void testCluster() {
int w=40;
string forced_edges = "" ;
map<string, string> labels;
WindowsStorage windows = WindowsStorage(labels);
Sequence seq = {"", "", "", "", NULL};
windows.add("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAT", seq, 0, 0);
windows.add("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", seq, 0, 0);
windows.add("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG", seq, 0, 0);
windows.add("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAC", seq, 0, 0);
windows.add("TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT", seq, 0, 0);
windows.add("TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAA", seq, 0, 0);
windows.add("TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGG", seq, 0, 0);
windows.add("TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCC", seq, 0, 0);
windows.add("GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTTTTTTTT", seq, 0, 0);
windows.add("GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAAAAAAAA", seq, 0, 0);
windows.add("GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG", seq, 0, 0);
windows.add("GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCCCCC", seq, 0, 0);
windows.add("CCCCCCCCCCCCCCCCCCCCCCCCCTTTTTTTTTTTTTTT", seq, 0, 0);
windows.add("CCCCCCCCCCCCCCCCCCCCCCCCCAAAAAAGCTAAAAAA", seq, 0, 0);
windows.add("CCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGTCTAGGGGG", seq, 0, 0);
windows.add("CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCATGCCCCCC", seq, 0, 0);
windows.sort();
list<pair <junction, size_t> > sort_clones = windows.getSortedList();
comp_matrix comp=comp_matrix(sort_clones);
//create matrix using junctions
comp.compare( cout, Cluster);
//save matrix file
comp.save("comp_matrix.data");
//reset matrix
comp.del();
//create matrix using matrix file
comp.load("comp_matrix.data");
//save matrix file
comp.save("comp_matrix2.data");
//test clustering
list <list <junction> > cluster ;
//0 différence admise / taille mini 10 / 0 cluster possible
cluster = comp.cluster(forced_edges, w, cout, 0, 10) ;
TAP_TEST(cluster.size()==0, TEST_CLUSTER,
"no cluster here (cluster.size()=" <<cluster.size() << ")" ) ;
//epsilon 0// taille mini 1 / 16 cluster possible
cluster = comp.cluster(forced_edges, w, cout, 0, 1) ;
TAP_TEST(cluster.size()==16, TEST_CLUSTER, "expected 16 clusters (cluster.size()=" <<cluster.size() << ")") ;
//epsilon 1// taille mini 3 / 1 cluster possible
cluster = comp.cluster(forced_edges, w, cout, 1, 3) ;
TAP_TEST(cluster.size()==1, TEST_CLUSTER, "expected 1 cluster (cluster.size()=" <<cluster.size() << ")") ;
//epsilon 3// taille mini 3 / 2 cluster possible
cluster = comp.cluster(forced_edges, w, cout, 3, 3) ;
TAP_TEST(cluster.size()==2, TEST_CLUSTER, "expected 2 clusters (cluster.size()=" <<cluster.size() << ")") ;
//epsilon 20 // taille mini 3 / 4 cluster possible
cluster = comp.cluster(forced_edges, w, cout, 20, 3) ;
TAP_TEST(cluster.size()==4, TEST_CLUSTER, "expected 4 clusters (cluster.size()=" <<cluster.size() << ")") ;
//del matrix
comp.del();
}
WindowsStorage *WindowExtractor::extract(OnlineFasta *reads,
size_t w,
map<string, string> &windows_labels, bool only_labeled_windows,
bool keep_unsegmented_as_clone,
double nb_expected, int nb_reads_for_evalue) {
init_stats();
WindowsStorage *windowsStorage = new WindowsStorage(windows_labels);
windowsStorage->setMaximalNbReadsPerWindow(max_reads_per_window);
unsigned long long int bp_total = 0;
while (reads->hasNext()) {
try {
reads->next();
}
catch (const invalid_argument e) {
cout << endl;
cerr << WARNING_STRING << "Error in getting a new read: " << e.what() << endl;
cerr << WARNING_STRING << "Vidjil stops the analysis here, after " << nb_reads << " reads." << endl;
break ;
}
nb_reads++;
if (out_affects) {
*out_affects << reads->getSequence();
}
KmerMultiSegmenter kmseg(reads->getSequence(), multigermline, out_affects, nb_expected, nb_reads_for_evalue);
KmerSegmenter *seg = kmseg.the_kseg ;
// Window length threshold
junction junc ;
if (seg->isSegmented()) {
junc = seg->getJunction(w);
if (!junc.size()) {
seg->setSegmentationStatus(UNSEG_TOO_SHORT_FOR_WINDOW);
}
}
int read_length = seg->getSequence().sequence.length();
// Update stats
stats[seg->getSegmentationStatus()].insert(read_length);
if (seg->isSegmented()) {
// Filter
if (!only_labeled_windows || windowsStorage->isInterestingJunction(junc))
// Store the window
windowsStorage->add(junc, reads->getSequence(), seg->getSegmentationStatus(), seg->segmented_germline);
// Update stats
stats[TOTAL_SEG_AND_WINDOW].insert(read_length) ;
stats_reads[seg->system].addScore(read_length);
if (out_segmented) {
*out_segmented << *seg ; // KmerSegmenter output (V/N/J)
}
} else {
if (keep_unsegmented_as_clone && (reads->getSequence().sequence.length() >= w))
{
// Keep the unsegmented read, taking the full sequence as the junction
windowsStorage->add(reads->getSequence().sequence, reads->getSequence(), seg->getSegmentationStatus(), seg->segmented_germline);
stats[TOTAL_SEG_AND_WINDOW].insert(read_length) ; // TODO: rather count that in a pseudo-germline such as 'TRG!'
}
if (out_unsegmented) {
*out_unsegmented << *seg ;
}
if (out_unsegmented_detail && (seg->getSegmentationStatus() >= STATS_FIRST_UNSEG)) {
if (unsegmented_detail_full || (seg->getSegmentationStatus() != UNSEG_TOO_FEW_ZERO && seg->getSegmentationStatus() != UNSEG_TOO_SHORT))
*out_unsegmented_detail[seg->getSegmentationStatus()] << *seg ;
}
}
// Last line of detailed affects output
if (out_affects) {
*out_affects << "#>" << seg->label << " " << seg->getInfoLine() << endl << endl;
}
// Progress bar
bp_total += read_length;
if (!(nb_reads % PROGRESS_POINT))
{
cout << "." ;
if (!(nb_reads % (PROGRESS_POINT * PROGRESS_LINE)))
cout << setw(10) << nb_reads / 1000 << "k reads " << fixed << setprecision(2) << setw(14) << bp_total / 1E6 << " Mbp" << endl ;
cout.flush() ;
}
}
cout << endl ;
fillStatsClones(windowsStorage);
return windowsStorage;
}