Commit 02f5237a authored by Elias Dohmen's avatar Elias Dohmen 🎓

add integration test

parent 7ace6193
test_DOMRATES:
stage: test
only:
- master
script:
- git submodule init
- git submodule update
- mkdir build
- cd build
- cmake -DCMAKE_BUILD_TYPE=Coverage -DWITH_UNIT_TEST=1 ..
- make
- make test
- cd ../tests/integrationTests
- ./runTests.sh
- cd ../..
- gcovr -r . -e "tests" -e "libs"
# pfam_scan.pl, run at Wed Sep 16 12:49:00 2015
#
# Copyright (c) 2009 Genome Research Ltd
# Freely distributed under the GNU
# General Public License
#
# Authors: Jaina Mistry (jm14@sanger.ac.uk), John Tate (jt6@sanger.ac.uk),
# Rob Finn (rdf@sanger.ac.uk)
#
# This is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>.
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
# query sequence file: /global/public/home/e_dohm01/annotation/Arabidopsis_thaliana.TAIR10.28.pep.all.fa
# searching against: /global/databases/pfam/v28.0//Pfam-A.hmm, with cut off --cut_ga
# resolve clan overlaps: on
# predict active sites: off
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
#
# <seq id> <alignment start> <alignment end> <envelope start> <envelope end> <hmm acc> <hmm name> <type> <hmm start> <hmm end> <hmm length> <bit score> <E-value> <significance> <clan>
A0001 1 10 1 10 PF00001 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0002 1 10 1 10 PF00001 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0002 11 20 11 20 PF00004 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0004 1 10 1 10 PF00006 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0004 11 20 11 20 PF00007 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0004 21 30 21 30 PF00008 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0004 31 40 31 40 PF00009 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0004 41 50 41 50 PF00010 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0007 1 10 1 10 PF00010 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0008 11 20 11 20 PF00009 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0008 21 30 21 30 PF00008 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0008 31 40 31 40 PF00007 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0008 41 50 41 50 PF00006 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0009 1 10 1 10 PF00011 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0009 11 20 11 20 PF00012 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0012 1 10 1 10 PF00013 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0012 11 20 11 20 PF00014 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0012 21 30 21 30 PF00015 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0013 1 10 1 10 PF00011 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0013 11 20 11 20 PF00012 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0013 21 30 21 30 PF00013 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0013 31 40 31 40 PF00014 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0013 41 50 41 50 PF00015 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0014 1 10 1 10 PF00016 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0014 11 20 11 20 PF00017 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0014 21 30 21 30 PF00018 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0014 31 40 31 40 PF00019 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0015 1 10 1 10 PF00016 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0015 11 20 11 20 PF00017 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0016 21 30 21 30 PF00018 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0017 21 30 21 30 PF00020 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0018 1 10 1 10 PF00021 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0018 11 20 11 20 PF00022 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0018 21 30 21 30 PF00023 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0019 11 20 11 20 PF00020 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0019 21 30 21 30 PF00021 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0020 11 20 11 20 PF00022 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
A0020 21 30 21 30 PF00023 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
# pfam_scan.pl, run at Wed Sep 16 12:49:00 2015
#
# Copyright (c) 2009 Genome Research Ltd
# Freely distributed under the GNU
# General Public License
#
# Authors: Jaina Mistry (jm14@sanger.ac.uk), John Tate (jt6@sanger.ac.uk),
# Rob Finn (rdf@sanger.ac.uk)
#
# This is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>.
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
# query sequence file: /global/public/home/e_dohm01/annotation/Arabidopsis_thaliana.TAIR10.28.pep.all.fa
# searching against: /global/databases/pfam/v28.0//Pfam-A.hmm, with cut off --cut_ga
# resolve clan overlaps: on
# predict active sites: off
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
#
# <seq id> <alignment start> <alignment end> <envelope start> <envelope end> <hmm acc> <hmm name> <type> <hmm start> <hmm end> <hmm length> <bit score> <E-value> <significance> <clan>
B0001 1 10 1 10 PF00001 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0002 1 10 1 10 PF00005 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0002 11 20 11 20 PF00001 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0004 1 10 1 10 PF00006 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0004 11 20 11 20 PF00007 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0004 21 30 21 30 PF00008 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0004 31 40 31 40 PF00009 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0004 41 50 41 50 PF00010 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0005 1 10 1 10 PF00006 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0005 11 20 11 20 PF00007 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0008 1 10 1 10 PF00010 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0008 11 20 11 20 PF00009 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0008 21 30 21 30 PF00008 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0008 31 40 31 40 PF00007 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0008 41 50 41 50 PF00006 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0009 1 10 1 10 PF00011 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0009 11 20 11 20 PF00012 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0010 1 10 1 10 PF00001 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0010 11 20 11 20 PF00011 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0010 21 30 21 30 PF00012 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0011 1 10 1 10 PF00011 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0011 11 20 11 20 PF00012 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0011 21 30 21 30 PF00001 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0012 1 10 1 10 PF00013 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0012 11 20 11 20 PF00014 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0012 21 30 21 30 PF00015 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0014 1 10 1 10 PF00016 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0014 11 20 11 20 PF00017 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0014 21 30 21 30 PF00018 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0014 31 40 31 40 PF00019 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0015 1 10 1 10 PF00016 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0015 11 20 11 20 PF00017 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0016 21 30 21 30 PF00018 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0017 21 30 21 30 PF00020 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0018 1 10 1 10 PF00021 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0018 11 20 11 20 PF00022 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0018 21 30 21 30 PF00023 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0019 11 20 11 20 PF00020 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0019 21 30 21 30 PF00021 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0020 11 20 11 20 PF00022 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
B0020 21 30 21 30 PF00023 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
# pfam_scan.pl, run at Wed Sep 16 12:49:00 2015
#
# Copyright (c) 2009 Genome Research Ltd
# Freely distributed under the GNU
# General Public License
#
# Authors: Jaina Mistry (jm14@sanger.ac.uk), John Tate (jt6@sanger.ac.uk),
# Rob Finn (rdf@sanger.ac.uk)
#
# This is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>.
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
# query sequence file: /global/public/home/e_dohm01/annotation/Arabidopsis_thaliana.TAIR10.28.pep.all.fa
# searching against: /global/databases/pfam/v28.0//Pfam-A.hmm, with cut off --cut_ga
# resolve clan overlaps: on
# predict active sites: off
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
#
# <seq id> <alignment start> <alignment end> <envelope start> <envelope end> <hmm acc> <hmm name> <type> <hmm start> <hmm end> <hmm length> <bit score> <E-value> <significance> <clan>
C0001 1 10 1 10 PF00001 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0004 11 20 11 20 PF00007 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0004 21 30 21 30 PF00008 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0004 31 40 31 40 PF00009 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0004 41 50 41 50 PF00010 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0005 11 20 11 20 PF00006 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0005 21 30 21 30 PF00007 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0005 31 40 31 40 PF00008 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0005 41 50 41 50 PF00009 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0006 11 20 11 20 PF00006 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0006 21 30 21 30 PF00007 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0006 31 40 31 40 PF00008 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0007 11 20 11 20 PF00008 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0007 21 30 21 30 PF00009 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0007 31 40 31 40 PF00010 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0008 1 10 1 10 PF00010 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0008 11 20 11 20 PF00009 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0008 21 30 21 30 PF00008 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0008 31 40 31 40 PF00007 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0008 41 50 41 50 PF00006 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0014 1 10 1 10 PF00016 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0014 11 20 11 20 PF00017 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0014 21 30 21 30 PF00018 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0014 31 40 31 40 PF00019 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0015 1 10 1 10 PF00016 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0015 11 20 11 20 PF00017 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0016 21 30 21 30 PF00018 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0017 21 30 21 30 PF00020 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0018 1 10 1 10 PF00021 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0018 11 20 11 20 PF00022 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0018 21 30 21 30 PF00023 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0019 11 20 11 20 PF00020 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0019 21 30 21 30 PF00021 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0020 11 20 11 20 PF00022 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
C0020 21 30 21 30 PF00023 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
# pfam_scan.pl, run at Wed Sep 16 12:49:00 2015
#
# Copyright (c) 2009 Genome Research Ltd
# Freely distributed under the GNU
# General Public License
#
# Authors: Jaina Mistry (jm14@sanger.ac.uk), John Tate (jt6@sanger.ac.uk),
# Rob Finn (rdf@sanger.ac.uk)
#
# This is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>.
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
# query sequence file: /global/public/home/e_dohm01/annotation/Arabidopsis_thaliana.TAIR10.28.pep.all.fa
# searching against: /global/databases/pfam/v28.0//Pfam-A.hmm, with cut off --cut_ga
# resolve clan overlaps: on
# predict active sites: off
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
#
# <seq id> <alignment start> <alignment end> <envelope start> <envelope end> <hmm acc> <hmm name> <type> <hmm start> <hmm end> <hmm length> <bit score> <E-value> <significance> <clan>
D0001 1 10 1 10 PF00001 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0002 1 10 1 10 PF00003 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0004 1 10 1 10 PF00006 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0004 11 20 11 20 PF00007 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0004 21 30 21 30 PF00008 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0004 31 40 31 40 PF00009 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0004 41 50 41 50 PF00010 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0008 1 10 1 10 PF00010 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0008 11 20 11 20 PF00009 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0008 21 30 21 30 PF00008 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0008 31 40 31 40 PF00007 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0008 41 50 41 50 PF00006 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0015 1 10 1 10 PF00016 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0015 11 20 11 20 PF00017 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0015 21 30 21 30 PF00018 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0016 1 10 1 10 PF00020 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0016 11 20 11 20 PF00021 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0016 21 30 21 30 PF00022 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
D0016 31 40 31 40 PF00023 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
# pfam_scan.pl, run at Wed Sep 16 12:49:00 2015
#
# Copyright (c) 2009 Genome Research Ltd
# Freely distributed under the GNU
# General Public License
#
# Authors: Jaina Mistry (jm14@sanger.ac.uk), John Tate (jt6@sanger.ac.uk),
# Rob Finn (rdf@sanger.ac.uk)
#
# This is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>.
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
# query sequence file: /global/public/home/e_dohm01/annotation/Arabidopsis_thaliana.TAIR10.28.pep.all.fa
# searching against: /global/databases/pfam/v28.0//Pfam-A.hmm, with cut off --cut_ga
# resolve clan overlaps: on
# predict active sites: off
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
#
# <seq id> <alignment start> <alignment end> <envelope start> <envelope end> <hmm acc> <hmm name> <type> <hmm start> <hmm end> <hmm length> <bit score> <E-value> <significance> <clan>
E0001 1 10 1 10 PF00001 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0002 1 10 1 10 PF00002 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0003 1 10 1 10 PF00003 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0004 1 10 1 10 PF00006 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0004 11 20 11 20 PF00007 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0004 21 30 21 30 PF00008 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0004 31 40 31 40 PF00009 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0004 41 50 41 50 PF00010 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0007 1 10 1 10 PF00010 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0007 11 20 11 20 PF00009 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0007 21 30 21 30 PF00008 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0008 31 40 31 40 PF00007 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0008 41 50 41 50 PF00006 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0014 1 10 1 10 PF00016 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0014 11 20 11 20 PF00017 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0014 21 30 21 30 PF00018 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0014 31 40 31 40 PF00019 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0015 1 10 1 10 PF00016 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0015 11 20 11 20 PF00017 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0016 21 30 21 30 PF00018 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0017 21 30 21 30 PF00020 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0018 1 10 1 10 PF00021 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0018 11 20 11 20 PF00022 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0018 21 30 21 30 PF00023 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0019 11 20 11 20 PF00020 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0019 21 30 21 30 PF00021 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0020 11 20 11 20 PF00022 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
E0020 21 30 21 30 PF00023 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
# pfam_scan.pl, run at Wed Sep 16 12:49:00 2015
#
# Copyright (c) 2009 Genome Research Ltd
# Freely distributed under the GNU
# General Public License
#
# Authors: Jaina Mistry (jm14@sanger.ac.uk), John Tate (jt6@sanger.ac.uk),
# Rob Finn (rdf@sanger.ac.uk)
#
# This is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>.
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
# query sequence file: /global/public/home/e_dohm01/annotation/Arabidopsis_thaliana.TAIR10.28.pep.all.fa
# searching against: /global/databases/pfam/v28.0//Pfam-A.hmm, with cut off --cut_ga
# resolve clan overlaps: on
# predict active sites: off
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
#
# <seq id> <alignment start> <alignment end> <envelope start> <envelope end> <hmm acc> <hmm name> <type> <hmm start> <hmm end> <hmm length> <bit score> <E-value> <significance> <clan>
OG0001 1 10 1 10 PF00001 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0002 1 10 1 10 PF00003 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0004 1 10 1 10 PF00006 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0004 11 20 11 20 PF00007 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0004 21 30 21 30 PF00008 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0004 31 40 31 40 PF00009 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0004 41 50 41 50 PF00010 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0008 1 10 1 10 PF00010 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0008 11 20 11 20 PF00009 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0008 21 30 21 30 PF00008 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0008 31 40 31 40 PF00007 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0008 41 50 41 50 PF00006 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0014 1 10 1 10 PF00016 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0014 11 20 11 20 PF00017 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0014 21 30 21 30 PF00018 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0014 31 40 31 40 PF00019 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0015 1 10 1 10 PF00016 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0015 11 20 11 20 PF00017 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0016 21 30 21 30 PF00018 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0017 21 30 21 30 PF00020 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0018 1 10 1 10 PF00021 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0018 11 20 11 20 PF00022 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0018 21 30 21 30 PF00023 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0019 11 20 11 20 PF00020 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0019 21 30 21 30 PF00021 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0020 11 20 11 20 PF00022 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
OG0020 21 30 21 30 PF00023 ATP-synt_C Family 3 46 63 26.4 5.3e-06 1 No_clan
(((C:2.000000,(A:1.000000,B:3.000000)AB)ABC,(D:1.000000,E:1.500000)DE),OG)R;
\ No newline at end of file
Exact solutions: 14
Non-ambiguous solutions: 1
Ambiguous solutions: 1
Complex solutions: 2
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%
#!/usr/bin/env bats
@test "run DomRates Integration Test" {
run ../../build/domRates -t ../data/test_tree.nwk -a ../data -g OG -o results/test_out.txt
[ $status == 0 ]
run diff <(results/compare_output.txt) <(results/test_out.txt)
[ $status == 0 ]
# run parallelization test with 4 threads
#run ../../build/domRates -t ../data/test_tree.nwk -a ../data -g OG -o results/test_out.txt -p 4
#[ $status == 0 ]
#run diff <(results/compare_output.txt) <(results/test_out.txt)
#[ $status == 0 ]
run ../../build/domRates -h
[ $status == 0 ]
rm results/test_out.txt
}
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