils.diff(self._expOutputFileName, self._outputFileName))
-
-    def _writeExpDefault(self, fileName):
-        f = open(fileName, 'w')
-        f.write("""chr1 S-MART match 6155418 6155441 24 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1
-chr2 S-MART match 26303950 26303981 32 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1
-chr3 S-MART match 28320540 28320574 35 + . occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1
-chr4 S-MART match 28565007 28565041 35 + . occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1
-chr6 S-MART match 48565007 48565041 35 + . occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=3;ID=test2/1-4;identity=80;Name=test2/1
-""")
-        f.close()
-
-    def _writeExpValueOption(self, fileName):
-        f = open(fileName, 'w')
-        f.write("""chr1 S-MART match 6155418 6155441 24 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1
-chr2 S-MART match 26303950 26303981 32 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1
-""")
-        f.close()
-
-    def _writeExpMinOption(self, fileName):
-        f = open(fileName, 'w')
-        f.write("""chr4 S-MART match 28565007 28565041 35 + . occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=4;ID=test2/1-3;identity=88;Name=test2/1
-chr6 S-MART match 48565007 48565041 35 + . occurrence=3;rank=3;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=3;ID=test2/1-4;identity=80;Name=test2/1
-""")
-        f.close()
-
-    def _writeExpMaxOption(self, fileName):
-        f = open(fileName, 'w')
-        f.write("""chr1 S-MART match 6155418 6155441 24 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1
-chr2 S-MART match 26303950 26303981 32 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1
-""")
-        f.close()
-
-    def _writeExpMaxMinOption(self, fileName):
-        f = open(fileName, 'w')
-        f.write("""chr1 S-MART match 6155418 6155441 24 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=1;nbMismatches=0;ID=test1/1;identity=100;Name=test1/1
-chr2 S-MART match 26303950 26303981 32 + . occurrence=1;rank=1;bestRegion=(self);nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-1;identity=93;Name=test2/1
-chr3 S-MART match 28320540 28320574 35 + . occurrence=2;bestRegion=chr2:26303950-26303981;nbGaps=0;nbOccurrences=3;nbMismatches=2;ID=test2/1-2;identity=94;Name=test2/1
-""")
-        f.close()
-
-if __name__ == "__main__":
-    unittest.main()

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_F_trimSequences.py
--- a/SMART/Java/Python/test/Test_F_trimSequences.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,28 +0,0 @@
-import unittest, os, os.path
-from SMART.Java.Python.misc import Utils
-SMART_PATH = os.environ["REPET_PATH"] + "/SMART"
-
-class Test_F_trimSequences(unittest.TestCase):
-
-    def setUp(self):
-        self._expOutputFileName = "expOutputFile.fasta"
-        self._obsOutputFileName = "obsOutputFile.mfa"
-        self._inputFileName     = "inputFile.fasta"
-
-    def tearDown(self):
-        for fileName in (self._expOutputFileName, self._obsOutputFileName, self._inputFileName):
-            if os.path.exists(fileName):
-                os.remove(fileName)
-
-    def test_simple(self):
-        expOutputFile = open(self._expOutputFileName, "w")
-        expOutputFile.write(">sequence1\nTTGCATAGCGCTACGTA\n")
-        expOutputFile.close()
-        inputFile = open(self._inputFileName, "w")
-        inputFile.write(">sequence1\nAGCTCGGGTATTGCATAGCGCTACGTACCCTTTATATC\n")
-        inputFile.close()
-        os.system("python %s/Java/Python/trimSequences.py -i %s -f fasta -3 CCCTTTATATC -5 AGCTCGGGTA -o %s -v 0" % (SMART_PATH, self._inputFileName, self._obsOutputFileName))
-        self.assertTrue(Utils.diff(self._expOutputFileName, self._obsOutputFileName))
-
-if __name__ == "__main__":
-    unittest.main()

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_FindOverlapsOptim.py
--- a/SMART/Java/Python/test/Test_FindOverlapsOptim.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,174 +0,0 @@\n-import unittest\n-import os\n-from SMART.Java.Python.FindOverlapsOptim import FindOverlapsOptim\n-from SMART.Java.Python.ncList.NCListCursor import NCListCursor\n-from SMART.Java.Python.ncList.test.MockFindOverlapsWithSeveralIntervals import *\n-\n-REFERENCE = 0\n-QUERY = 1\n-\n-class Test_FindOverlapsOptim(unittest.TestCase):\n-\n- def setUp(self):\n- self._inputRefGff3FileName = \'sorted_Ref.gff3\'\n- self._inputQueryGff3FileName = \'sorted_Query.gff3\'\n- self._writeQueryGff3File(self._inputQueryGff3FileName)\n- self._outputGff3FileName = \'overlaps.gff3\'\n- iMock = MockFindOverlapsWithServeralIntervals_case1()\n- iMock.write(self._inputRefGff3FileName)\n- self._iFOO = FindOverlapsOptim(0)\n- self._iFOO.setRefFileName(self._inputRefGff3FileName, "gff3")\n- self._iFOO.setQueryFileName(self._inputQueryGff3FileName, "gff3")\n- self._iFOO.setOutputFileName(self._outputGff3FileName)\n- self._iFOO.prepareIntermediateFiles()\n- self._iFOO.createNCLists()\n- self._queryNcList = self._iFOO._ncLists[QUERY]["chr1"]\n- self._refNcList = self._iFOO._ncLists[REFERENCE]["chr1"]\n- \n- def tearDown(self):\n- os.remove(self._inputRefGff3FileName)\n- os.remove(self._inputQueryGff3FileName)\n- os.remove(self._outputGff3FileName)\n- \n- def test_isOverlapping_true(self):\n- queryCursor = NCListCursor(None, self._queryNcList, 5, 0)\n- refCursor = NCListCursor(None, self._refNcList, 4, 0)\n- obs = self._iFOO.isOverlapping(queryCursor, refCursor)\n- exp = 0\n- self.assertEquals(exp, obs)\n- \n- def test_isOverlapping_false_left(self):\n- queryCursor = NCListCursor(None, self._queryNcList, 5, 0)\n- refCursor = NCListCursor(None, self._refNcList, 2, 0)\n- obs = self._iFOO.isOverlapping(queryCursor, refCursor)\n- exp = -1\n- self.assertEquals(exp, obs)\n- \n- def test_isOverlapping_false_right(self):\n- queryCursor = NCListCursor(None, self._queryNcList, 5, 0)\n- refCursor = NCListCursor(None, self._refNcList, 1, 0)\n- obs = self._iFOO.isOverlapping(queryCursor, refCursor)\n- exp = 1\n- self.assertEquals(exp, obs) \n- \n- def test_isLastElement_true(self):\n- refCursor = NCListCursor(None, self._refNcList, 4, 0)\n- obsBool = refCursor.isLast()\n- expBool = True\n- self.assertEquals(expBool, obsBool)\n- \n- def test_isLastElement_false(self):\n- refCursor = NCListCursor(None, self._refNcList, 3, 0)\n- obsBool = refCursor.isLast()\n- expBool = False\n- self.assertEquals(expBool, obsBool) \n- \n- def test_isLastElement_highestLevel_true(self):\n- refCursor = NCListCursor(None, self._refNcList, 1, 0)\n- obsBool = refCursor.isLast()\n- expBool = True\n- self.assertEquals(expBool, obsBool)\n- \n- def test_isLastElement_highestLevel_false(self):\n- refCursor = NCListCursor(None, self._refNcList, 0, 0)\n- obsBool = refCursor.isLast()\n- expBool = False\n- self.assertEquals(expBool, obsBool) \n-\n- def test_findOverlapIter(self):\n- queryCursor = NCListCursor(None, self._queryNcList, 2, 0)\n- refCursor = NCListCursor(None, self._refNcList, 0, 0)\n- queryTranscript = queryCursor.getTranscript()\n- done = False\n- (cursor, done, empty) = self._iFOO.findOverlapIter(queryTranscript, refCursor, done)\n- obsFirstOverlapLAddr = (cursor._lIndex, done, empty)\n- expFirstOverlapLAddr = 4, True, False\n- self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)\n- \n- def test_not_findOverlapIter(self):\n- queryCursor = NCListCursor(None, self._queryNcList, 4, 0)\n- refCursor = NCListCursor(None, self._refNcList, 1, 0)\n- queryTranscript '..b' done, empty)\n- expFirstOverlapLAddr = -1, False, True\n- self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)\n- \n- def test_findOverlapIter_not_the_first_RefOverlap(self):\n- queryCursor = NCListCursor(None, self._queryNcList, 3, 0)\n- refCursor = NCListCursor(None, self._refNcList, 4, 0)\n- queryTranscript = queryCursor.getTranscript()\n- done = True\n- (cursor, done, empty) = self._iFOO.findOverlapIter(queryTranscript, refCursor, done)\n- obsFirstOverlapLAddr = (cursor._lIndex, done, empty)\n- expFirstOverlapLAddr = 1, True, False\n- self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)\n- \n- def test_moveDown(self):\n- refCursor = NCListCursor(None, self._refNcList, 0, 0)\n- refCursor.moveDown()\n- expFirstChildLAddr = 2\n- self.assertEquals(expFirstChildLAddr, refCursor._lIndex) \n- \n- def test_moveUp(self):\n- refCursor = NCListCursor(None, self._refNcList, 4, 0)\n- refCursor.moveUp()\n- expFirstChildLAddr = 0\n- self.assertEquals(expFirstChildLAddr, refCursor._lIndex) \n- \n- def test_moveRight(self):\n- refCursor = NCListCursor(None, self._refNcList, 3, 0)\n- refCursor.moveRight()\n- expFirstChildLAddr = 4\n- self.assertEquals(expFirstChildLAddr, refCursor._lIndex) \n- \n- def test_moveNext(self):\n- refCursor = NCListCursor(None, self._refNcList, 6, 0)\n- refCursor.moveNext()\n- expFirstChildLAddr = 1\n- self.assertEquals(expFirstChildLAddr, refCursor._lIndex) \n-\n- def test_not_findOverlapIter_between2RefIntervals(self):\n- inputQueryGff3FileName = \'query2.gff3\'\n- self._writeQueryGff3File2(inputQueryGff3FileName)\n- self._outputGff3FileName = \'overlaps.gff3\'\n- iMock = MockFindOverlapsWithServeralIntervals_case1()\n- iMock.write(self._inputRefGff3FileName)\n- _iFOO = FindOverlapsOptim(0)\n- _iFOO.setRefFileName(self._inputRefGff3FileName, "gff3")\n- _iFOO.setQueryFileName(inputQueryGff3FileName, "gff3")\n- _iFOO.setOutputFileName(self._outputGff3FileName)\n- _iFOO.prepareIntermediateFiles()\n- _iFOO.createNCLists()\n- _queryNcList = _iFOO._ncLists[QUERY]["chr1"]\n- _refNcList = _iFOO._ncLists[REFERENCE]["chr1"]\n- queryCursor = NCListCursor(None, _queryNcList, 0, 0)\n- refCursor = NCListCursor(None, _refNcList, 0, 0)\n- queryTranscript = queryCursor.getTranscript()\n- done = True\n- (cursor, done, empty) = _iFOO.findOverlapIter(queryTranscript, refCursor, done)\n- lIndex = cursor._lIndex\n- obsFirstOverlapLAddr = (lIndex, done, empty)\n- expFirstOverlapLAddr = 1, False, True\n- self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)\n- os.remove(inputQueryGff3FileName) \n-\n- def _writeQueryGff3File2(self, fileName):\n- f = open(fileName, \'w\')\n- f.write("chr1\\tquery\\ttest1\\t1100\\t1150\\t126\\t+\\t.\\tID=test1.1;Name=test1.1\\n")\n- f.write("chr1\\tquery\\ttest2\\t1250\\t1300\\t781\\t+\\t.\\tID=test1.2;Name=test1.2\\n")\n- f.close() \n- \n- def _writeQueryGff3File(self, fileName):\n- f = open(fileName, \'w\')\n- f.write("chr1\\tquery\\ttest1.1\\t25\\t150\\t126\\t+\\t.\\tID=test1.1;Name=test1.1\\n")\n- f.write("chr1\\tquery\\ttest1.2\\t70\\t850\\t781\\t+\\t.\\tID=test1.2;Name=test1.2\\n")\n- f.write("chr1\\tquery\\ttest1.3\\t550\\t850\\t201\\t+\\t.\\tID=test1.3;Name=test1.3\\n")\n- f.write("chr1\\tquery\\ttest1.4\\t925\\t1025\\t101\\t+\\t.\\tID=test1.4;Name=test1.4\\n")\n- f.write("chr1\\tquery\\ttest1.5\\t1201\\t1210\\t10\\t+\\t.\\tID=test1.5;Name=test1.5\\n")\n- f.write("chr1\\tquery\\ttest1.6\\t1500\\t1600\\t101\\t+\\t.\\tID=test1.6;Name=test1.6\\n")\n- f.close()\n- \n-if __name__ == "__main__":\n- unittest.main()\n'

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/Test_FindOverlaps_optim.py
--- a/SMART/Java/Python/test/Test_FindOverlaps_optim.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,149 +0,0 @@
-import unittest
-import os
-from SMART.Java.Python.FindOverlapsOptim import FindOverlapsOptim
-from SMART.Java.Python.ncList.test.MockFindOverlapsWithSeveralIntervals import *
-
-class Test_FindOverlaps_optim(unittest.TestCase):
-
-    def setUp(self):
-        self._inputRefGff3FileName = 'sorted_Ref.gff3'
-        iMock = MockFindOverlapsWithServeralIntervals_case1()
-        iMock.write(self._inputRefGff3FileName)
-        self._inputQueryGff3FileName = 'sorted_Query.gff3'
-        self._writeQueryGff3File(self._inputQueryGff3FileName)
-        self._outputGff3FileName = 'overlaps.gff3'
-        self._iFOO = FindOverlaps_optim(self._inputRefGff3FileName, self._inputQueryGff3FileName)
-        self._iFOO.prepareIntermediateFiles_sorted()
-        self._iFOO.setOutputGff3FileName(self._outputGff3FileName)
-
-    def tearDown(self):
-        os.remove(self._inputRefGff3FileName)
-        os.remove(self._inputQueryGff3FileName)
-        os.remove(self._outputGff3FileName)
-        self._iFOO.deletIntermediateFiles()
-
-    def test_isOverlapping_true(self):
-        queryGff3Addr = 116
-        RefGff3Addr = 231
-        obs = self._iFOO.isOverlapping(queryGff3Addr, RefGff3Addr)
-        exp = 0
-        self.assertEquals(exp, obs)
-
-    def test_isOverlapping_false_left(self):
-        queryGff3Addr = 116
-        RefGff3Addr = 58
-        obs = self._iFOO.isOverlapping(queryGff3Addr, RefGff3Addr)
-        exp = -1
-        self.assertEquals(exp, obs)
-
-    def test_isOverlapping_false_right(self):
-        queryGff3Addr = 116
-        RefGff3Addr = 347
-        obs = self._iFOO.isOverlapping(queryGff3Addr, RefGff3Addr)
-        exp = 1
-        self.assertEquals(exp, obs)
-
-    def test_getHisFirstChild(self):
-        firstRefLAddr = 0
-        obsFirstChildLAddr = self._iFOO.getHisFirstChild(firstRefLAddr)
-        expFirstChildLAddr = 48
-        self.assertEquals(expFirstChildLAddr, obsFirstChildLAddr)
-
-    def test_isLastElement_true(self):
-        refLAddr = 96
-        obsBool = self._iFOO.isLastElement(refLAddr)
-        expBool = True
-        self.assertEquals(expBool, obsBool)
-
-    def test_isLastElement_false(self):
-        refLAddr = 72
-        obsBool = self._iFOO.isLastElement(refLAddr)
-        expBool = False
-        self.assertEquals(expBool, obsBool)
-
-    def test_isLastElement_highestLevel_true(self):
-        refLAddr = 24
-        obsBool = self._iFOO.isLastElement(refLAddr)
-        expBool = True
-        self.assertEquals(expBool, obsBool)
-
-    def test_isLastElement_highestLevel_false(self):
-        refLAddr = 0
-        obsBool = self._iFOO.isLastElement(refLAddr)
-        expBool = False
-        self.assertEquals(expBool, obsBool)
-
-    def test_findOverlapIter(self):
-        queryGff3Addr = 175
-        firstRefLAddr = 0
-        done = False
-        obsFirstOverlapLAddr = self._iFOO.findOverlapIter(queryGff3Addr, firstRefLAddr, done)
-        expFirstOverlapLAddr = 96, True
-        self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
-
-    def test_not_findOverlapIter(self):
-        queryGff3Addr = 295
-        firstRefLAddr = 24
-        done = False
-        obsFirstOverlapLAddr = self._iFOO.findOverlapIter(queryGff3Addr, firstRefLAddr, done)
-        expFirstOverlapLAddr = None, False
-        self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
-
-    def test_findOverlapIter_not_the_first_RefOverlap(self):
-        queryGff3Addr = 235
-        firstRefLAddr = 96
-        done = True
-        obsFirstOverlapLAddr = self._iFOO.findOverlapIter(queryGff3Addr, firstRefLAddr, done)
-        expFirstOverlapLAddr = 24, False
-        self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
-
-    def test_changeToNewSubEndLAddr(self):
-        firstChildLAddr = 48
-        subEndLAddr = 48
-        expSubEndLAddr = 120
-        obsSubEndLAddr = self._iFOO.changeToNewSubEndLAddr(firstChildLAddr, subEndLAddr)
-        self.assertEquals(expSubEndLAddr, obsSubEndLAddr)
-
-    def test_defineSubEndLaddr(self):
-        parentLAddr = -1
-        expSubEndLAddr = 48
-        obsSubEndLAddr = self._iFOO.defineSubEndLaddr(parentLAddr)
-        self.assertEquals(expSubEndLAddr, obsSubEndLAddr)
-
-    def test_getNextRefIntervalInCaseNotOverLap(self):
-        firstRefLAddr = 96
-        expRefLAddr = 24
-        obsRefLAddr = self._iFOO.getNext(firstRefLAddr)
-        self.assertEquals(expRefLAddr, obsRefLAddr)
-
-
-    def test_not_findOverlapIter_between2RefIntervals(self):
-        inputQueryGff3FileName = 'query2.gff3'
-        self._writeQueryGff3File2(inputQueryGff3FileName)
-        self._iFOO.setQueryGff3FileName(inputQueryGff3FileName)
-        queryGff3Addr = 0
-        firstRefLAddr = 0
-        done = False
-        obsFirstOverlapLAddr = self._iFOO.findOverlapIter(queryGff3Addr, firstRefLAddr, done)
-        expFirstOverlapLAddr = 24, False
-        self.assertEquals(expFirstOverlapLAddr, obsFirstOverlapLAddr)
-        os.remove(inputQueryGff3FileName)
-
-    def _writeQueryGff3File2(self, fileName):
-        f = open(fileName, 'w')
-        f.write("chr1\tquery\ttest1\t1100\t1150\t126\t+\t.\tID=test1.1;Name=test1.1\n")
-        f.write("chr1\tquery\ttest2\t1250\t1300\t781\t+\t.\tID=test1.2;Name=test1.2\n")
-        f.close()
-
-    def _writeQueryGff3File(self, fileName):
-        f = open(fileName, 'w')
-        f.write("chr1\tquery\ttest1.1\t25\t150\t126\t+\t.\tID=test1.1;Name=test1.1\n")
-        f.write("chr1\tquery\ttest1.2\t70\t850\t781\t+\t.\tID=test1.2;Name=test1.2\n")
-        f.write("chr1\tquery\ttest1.3\t550\t850\t201\t+\t.\tID=test1.3;Name=test1.3\n")
-        f.write("chr1\tquery\ttest1.4\t925\t1025\t101\t+\t.\tID=test1.4;Name=test1.4\n")
-        f.write("chr1\tquery\ttest1.5\t1201\t1210\t10\t+\t.\tID=test1.5;Name=test1.5\n")
-        f.write("chr1\tquery\ttest1.6\t1500\t1600\t101\t+\t.\tID=test1.6;Name=test1.6\n")
-        f.close()
-
-if __name__ == "__main__":
-    unittest.main()
\ No newline at end of file

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test/timeResults.R
--- a/SMART/Java/Python/test/timeResults.R Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
-data <- read.table("timeResults.dat", header=TRUE)
-attach(data)
-plot(numberOfReads, time, xlab="number of reads", ylab="time used")
-title("7 overlaps and random reference input fixed")

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/test3.gff3
--- a/SMART/Java/Python/test3.gff3 Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,3 +0,0 @@
-dmel_chr4 S-MART match 228977 229472 . - . Target=DmelChr4Mask-B-G20-MAP3_classII-TIR-comp 559 1044;ID=ms108_dmel_chr4_DmelChr4Mask-B-G20-MAP3_classII-TIR-comp;Name=unnamed transcript
-dmel_chr4 S-MART exon 228977 229302 . - . ID=ms108_dmel_chr4_DmelChr4Mask-B-G20-MAP3_classII-TIR-comp-exon1;Name=unnamed transcript-exon1;Parent=ms108_dmel_chr4_DmelChr4Mask-B-G20-MAP3_classII-TIR-comp
-dmel_chr4 S-MART exon 229384 229472 . - . ID=ms108_dmel_chr4_DmelChr4Mask-B-G20-MAP3_classII-TIR-comp-exon2;Name=unnamed transcript-exon2;Parent=ms108_dmel_chr4_DmelChr4Mask-B-G20-MAP3_classII-TIR-comp

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/testInstall.py
--- a/SMART/Java/Python/testInstall.py Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,103 +0,0 @@
-#! /usr/bin/env python
-#
-# Copyright INRA-URGI 2009-2010
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software. You can use,
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info".
-#
-# As a counterpart to the access to the source code and rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty and the software's author, the holder of the
-# economic rights, and the successive licensors have only limited
-# liability.
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading, using, modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean that it is complicated to manipulate, and that also
-# therefore means that it is reserved for developers and experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or
-# data to be ensured and, more generally, to use and operate it in the
-# same conditions as regards security.
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-#
-"""
-Test if the configuration is sound
-"""
-
-import sys
-import os
-import subprocess
-
-# Test Python files
-try :
-    from SMART.Java.Python.misc.RPlotter import *
-except:
-    print "Cannot find Python scripts! Update PYTHONPATH (currently %s) environment variable and see configuration in the documentation!" % (os.environ["PYTHONPATH"] if "PYTHONPATH" in os.environ else "empty")
-    sys.exit(3)
-
-try :
-    from SMART.Java.Python.mySql.MySqlTranscriptTable import *
-    from SMART.Java.Python.mySql.MySqlConnection import *
-except:
-    print "SQLite is not installed ! Please read the documentation!"
-    sys.exit(4)
-
-
-if __name__ == "__main__":
-
-    print "Python scripts are correctly read."
-
-    # Test mySQL
-    connection = MySqlConnection()
-    table = MySqlTranscriptTable(connection)
-
-    try:
-        table.createTranscriptTable()
-    except:
-        print "Cannot connect to the SQLite database! See configuration in the documentation!"
-        sys.exit(5)
-
-    print "SQLite database is correctly set up."
-
-
-    # Test R
-    fileName = "tmpFile.R"
-    file = open(fileName, "w")
-    file.write("?licence\n")
-    file.close()
-    rCommand = "R"
-    if "SMARTRPATH" in os.environ:
-        rCommand = os.environ["SMARTRPATH"]
-    command = "\"%s\" CMD BATCH %s" % (rCommand, fileName)
-    status    = subprocess.call(command, shell=True)
-    os.remove(fileName)
-    outputFileName = "%sout" % (fileName)
-    if os.path.exists(outputFileName):
-        os.remove(outputFileName)
-
-    if status != 0:
-        print "Problem with the execution of R script (command '%s' did not work, current directory is %s, status is %d)! See configuration in the documentation!" % (command, os.getcwd(), status)
-        sys.exit(6)
-
-    line = {0: 1, 1: 2}
-    pngFileName = "tmpFile.png"
-    plotter = RPlotter(pngFileName)
-    plotter.addLine(line)
-    try:
-        plotter.plot()
-    except:
-        print "Problem with the execution of R script: library 'RColorBrewer' is missing! See configuration in the documentation!"
-        sys.exit(7)
-    os.remove(pngFileName)
-
-    print "R is available."
-
-    print "Set up is fine! Enjoy S-MART!"

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/testPC_unnamed transcript_coverage.png

Binary file SMART/Java/Python/testPC_unnamed transcript_coverage.png has changed

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/testPC_unnamed transcript_overlap.png

Binary file SMART/Java/Python/testPC_unnamed transcript_overlap.png has changed

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/tmpFile26845.R
--- a/SMART/Java/Python/tmpFile26845.R Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,8 +0,0 @@
-library(extrafont)
-loadfonts()
-library(ggplot2)
-data <- read.table("tmpFile26845.dat", header = T)
-data$Sample <- factor(data$Sample, levels=c("Col"))
-png("test.png", width = 800, height = 300)
-ggplot(data, aes(x = Pos/1000000, y = Count, fill = Sample, color = Sample)) + opts(title = "Distribution") + geom_bar(stat = "identity") + facet_grid(Sample ~ Chr, space="free") + xlab(" (in Gbp)") + ylab("# reads") + scale_fill_manual(values = c("red")) + scale_color_manual(values = c("red")) + opts(legend.position = "none", panel.grid.major = theme_blank(), panel.grid.minor = theme_blank(), panel.background = theme_blank()) + theme(text=element_text(family="Arial", size=12))
-dev.off()

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/tmpFile26845.Rout
--- a/SMART/Java/Python/tmpFile26845.Rout Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,24 +0,0 @@
-
-R version 2.11.1 (2010-05-31)
-Copyright (C) 2010 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
-
-R is free software and comes with ABSOLUTELY NO WARRANTY.
-You are welcome to redistribute it under certain conditions.
-Type 'license()' or 'licence()' for distribution details.
-
- Natural language support but running in an English locale
-
-R is a collaborative project with many contributors.
-Type 'contributors()' for more information and
-'citation()' on how to cite R or R packages in publications.
-
-Type 'demo()' for some demos, 'help()' for on-line help, or
-'help.start()' for an HTML browser interface to help.
-Type 'q()' to quit R.
-
-[Previously saved workspace restored]
-
-> library(extrafont)
-Error in library(extrafont) : there is no package called 'extrafont'
-Execution halted

diff -r 4e7ee5683ef1 -r 2a3fdec156e0 SMART/Java/Python/tmpFile26845.dat
--- a/SMART/Java/Python/tmpFile26845.dat Mon Apr 29 03:30:11 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,23741 +0,0 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