//***************************************************************************************************************
void ChimeraSlayer::print(ostream& out) {
try {
-
mothurOutEndLine();
+ for (int i = 0; i < querySeqs.size(); i++) {
+
+ if (chimeraFlags[i] == "yes") {
+ mothurOut(querySeqs[i]->getName() + "\tyes"); mothurOutEndLine();
+
+ }else{
+ out << querySeqs[i]->getName() << "\tno" << endl;
+ mothurOut("no");
+ }
+ }
+/*
+
+ my $div_ratio_QLA_QRB = $data_struct->{div_ratio_QLA_QRB};
+ my $div_ratio_QRA_QLB = $data_struct->{div_ratio_QLB_QRA};
+
+ my $per_id_QLA = $data_struct->{per_id_QLA};
+ my $per_id_QRB = $data_struct->{per_id_QRB};
+ my $per_id_AB = $data_struct->{per_id_AB};
+ my $per_id_QA = $data_struct->{per_id_QA};
+ my $per_id_QB = $data_struct->{per_id_QB};
+ my $per_id_LAB = $data_struct->{per_id_LAB};
+ my $per_id_RAB = $data_struct->{per_id_RAB};
+ my $per_id_QRA = $data_struct->{per_id_QRA};
+ my $per_id_QLB = $data_struct->{per_id_QLB};
+ my $per_id_QLB_QRA = $data_struct->{per_id_QLB_QRA};
+ my $per_id_QLA_QRB = $data_struct->{per_id_QLA_QRB};
+
+ my $win_left_end5 = $data_struct->{win_left_end5};
+ my $win_left_end3 = $data_struct->{win_left_end3};
+ my $win_right_end5 = $data_struct->{win_right_end5};
+ my $win_right_end3 = $data_struct->{win_right_end3};
+ my $Q = $data_struct->{query_alignment};
+ my $A = $data_struct->{parent_A_alignment};
+ my $B = $data_struct->{parent_B_alignment};
+ my $BS_A = $data_struct->{BS_A};
+ my $BS_B = $data_struct->{BS_B};
+
+ my @Q_chars = @{$Q->{align}};
+ my @A_chars = @{$A->{align}};
+ my @B_chars = @{$B->{align}};
+
+ my $query_acc = $Q->{acc};
+ my $A_acc = $A->{acc};
+ my $B_acc = $B->{acc};
+
+ my $break_left = $Q->{seqPos}->[$win_left_end3];
+ my $break_right = $Q->{seqPos}->[$win_right_end5];
+
+
+ cout << "//\n## CHIMERA\t" << querySeqs[i]->getName() << "\t" << $break_left-$break_right" << endl
+ << "\tDIV_QLARB: ". sprintf("%.3f", $div_ratio_QLA_QRB)
+ << "\tBS_QLARB: " . sprintf("%.2f", $BS_A)
+ << "\tDIV_QRALB: " . sprintf("%.3f", $div_ratio_QRA_QLB)
+ << "\tBS_QRALB: " . sprintf("%.2f", $BS_B)
+ << "\t$A_acc\t$B_acc"
+ << "\tbreakpoint: $break_left-$break_right\n\n";
+
+ ## draw illustration:
+
+ print " Per_id parents: " . sprintf("%.2f", $per_id_AB) . "\n\n";
+ print " Per_id(Q,A): " . sprintf("%.2f", $per_id_QA) . "\n";
+ print "--------------------------------------------------- A: $A_acc\n"
+ . " " . sprintf("%.2f", $per_id_QLA) . " " . sprintf("%.2f", $per_id_QRA) . "\n"
+ . "~~~~~~~~~~~~~~~~~~~~~~~~\\ /~~~~~~~~~~~~~~~~~~~~~~~~ Q: $query_acc\n"
+ . "DivR: " . sprintf("%.3f", $div_ratio_QLA_QRB) . " BS: " . sprintf("%.2f", $BS_A) . " |\n"
+ . "Per_id(QLA,QRB): " . sprintf("%.2f", $per_id_QLA_QRB) . " |\n"
+ . " |\n"
+ . " (L-AB: " . sprintf("%.2f", $per_id_LAB) . ") | (R-AB: " . sprintf("%.2f", $per_id_RAB) . ")\n"
+ . " WinL:$win_left_end5-$win_left_end3 | WinR:$win_right_end5-$win_right_end3\n"
+ . " |\n"
+ . "Per_id(QLB,QRA): " . sprintf("%.2f", $per_id_QLB_QRA) . " |\n"
+ . "DivR: " . sprintf("%.3f", $div_ratio_QRA_QLB) . " BS: " . sprintf("%.2f", $BS_B) . " |\n"
+ . "~~~~~~~~~~~~~~~~~~~~~~~~/ \\~~~~~~~~~~~~~~~~~~~~~~~~~ Q: $query_acc\n"
+ . " " . sprintf("%.2f", $per_id_QLB) . " " . sprintf("%.2f", $per_id_QRB) . "\n"
+ . "---------------------------------------------------- B: $B_acc\n";
+ print " Per_id(Q,B): ". sprintf("%.2f", $per_id_QB) . "\n\n";
+
+ my $deltaL = $per_id_QLA - $per_id_QLB;
+ my $deltaR = $per_id_QRA - $per_id_QRB;
+
+ print "DeltaL: " . sprintf("%.2f", $deltaL) . " DeltaR: " . sprintf("%.2f", $deltaR) . "\n\n";
+
+ unless ($printAlignmentsFlag) { return; }
+
+
+ ## build the left windows:
+ my @Q_left_win = @Q_chars[$win_left_end5..$win_left_end3];
+ my @A_left_win = @A_chars[$win_left_end5..$win_left_end3];
+ my @B_left_win = @B_chars[$win_left_end5..$win_left_end3];
+
+ &print_alignment($A_acc, \@A_left_win,
+ $query_acc, \@Q_left_win,
+ $B_acc, \@B_left_win);
+
+ print "\t\t** Breakpoint **\n\n";
+
+ my @Q_right_win = @Q_chars[$win_right_end5..$win_right_end3];
+ my @A_right_win = @A_chars[$win_right_end5..$win_right_end3];
+ my @B_right_win = @B_chars[$win_right_end5..$win_right_end3];
+
+ &print_alignment($A_acc, \@A_right_win,
+ $query_acc, \@Q_right_win,
+ $B_acc, \@B_right_win);
+
+ return;
+}
+
+
+####
+
+ */
}
catch(exception& e) {
int numSeqs = querySeqs.size();
+ chimeraResults.resize(numSeqs);
+ chimeraFlags.resize(numSeqs, "no");
+
//break up file if needed
int linesPerProcess = numSeqs / processors ;
float percentIdentical = maligner->getPercentID();
vector<results> Results = maligner->getOutput();
- cout << querySeqs[4]->getName() << '\t' << chimeraFlag << '\t' << percentIdentical << endl;
+ //cout << querySeqs[i]->getName() << '\t' << chimeraFlag << '\t' << percentIdentical << endl;
for (int j = 0; j < Results.size(); j++) {
- cout << "regionStart = " << Results[j].regionStart << "\tRegionEnd = " << Results[j].regionEnd << "\tName = " << Results[j].parent << "\tPerQP = " << Results[j].queryToParent << "\tLocalPerQP = " << Results[j].queryToParentLocal << "\tdivR = " << Results[j].divR << endl;
-
+ //cout << "regionStart = " << Results[j].regionStart << "\tRegionEnd = " << Results[j].regionEnd << "\tName = " << Results[j].parent << "\tPerQP = " << Results[j].queryToParent << "\tLocalPerQP = " << Results[j].queryToParentLocal << "\tdivR = " << Results[j].divR << endl;
}
if (chimeraFlag == "yes") {
seqs.pop_back();
}
}
-
+
//put seqs into vector to send to slayer
vector<Sequence*> seqsForSlayer;
for (int k = 0; k < seqs.size(); k++) { seqsForSlayer.push_back(seqs[k].seq); }
}
//send to slayer
- slayer->getResults(querySeqs[i], seqsForSlayer);
-
+ chimeraFlags[i] = slayer->getResults(querySeqs[i], seqsForSlayer);
+ chimeraResults[i] = slayer->getOutput();
+
//free memory
for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; }
}
projects / mothur.git / blobdiff