Commit 37d07578 authored by Elias Dohmen's avatar Elias Dohmen 🎓

output format + integrationTest update

parent c32ba7dd
......@@ -791,9 +791,9 @@ check_termGain(map< unsigned int,vector<string>> posorder, vector<int> singleDom
fout << "# Domain accession\t#Fusions\t#Fissions\t#TerminalLosses\t#TerminalEmergences\t#SingleDomainLosses\t#SingleDomainEmergences\t#Identities" << endl;
for (auto domcount = events_per_domain.begin(); domcount != events_per_domain.end(); ++domcount) {
fout << domcount->first << "\t";
fout << domcount->first;
for (auto countvec = domcount->second.begin(); countvec != domcount->second.end(); ++countvec) {
fout << *countvec << "\t";
fout << "\t" << *countvec;
}
fout << endl;
}
......@@ -811,9 +811,9 @@ check_termGain(map< unsigned int,vector<string>> posorder, vector<int> singleDom
fout << "# Domain accession\t#Fusions\t#Fissions\t#TerminalLosses\t#TerminalEmergences\t#SingleDomainLosses\t#SingleDomainEmergences" << endl;
for (auto domcount = events_per_domain.begin(); domcount != events_per_domain.end(); ++domcount) {
fout << domcount->first << "\t";
fout << domcount->first;
for (auto countvec = domcount->second.begin(); countvec != std::prev(domcount->second.end()); ++countvec) {
fout << *countvec;
fout << "\t" << *countvec;
}
fout << endl;
}
......@@ -829,9 +829,8 @@ check_termGain(map< unsigned int,vector<string>> posorder, vector<int> singleDom
for (auto da = lca_c->first.begin(); da != lca_c->first.end(); ++da) {
fout << *da << " ";
}
fout << "\t";
for (auto ne = lca_c->second.begin(); ne != lca_c->second.end(); ++ne) {
fout << *ne << "\t";
fout << "\t" << *ne;
}
fout << endl;
}
......@@ -845,9 +844,8 @@ check_termGain(map< unsigned int,vector<string>> posorder, vector<int> singleDom
for (auto da = lca_c->first.begin(); da != lca_c->first.end(); ++da) {
fout << *da << " ";
}
fout << "\t";
for (auto ne = lca_c->second.begin(); ne != std::prev(lca_c->second.end()); ++ne) {
fout << *ne << "\t";
fout << "\t" << *ne;
}
fout << endl;
}
......@@ -868,9 +866,8 @@ check_termGain(map< unsigned int,vector<string>> posorder, vector<int> singleDom
for (auto da = lca_c->first.begin(); da != lca_c->first.end(); ++da) {
asout << *da << " ";
}
asout << "\t";
for (auto ne = lca_c->second.begin(); ne != lca_c->second.end(); ++ne) {
asout << *ne << "\t";
asout << "\t" << *ne;
}
asout << endl;
}
......@@ -883,7 +880,6 @@ check_termGain(map< unsigned int,vector<string>> posorder, vector<int> singleDom
for (auto da = va->first.begin(); da != va->first.end(); ++da) {
asout << *da << " ";
}
for (auto ne = va->second.begin(); ne != va->second.end(); ++ne) {
asout << "\t" << *ne;
}
......@@ -902,9 +898,8 @@ check_termGain(map< unsigned int,vector<string>> posorder, vector<int> singleDom
for (auto da = lca_c->first.begin(); da != lca_c->first.end(); ++da) {
asout << *da << " ";
}
asout << "\t";
for (auto ne = lca_c->second.begin(); ne != std::prev(lca_c->second.end()); ++ne) {
asout << *ne << "\t";
asout << "\t" << *ne;
}
asout << endl;
}
......
Exact solutions: 14
Non-ambiguous solutions: 1
Ambiguous solutions: 1
Complex solutions: 2
Identities total: 77
Fusions: 4
Fissions: 2
Terminal Loss: 5
Terminal Emergences: 2
Single Domain Losses: 1
Single Domain Emergences: 1
Exact and non-ambiguous solutions: 15
Fusion rate: 26.67%
Fission rate: 13.33%
Terminal Loss rate: 33.33%
Terminal Emergence rate: 13.33%
Single Domain Loss rate: 6.67%
Single Domain Emergence rate: 6.67%
# Number of events per node.
# Node ID #Fusions #Fissions #TerminalLosses #TerminalEmergences #SingleDomainLosses #SingleDomainEmergences #Identities
0 0 0 0 0 0 0 0
1 0 0 0 0 0 0 0
2 0 0 0 0 1 0 10
3 0 0 4 0 0 0 9
4 0 0 0 0 0 0 10
5 1 1 0 1 0 0 11
6 2 0 1 1 0 0 12
7 0 0 0 0 0 0 11
8 1 0 0 0 0 0 4
9 0 1 0 0 0 1 10
10 0 0 0 0 0 0 0
# Number of events per domain.
# Domain accession #Fusions #Fissions #TerminalLosses #TerminalEmergences #SingleDomainLosses #SingleDomainEmergences #Identities
PF00001 2 0 0 0 0 0 8
PF00002 0 0 0 0 0 1 0
PF00003 0 0 0 0 1 0 3
PF00004 0 0 0 1 0 0 0
PF00005 0 0 0 1 0 0 0
PF00006 0 2 2 0 0 0 13
PF00007 0 2 1 0 0 0 13
PF00008 0 2 1 0 0 0 13
PF00009 0 2 2 0 0 0 13
PF00010 0 2 3 0 0 0 13
PF00011 3 0 0 0 0 0 2
PF00012 3 0 0 0 0 0 2
PF00013 1 0 0 0 0 0 2
PF00014 1 0 0 0 0 0 2
PF00015 1 0 0 0 0 0 2
PF00016 1 0 0 0 0 0 14
PF00017 1 0 0 0 0 0 14
PF00018 1 0 0 0 0 0 14
PF00019 0 0 1 0 0 0 7
PF00020 1 0 0 0 0 0 14
PF00021 1 0 0 0 0 0 14
PF00022 1 0 0 0 0 0 14
PF00023 1 0 0 0 0 0 14
# Number of events per domain arrangement.
# Node Domain arrangement #Fusions #Fissions #TerminalLosses #TerminalEmergences #SingleDomainLosses #SingleDomainEmergences #Identities
2 PF00001 0 0 0 0 0 0 1
2 PF00003 0 0 0 0 1 0 0
2 PF00006 PF00007 PF00008 PF00009 PF00010 0 0 0 0 0 0 1
2 PF00010 PF00009 PF00008 PF00007 PF00006 0 0 0 0 0 0 1
2 PF00016 PF00017 0 0 0 0 0 0 1
2 PF00016 PF00017 PF00018 PF00019 0 0 0 0 0 0 1
2 PF00018 0 0 0 0 0 0 1
2 PF00020 0 0 0 0 0 0 1
2 PF00020 PF00021 0 0 0 0 0 0 1
2 PF00021 PF00022 PF00023 0 0 0 0 0 0 1
2 PF00022 PF00023 0 0 0 0 0 0 1
3 PF00001 0 0 0 0 0 0 1
3 PF00006 PF00007 PF00008 0 0 2 0 0 0 0
3 PF00006 PF00007 PF00008 PF00009 0 0 1 0 0 0 0
3 PF00007 PF00008 PF00009 PF00010 0 0 1 0 0 0 0
3 PF00008 PF00009 PF00010 0 0 2 0 0 0 0
3 PF00010 PF00009 PF00008 PF00007 PF00006 0 0 0 0 0 0 1
3 PF00016 PF00017 0 0 0 0 0 0 1
3 PF00016 PF00017 PF00018 PF00019 0 0 0 0 0 0 1
3 PF00018 0 0 0 0 0 0 1
3 PF00020 0 0 0 0 0 0 1
3 PF00020 PF00021 0 0 0 0 0 0 1
3 PF00021 PF00022 PF00023 0 0 0 0 0 0 1
3 PF00022 PF00023 0 0 0 0 0 0 1
4 PF00001 0 0 0 0 0 0 1
4 PF00006 PF00007 PF00008 PF00009 PF00010 0 0 0 0 0 0 1
4 PF00010 PF00009 PF00008 PF00007 PF00006 0 0 0 0 0 0 1
4 PF00016 PF00017 0 0 0 0 0 0 1
4 PF00016 PF00017 PF00018 PF00019 0 0 0 0 0 0 1
4 PF00018 0 0 0 0 0 0 1
4 PF00020 0 0 0 0 0 0 1
4 PF00020 PF00021 0 0 0 0 0 0 1
4 PF00021 PF00022 PF00023 0 0 0 0 0 0 1
4 PF00022 PF00023 0 0 0 0 0 0 1
5 PF00001 0 0 0 0 0 0 1
5 PF00001 PF00004 0 0 0 1 0 0 0
5 PF00006 PF00007 PF00008 PF00009 PF00010 0 0 0 0 0 0 1
5 PF00009 PF00008 PF00007 PF00006 0 1 0 0 0 0 0
5 PF00010 0 1 0 0 0 0 0
5 PF00011 PF00012 0 0 0 0 0 0 1
5 PF00011 PF00012 PF00013 PF00014 PF00015 1 0 0 0 0 0 0
5 PF00013 PF00014 PF00015 0 0 0 0 0 0 1
5 PF00016 PF00017 0 0 0 0 0 0 1
5 PF00016 PF00017 PF00018 PF00019 0 0 0 0 0 0 1
5 PF00018 0 0 0 0 0 0 1
5 PF00020 0 0 0 0 0 0 1
5 PF00020 PF00021 0 0 0 0 0 0 1
5 PF00021 PF00022 PF00023 0 0 0 0 0 0 1
5 PF00022 PF00023 0 0 0 0 0 0 1
6 PF00001 0 0 0 0 0 0 1
6 PF00001 PF00011 PF00012 1 0 0 0 0 0 0
6 PF00005 PF00001 0 0 0 1 0 0 0
6 PF00006 PF00007 0 0 3 0 0 0 0
6 PF00006 PF00007 PF00008 PF00009 PF00010 0 0 0 0 0 0 1
6 PF00010 PF00009 PF00008 PF00007 PF00006 0 0 0 0 0 0 1
6 PF00011 PF00012 0 0 0 0 0 0 1
6 PF00011 PF00012 PF00001 1 0 0 0 0 0 0
6 PF00013 PF00014 PF00015 0 0 0 0 0 0 1
6 PF00016 PF00017 0 0 0 0 0 0 1
6 PF00016 PF00017 PF00018 PF00019 0 0 0 0 0 0 1
6 PF00018 0 0 0 0 0 0 1
6 PF00020 0 0 0 0 0 0 1
6 PF00020 PF00021 0 0 0 0 0 0 1
6 PF00021 PF00022 PF00023 0 0 0 0 0 0 1
6 PF00022 PF00023 0 0 0 0 0 0 1
7 PF00001 0 0 0 0 0 0 1
7 PF00003 0 0 0 0 0 0 1
7 PF00006 PF00007 PF00008 PF00009 PF00010 0 0 0 0 0 0 1
7 PF00010 PF00009 PF00008 PF00007 PF00006 0 0 0 0 0 0 1
7 PF00016 PF00017 0 0 0 0 0 0 1
7 PF00016 PF00017 PF00018 PF00019 0 0 0 0 0 0 1
7 PF00018 0 0 0 0 0 0 1
7 PF00020 0 0 0 0 0 0 1
7 PF00020 PF00021 0 0 0 0 0 0 1
7 PF00021 PF00022 PF00023 0 0 0 0 0 0 1
7 PF00022 PF00023 0 0 0 0 0 0 1
8 PF00001 0 0 0 0 0 0 1
8 PF00003 0 0 0 0 0 0 1
8 PF00006 PF00007 PF00008 PF00009 PF00010 0 0 0 0 0 0 1
8 PF00010 PF00009 PF00008 PF00007 PF00006 0 0 0 0 0 0 1
8 PF00016 PF00017 PF00018 1 0 1 0 0 0 0
8 PF00020 PF00021 PF00022 PF00023 1 0 0 0 0 0 0
9 PF00001 0 0 0 0 0 0 1
9 PF00002 0 0 0 0 0 1 0
9 PF00003 0 0 0 0 0 0 1
9 PF00006 PF00007 PF00008 PF00009 PF00010 0 0 0 0 0 0 1
9 PF00007 PF00006 0 1 0 0 0 0 0
9 PF00010 PF00009 PF00008 0 1 0 0 0 0 0
9 PF00016 PF00017 0 0 0 0 0 0 1
9 PF00016 PF00017 PF00018 PF00019 0 0 0 0 0 0 1
9 PF00018 0 0 0 0 0 0 1
9 PF00020 0 0 0 0 0 0 1
9 PF00020 PF00021 0 0 0 0 0 0 1
9 PF00021 PF00022 PF00023 0 0 0 0 0 0 1
9 PF00022 PF00023 0 0 0 0 0 0 1
# Complex solutions:
4 PF00011 PF00012 0 0 0 0 0 0 0
4 PF00013 PF00014 PF00015 0 0 0 0 0 0 0
# Number of events per node.
# Node ID #Fusions #Fissions #TerminalLosses #TerminalEmergences #SingleDomainLosses #SingleDomainEmergences
0 0 0 0 0 0 0
1 0 0 0 0 0 0
2 0 0 0 0 1 0
3 0 0 4 0 0 0
4 0 0 0 0 0 0
5 1 1 0 1 0 0
6 2 0 1 1 0 0
7 0 0 0 0 0 0
8 1 0 0 0 0 0
9 0 1 0 0 0 1
10 0 0 0 0 0 0
# Number of events per domain.
# Domain accession #Fusions #Fissions #TerminalLosses #TerminalEmergences #SingleDomainLosses #SingleDomainEmergences
PF00001 2 0 0 0 0 0
PF00002 0 0 0 0 0 1
PF00003 0 0 0 0 1 0
PF00004 0 0 0 1 0 0
PF00005 0 0 0 1 0 0
PF00006 0 2 2 0 0 0
PF00007 0 2 1 0 0 0
PF00008 0 2 1 0 0 0
PF00009 0 2 2 0 0 0
PF00010 0 2 3 0 0 0
PF00011 3 0 0 0 0 0
PF00012 3 0 0 0 0 0
PF00013 1 0 0 0 0 0
PF00014 1 0 0 0 0 0
PF00015 1 0 0 0 0 0
PF00016 1 0 0 0 0 0
PF00017 1 0 0 0 0 0
PF00018 1 0 0 0 0 0
PF00019 0 0 1 0 0 0
PF00020 1 0 0 0 0 0
PF00021 1 0 0 0 0 0
PF00022 1 0 0 0 0 0
PF00023 1 0 0 0 0 0
# Number of events per domain arrangement.
# Node Domain arrangement #Fusions #Fissions #TerminalLosses #TerminalEmergences #SingleDomainLosses #SingleDomainEmergences
2 PF00003 0 0 0 0 1 0
3 PF00006 PF00007 PF00008 0 0 2 0 0 0
3 PF00006 PF00007 PF00008 PF00009 0 0 1 0 0 0
3 PF00007 PF00008 PF00009 PF00010 0 0 1 0 0 0
3 PF00008 PF00009 PF00010 0 0 2 0 0 0
5 PF00001 PF00004 0 0 0 1 0 0
5 PF00009 PF00008 PF00007 PF00006 0 1 0 0 0 0
5 PF00010 0 1 0 0 0 0
5 PF00011 PF00012 PF00013 PF00014 PF00015 1 0 0 0 0 0
6 PF00001 PF00011 PF00012 1 0 0 0 0 0
6 PF00005 PF00001 0 0 0 1 0 0
6 PF00006 PF00007 0 0 3 0 0 0
6 PF00011 PF00012 PF00001 1 0 0 0 0 0
8 PF00016 PF00017 PF00018 1 0 1 0 0 0
8 PF00020 PF00021 PF00022 PF00023 1 0 0 0 0 0
9 PF00002 0 0 0 0 0 1
9 PF00007 PF00006 0 1 0 0 0 0
9 PF00010 PF00009 PF00008 0 1 0 0 0 0
#!/usr/bin/env bats
@test "run DomRates Integration Test" {
@test "run DomRates IntegrationTest" {
run ../../build/domRates -t ../data/test_tree.nwk -a ../data/ -g OG -o results/test_out.txt
run ../../build/domRates -t ../data/test_tree.nwk -a ../data/ -g OG -o results/test_out.txt -s results/test_out_stats.txt
[ $status == 0 ]
run diff <(results/compare_output.txt) <(results/test_out.txt)
run diff results/compare_out.txt results/test_out.txt
[ $status == 0 ]
run diff results/compare_out_stats.txt results/test_out_stats.txt
[ $status == 0 ]
run diff results/compare_out_stats_epd.txt results/test_out_stats_epd.txt
[ $status == 0 ]
# run parallelization test with 4 threads
......@@ -13,9 +17,25 @@
#run diff <(results/compare_output.txt) <(results/test_out.txt)
#[ $status == 0 ]
run ../../build/domRates -t ../data/test_tree.nwk -a ../data/ -g OG -o results/test_ident_out.txt -s results/test_ident_out_stats.txt -i
[ $status == 0 ]
run diff results/compare_ident_out.txt results/test_ident_out.txt
[ $status == 0 ]
run diff results/compare_ident_out_stats.txt results/test_ident_out_stats.txt
[ $status == 0 ]
run diff results/compare_ident_out_stats_epd.txt results/test_ident_out_stats_epd.txt
[ $status == 0 ]
run ../../build/domRates -h
[ $status == 0 ]
rm results/test_out.txt
rm results/test_out_stats.txt
rm results/test_out_stats_epd.txt
rm results/test_ident_out.txt
rm results/test_ident_out_stats.txt
rm results/test_ident_out_stats_epd.txt
}
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