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fix numeric output in logfile
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@fungs
fungs committed Oct 7, 2021
1 parent d903b04 commit da445fe
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Showing 2 changed files with 11 additions and 12 deletions.
19 changes: 10 additions & 9 deletions core/src/taxonpredictionmodelsequence.hh
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Original file line number Diff line number Diff line change
Expand Up @@ -344,6 +344,7 @@ public:
boost::format seqname_fmt("%d:%d@%s"); // local variable because not thread-safe
StopWatchCPUTime stopwatch_init("initializing this record"); // log overall time for this predict phase
stopwatch_init.start();
logsink << std::fixed << std::setprecision(2); // TODO: reverse/clear flags afterwards

// push records into active_records TODO: remove intermediate active_records?
active_list_type_ active_records;
Expand Down Expand Up @@ -512,7 +513,7 @@ public:
qgroup.insert(i);
dist = 0;
sim = records[i]->getIdentities();
logsink << std::setprecision(2) << " *ALN " << i << " <=> query" << tab << "dist=" << dist << "; sim=" << sim << "; qsearchscore=" << qsearchscore << "; qsearchmatch=" << qsearchmatch << "; qpid=1.0" << std::endl;
logsink << " *ALN " << i << " <=> query" << tab << "dist=" << dist << "; sim=" << sim << "; qsearchscore=" << qsearchscore << "; qsearchmatch=" << qsearchmatch << "; qpid=1.0" << std::endl;
++pass_0_counter_naive;
} else if (records[i]->getScore() >= dbalignment_searchscore_threshold) {

Expand All @@ -529,7 +530,7 @@ public:

sim = std::max(queryalignment.similarity, static_cast<float>(records[i]->getIdentities()));
double qpid = static_cast<double>(sim)/qrlength;
logsink << std::setprecision(2) << " +ALN " << i << " <=> query" << tab << "dist=" << dist << "; sim=" << sim << "; qsearchscore=" << qsearchscore << "; qsearchmatch=" << qsearchmatch << "; qsearchpid=" << qsearchpid << "; qpid=" << qpid << std::endl;
logsink << " +ALN " << i << " <=> query" << tab << "dist=" << dist << "; sim=" << sim << "; qsearchscore=" << qsearchscore << "; qsearchmatch=" << qsearchmatch << "; qsearchpid=" << qsearchpid << "; qpid=" << qpid << std::endl;
logsink << queryalignment << std::endl;

} else { // not similar -> fill in some dummy values
Expand Down Expand Up @@ -591,7 +592,7 @@ public:
std::list< boost::tuple< uint, int > > outgroup_tmp;

// align all others <=> anchor TODO: adaptive cut-off
logsink << std::setprecision(2) << " query: (" << qdist << ") unknown" << std::endl;
logsink << " query: (" << qdist << ") unknown" << std::endl;
pass_1_counter_naive += n - 1;

// TODO: implement heuristic cut-off
Expand Down Expand Up @@ -632,7 +633,7 @@ public:
++pass_1_counter;
float sim = segmentalignment.similarity;

logsink << std::setprecision(2) << " +ALN " << i << " <=> " << index_anchor << tab << "dist=" << dist << "; sim=" << sim << "; qsearchscore=" << qsearchscore << "; qsearchmatch=" << qsearchmatch << "; qsearchpid=" << qsearchpid << "; qpid=" << qpid << "; qsearchscore_cut=" << qsearchscore_thresh_heuristic << "; qpid_cutg=" << qpid_thresh_guarantee << "; qpid_cut_h=" << qpid_thresh_heuristic << std::endl;
logsink << " +ALN " << i << " <=> " << index_anchor << tab << "dist=" << dist << "; sim=" << sim << "; qsearchscore=" << qsearchscore << "; qsearchmatch=" << qsearchmatch << "; qsearchpid=" << qsearchpid << "; qpid=" << qpid << "; qsearchscore_cut=" << qsearchscore_thresh_heuristic << "; qpid_cutg=" << qpid_thresh_guarantee << "; qpid_cut_h=" << qpid_thresh_heuristic << std::endl;
logsink << segmentalignment << std::endl;
}
}
Expand All @@ -645,7 +646,7 @@ public:
if(dist <= qdist) {
lnode = this->taxinter_.getLCA(lnode, cnode);
if(dist > ldist) ldist = dist;
logsink << std::setprecision(2) << " current lower node: " << "("<< dist <<") "<<lnode->data->annotation->name << " (+ " << cnode->data->annotation->name << " at " << static_cast<int>(this->taxinter_.getLCA(cnode, rnode)->data->root_pathlength) << " )" << std::endl;
logsink << " current lower node: " << "("<< dist <<") "<<lnode->data->annotation->name << " (+ " << cnode->data->annotation->name << " at " << static_cast<int>(this->taxinter_.getLCA(cnode, rnode)->data->root_pathlength) << " )" << std::endl;
}
else {
if(dist < udist) { // true if we find a segment with a lower dist than query
Expand Down Expand Up @@ -717,7 +718,7 @@ public:
ival = 1.;
} else if(unode != lnode && ldist < qdist) ival = (qdist - ldist)/(udist - ldist);

logsink << std::endl << std::setprecision(2) << " SCORE\tldist = " << ldist << "; udist = " << udist << "; querydist = " << qdist << "; querydist_ex = " << qdist_ex << "; ival = " << ival << std::endl << std::endl;
logsink << std::endl << " SCORE\tldist = " << ldist << "; udist = " << udist << "; querydist = " << qdist << "; querydist_ex = " << qdist_ex << "; ival = " << ival << std::endl << std::endl;
const float taxsig = .0; // TODO: placer.getTaxSignal(qdist);

ival_global = std::max(ival, ival_global); // combine interpolation values conservatively
Expand Down Expand Up @@ -778,7 +779,7 @@ public:
dist = segmentalignment.distance;
sim = segmentalignment.similarity;

logsink << std::setprecision(2) << " +ALN " << i << " <=> " << index_anchor << tab << "dist=" << dist << "; sim=" << sim << "; qsearchscore=" << qsearchscore << "; qsearchmatch=" << qsearchmatch << "; qpid=" << qpid << std::endl;
logsink << " +ALN " << i << " <=> " << index_anchor << tab << "dist=" << dist << "; sim=" << sim << "; qsearchscore=" << qsearchscore << "; qsearchmatch=" << qsearchmatch << "; qpid=" << qpid << std::endl;
logsink << segmentalignment << std::endl;
++pass_2_counter;
querydistance[i] = dist;
Expand All @@ -798,7 +799,7 @@ public:
float sim = std::max(segmentalignment.similarity, querysimilarity[index_anchor]);

double qpid = static_cast<double>(sim)/qrlength;
logsink << std::setprecision(2) << " +ALN query <=> " << index_anchor << tab << "dist=" << dist << "; sim=" << sim << "; qsearchscore=" << records[index_anchor]->getScore() << "; qsearchmatch=" << qsearchmatch << "; qpid=" << qpid << std::endl;
logsink << " +ALN query <=> " << index_anchor << tab << "dist=" << dist << "; sim=" << sim << "; qsearchscore=" << records[index_anchor]->getScore() << "; qsearchmatch=" << qsearchmatch << "; qpid=" << qpid << std::endl;
logsink << segmentalignment << std::endl;
querydistance[index_anchor] = dist;
querysimilarity[index_anchor] = sim;
Expand Down Expand Up @@ -833,7 +834,7 @@ public:
gcounter = pass_0_counter + pass_1_counter + pass_2_counter;
float normalised_rt = (float)gcounter/(float)n;
stopwatch_process.stop();
logsink << "STATS" << tab << qrseqname << tab << n << tab << pass_0_counter << tab << pass_1_counter << tab << pass_2_counter << tab << gcounter << tab << stopwatch_init.read() << tab << stopwatch_seqret.read() << tab << stopwatch_process.read() << tab << std::setprecision(2) << std::fixed << normalised_rt << std::endl << std::endl;
logsink << "STATS" << tab << qrseqname << tab << n << tab << pass_0_counter << tab << pass_1_counter << tab << pass_2_counter << tab << gcounter << tab << stopwatch_init.read() << tab << stopwatch_seqret.read() << tab << stopwatch_process.read() << tab << normalised_rt << std::endl << std::endl;
}

protected:
Expand Down
4 changes: 1 addition & 3 deletions core/taxator.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -339,10 +339,8 @@ int main( int argc, char** argv ) {
// std::cerr << "end load taxonomy\n";
if( delete_unmarked ) tax->deleteUnmarkedNodes(); // do everything only with the major NCBI ranks given by "ranks"

// std::cerr << "load idtotax\n";
boost::scoped_ptr< StrIDConverter > seqid2taxid( loadStrIDConverterFromFile( accessconverter_filename, 1000 ) );
std::ofstream logsink( log_filename.c_str(), std::ios_base::app );
// std::cerr << "end load idtotax\n";
std::ofstream logsink( log_filename.c_str(), std::ios_base::app); // TODO: is ::ate more appropriate?

try {
// choose appropriate prediction model from command line parameters
Expand Down

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