[med-svn] [macsyfinder] branch upstream updated (579efa8 -> e67d1ad)
Andreas Tille
tille at debian.org
Tue Feb 6 16:15:48 UTC 2018
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository macsyfinder.
from 579efa8 New upstream version 1.0.2
new e67d1ad New upstream version 1.0.5
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 24 +
.gitlab-ci.yml | 50 +
.travis.yml | 13 +-
CITATION => CITATION.yml | 12 +-
CONTRIB | 11 +
Docker/coverage/Dockerfile | 10 +
Docker/pages/Dockerfile | 10 +
Docker/run_dep/Dockerfile | 11 +
INSTALL | 88 -
INSTALL.md | 144 +
MANIFEST.in | 18 +-
NEWS | 15 +-
README.md | 66 +-
bin/macsyfinder | 95 +-
data/sequence_data/datatest_gembase.fasta.idx | 7219 ------
data/sequence_data/datatest_gembase.fasta.phr | Bin 1544922 -> 0 bytes
data/sequence_data/datatest_gembase.fasta.pin | Bin 57840 -> 0 bytes
data/sequence_data/datatest_gembase.fasta.pog | Bin 28908 -> 0 bytes
data/sequence_data/datatest_gembase.fasta.psd | 14438 -----------
data/sequence_data/datatest_gembase.fasta.psi | Bin 7691 -> 0 bytes
data/sequence_data/datatest_gembase.fasta.psq | Bin 2344444 -> 0 bytes
doc/conf.py | 2 +-
doc/gembase_convention.rst | 8 +-
doc/input.rst | 4 +
doc/installation.rst | 130 +-
doc/macsyview.rst | 21 +-
macsypy/__init__.py | 1 +
macsypy/config.py | 340 +-
macsypy/database.py | 139 +-
macsypy/gene.py | 122 +-
macsypy/registries.py | 8 +-
macsypy/report.py | 110 +-
macsypy/search_genes.py | 42 +-
macsypy/search_systems.py | 375 +-
macsypy/system.py | 13 +-
macsypy/system_parser.py | 136 +-
test/__init__.py => macsypy/utils.py | 20 +-
setup.py | 269 +-
test/datatest/outputs_control/log_prru_psae | 341 -
test/log_test | 310 -
test/script_test.csh | 4 -
test/test_Config.py | 661 -
test/test_Hit.py | 114 -
tests.py | 168 +
tests/__init__.py | 18 +
.../data}/DEF/bad_max_nb_genes.xml | 0
.../data}/DEF/bad_min_genes_required.xml | 0
.../data}/DEF/bad_min_mandatory_genes_required.xml | 0
.../DEF/bad_min_mandatory_genes_required_2.xml | 0
{test/datatest => tests/data}/DEF/bad_sys_ref.xml | 0
.../data}/DEF/fail_invalid_presence.xml | 0
.../data}/DEF/fail_wo_presence.xml | 0
{test/datatest => tests/data}/DEF/gene_no_name.xml | 0
.../data}/DEF/invalid_aligned.xml | 0
.../data}/DEF/invalid_homolog.xml | 0
{test/datatest => tests/data}/DEF/system_1.xml | 0
{test/datatest => tests/data}/DEF/system_2.xml | 0
tests/data/base/formatdb.err | 10 +
.../data}/base/ordered_replicon_base | 0
tests/data/base/test_aesu.fa | 25513 +++++++++++++++++++
tests/data/base/test_aesu.fa.idx | 3140 +++
tests/data/base/test_aesu.fa.phr | Bin 0 -> 178980 bytes
tests/data/base/test_aesu.fa.pin | Bin 0 -> 25200 bytes
tests/data/base/test_aesu.fa.pog | Bin 0 -> 12592 bytes
tests/data/base/test_aesu.fa.psd | 6280 +++++
tests/data/base/test_aesu.fa.psi | Bin 0 -> 3373 bytes
tests/data/base/test_aesu.fa.psq | Bin 0 -> 1044806 bytes
{test/datatest => tests/data}/base/test_base.fa | 68 +-
.../data_set_1/basic_run_results/macsyfinder.conf | 26 +
.../data_set_1/basic_run_results/macsyfinder.out | 147 +
.../basic_run_results/macsyfinder.report | 13 +
.../basic_run_results/macsyfinder.summary | 2 +
.../data_set_1/basic_run_results/macsyfinder.tab | 2 +
.../basic_run_results/results.macsyfinder.json | 1 +
tests/data/data_set_1/def/CONJ.xml | 27 +
tests/data/data_set_1/def/Flagellum.xml | 40 +
tests/data/data_set_1/def/T2SS.xml | 50 +
tests/data/data_set_1/def/T3SS.xml | 52 +
tests/data/data_set_1/def/T4P.xml | 49 +
tests/data/data_set_1/def/T4SS_typeF.xml | 20 +
tests/data/data_set_1/def/T4SS_typeI.xml | 21 +
tests/data/data_set_1/def/T9SS.xml | 25 +
tests/data/data_set_1/def/Tad.xml | 17 +
.../data/data_set_1/profiles/Flg_flgB.hmm | 0
.../data/data_set_1/profiles/Flg_flgC.hmm | 0
.../data/data_set_1/profiles/Flg_fliE.hmm | 0
.../data/data_set_1/profiles/Flg_sctJ_FLG.hmm | 0
.../data/data_set_1/profiles/Flg_sctN_FLG.hmm | 0
tests/data/data_set_1/profiles/Flg_sctQ_FLG.hmm | 245 +
tests/data/data_set_1/profiles/Flg_sctR_FLG.hmm | 626 +
tests/data/data_set_1/profiles/Flg_sctS_FLG.hmm | 287 +
tests/data/data_set_1/profiles/Flg_sctT_FLG.hmm | 797 +
tests/data/data_set_1/profiles/Flg_sctU_FLG.hmm | 1052 +
tests/data/data_set_1/profiles/Flg_sctV_FLG.hmm | 2033 ++
tests/data/data_set_1/profiles/T2SS_gspC.hmm | 248 +
.../data/data_set_1/profiles/T2SS_gspD.hmm | 0
tests/data/data_set_1/profiles/T2SS_gspE.hmm | 1154 +
tests/data/data_set_1/profiles/T2SS_gspF.hmm | 1202 +
tests/data/data_set_1/profiles/T2SS_gspG.hmm | 413 +
tests/data/data_set_1/profiles/T2SS_gspH.hmm | 479 +
tests/data/data_set_1/profiles/T2SS_gspI.hmm | 347 +
tests/data/data_set_1/profiles/T2SS_gspJ.hmm | 389 +
tests/data/data_set_1/profiles/T2SS_gspK.hmm | 761 +
tests/data/data_set_1/profiles/T2SS_gspL.hmm | 782 +
tests/data/data_set_1/profiles/T2SS_gspM.hmm | 422 +
tests/data/data_set_1/profiles/T2SS_gspN.hmm | 671 +
tests/data/data_set_1/profiles/T2SS_gspO.hmm | 719 +
.../data/data_set_1/profiles/T3SS_sctC.hmm | 0
.../data/data_set_1/profiles/T3SS_sctJ.hmm | 0
.../data/data_set_1/profiles/T3SS_sctN.hmm | 0
tests/data/data_set_1/profiles/T3SS_sctQ.hmm | 227 +
tests/data/data_set_1/profiles/T3SS_sctR.hmm | 617 +
tests/data/data_set_1/profiles/T3SS_sctS.hmm | 263 +
tests/data/data_set_1/profiles/T3SS_sctT.hmm | 785 +
tests/data/data_set_1/profiles/T3SS_sctU.hmm | 1031 +
tests/data/data_set_1/profiles/T3SS_sctV.hmm | 2024 ++
tests/data/data_set_1/profiles/T4P_pilAE.hmm | 515 +
tests/data/data_set_1/profiles/T4P_pilB.hmm | 1169 +
tests/data/data_set_1/profiles/T4P_pilC.hmm | 1037 +
tests/data/data_set_1/profiles/T4P_pilD.hmm | 716 +
tests/data/data_set_1/profiles/T4P_pilI_pilV.hmm | 533 +
tests/data/data_set_1/profiles/T4P_pilM.hmm | 1034 +
tests/data/data_set_1/profiles/T4P_pilN.hmm | 599 +
tests/data/data_set_1/profiles/T4P_pilO.hmm | 581 +
.../data/data_set_1/profiles/T4P_pilP.hmm | 362 +-
tests/data/data_set_1/profiles/T4P_pilQ.hmm | 857 +
tests/data/data_set_1/profiles/T4P_pilT_pilU.hmm | 1019 +
tests/data/data_set_1/profiles/T4SS_F_traB.hmm | 1313 +
tests/data/data_set_1/profiles/T4SS_F_traE.hmm | 599 +
tests/data/data_set_1/profiles/T4SS_F_traF.hmm | 848 +
tests/data/data_set_1/profiles/T4SS_F_traG.hmm | 2864 +++
tests/data/data_set_1/profiles/T4SS_F_traH.hmm | 1403 +
tests/data/data_set_1/profiles/T4SS_F_traK.hmm | 854 +
tests/data/data_set_1/profiles/T4SS_F_traL.hmm | 320 +
tests/data/data_set_1/profiles/T4SS_F_traN.hmm | 1985 ++
tests/data/data_set_1/profiles/T4SS_F_traU.hmm | 1022 +
tests/data/data_set_1/profiles/T4SS_F_traV.hmm | 755 +
tests/data/data_set_1/profiles/T4SS_F_traW.hmm | 656 +
tests/data/data_set_1/profiles/T4SS_F_trbC.hmm | 707 +
tests/data/data_set_1/profiles/T4SS_G_tfc7.hmm | 767 +
tests/data/data_set_1/profiles/T4SS_I_traE.hmm | 842 +
tests/data/data_set_1/profiles/T4SS_I_traI.hmm | 839 +
tests/data/data_set_1/profiles/T4SS_I_traK.hmm | 281 +
tests/data/data_set_1/profiles/T4SS_I_traL.hmm | 488 +
tests/data/data_set_1/profiles/T4SS_I_traM.hmm | 707 +
tests/data/data_set_1/profiles/T4SS_I_traN.hmm | 1028 +
tests/data/data_set_1/profiles/T4SS_I_traO.hmm | 1343 +
tests/data/data_set_1/profiles/T4SS_I_traP.hmm | 737 +
tests/data/data_set_1/profiles/T4SS_I_traQ.hmm | 557 +
tests/data/data_set_1/profiles/T4SS_I_traR.hmm | 422 +
tests/data/data_set_1/profiles/T4SS_I_traT.hmm | 818 +
tests/data/data_set_1/profiles/T4SS_I_traU.hmm | 3044 +++
tests/data/data_set_1/profiles/T4SS_I_traW.hmm | 1235 +
tests/data/data_set_1/profiles/T4SS_I_traY.hmm | 2255 ++
tests/data/data_set_1/profiles/T4SS_I_trbA.hmm | 1259 +
tests/data/data_set_1/profiles/T4SS_I_trbB.hmm | 1061 +
tests/data/data_set_1/profiles/T4SS_MOBB.hmm | 692 +
tests/data/data_set_1/profiles/T4SS_MOBC.hmm | 653 +
tests/data/data_set_1/profiles/T4SS_MOBF.hmm | 2660 ++
tests/data/data_set_1/profiles/T4SS_MOBH.hmm | 632 +
tests/data/data_set_1/profiles/T4SS_MOBP1.hmm | 719 +
tests/data/data_set_1/profiles/T4SS_MOBP2.hmm | 1547 ++
tests/data/data_set_1/profiles/T4SS_MOBP3.hmm | 944 +
tests/data/data_set_1/profiles/T4SS_MOBQ.hmm | 671 +
tests/data/data_set_1/profiles/T4SS_MOBT.hmm | 1118 +
tests/data/data_set_1/profiles/T4SS_MOBV.hmm | 632 +
tests/data/data_set_1/profiles/T4SS_T_virB1.hmm | 449 +
tests/data/data_set_1/profiles/T4SS_t4cp1.hmm | 350 +
tests/data/data_set_1/profiles/T4SS_t4cp2.hmm | 686 +
tests/data/data_set_1/profiles/T4SS_tcpA.hmm | 1412 +
tests/data/data_set_1/profiles/T4SS_virb4.hmm | 2849 +++
.../data_set_1/profiles/T9SS_gldJ_TIGR03524.hmm | 1697 ++
.../data_set_1/profiles/T9SS_gldK_TIGR03525.hmm | 1367 +
.../data_set_1/profiles/T9SS_gldL_TIGR03513.hmm | 761 +
.../data_set_1/profiles/T9SS_gldM_TIGR03517.hmm | 1592 ++
.../data_set_1/profiles/T9SS_gldN_TIGR03523.hmm | 860 +
tests/data/data_set_1/profiles/T9SS_porQ.hmm | 1018 +
tests/data/data_set_1/profiles/T9SS_porU.hmm | 3352 +++
tests/data/data_set_1/profiles/T9SS_porV.hmm | 1168 +
.../data_set_1/profiles/T9SS_sprA-2_PF12118.hmm | 912 +
.../data_set_1/profiles/T9SS_sprA-3_TIGR04189.hmm | 6982 +++++
.../data/data_set_1/profiles/T9SS_sprA_PF14349.hmm | 1305 +
tests/data/data_set_1/profiles/T9SS_sprE.hmm | 2161 ++
tests/data/data_set_1/profiles/T9SS_sprT.hmm | 730 +
tests/data/data_set_1/profiles/Tad_flp.hmm | 188 +
tests/data/data_set_1/profiles/Tad_rcpA.hmm | 1235 +
tests/data/data_set_1/profiles/Tad_tadA.hmm | 1127 +
tests/data/data_set_1/profiles/Tad_tadB.hmm | 680 +
tests/data/data_set_1/profiles/Tad_tadC.hmm | 905 +
tests/data/data_set_1/profiles/Tad_tadE.hmm | 476 +
tests/data/data_set_1/profiles/Tad_tadF.hmm | 608 +
tests/data/data_set_1/profiles/Tad_tadV.hmm | 476 +
.../data/data_set_1/profiles/Tad_tadZ.hmm | 0
.../data}/hmm/flp.res_hmm_extract | 0
.../datatest => tests/data}/hmm/flp.search_hmm.out | 0
.../data}/hmm/gspC.res_hmm_extract | 0
.../data}/hmm/gspC.search_hmm.out | 0
.../data}/hmm/gspD.res_hmm_extract | 0
.../data}/hmm/gspD.search_hmm.out | 48 +
.../data}/hmm/gspE.res_hmm_extract | 0
.../data}/hmm/gspE.search_hmm.out | 0
.../data}/hmm/gspF.res_hmm_extract | 0
.../data}/hmm/gspF.search_hmm.out | 0
.../data}/hmm/gspG.res_hmm_extract | 0
.../data}/hmm/gspG.search_hmm.out | 0
.../data}/hmm/gspH.res_hmm_extract | 0
.../data}/hmm/gspH.search_hmm.out | 0
.../data}/hmm/gspI.res_hmm_extract | 0
.../data}/hmm/gspI.search_hmm.out | 0
.../data}/hmm/gspJ.res_hmm_extract | 0
.../data}/hmm/gspJ.search_hmm.out | 0
.../data}/hmm/gspK.res_hmm_extract | 0
.../data}/hmm/gspK.search_hmm.out | 0
.../data}/hmm/gspL.res_hmm_extract | 0
.../data}/hmm/gspL.search_hmm.out | 0
.../data}/hmm/gspM.res_hmm_extract | 0
.../data}/hmm/gspM.search_hmm.out | 0
.../data}/hmm/gspO.res_hmm_extract | 0
.../data}/hmm/gspO.search_hmm.out | 0
.../data}/hmm/pilAE.res_hmm_extract | 0
.../data}/hmm/pilAE.search_hmm.out | 0
.../data}/hmm/pilB.res_hmm_extract | 0
.../data}/hmm/pilB.search_hmm.out | 0
.../data}/hmm/pilC.res_hmm_extract | 0
.../data}/hmm/pilC.search_hmm.out | 0
.../data}/hmm/pilD.res_hmm_extract | 0
.../data}/hmm/pilD.search_hmm.out | 0
.../data}/hmm/pilI_pilV.res_hmm_extract | 0
.../data}/hmm/pilI_pilV.search_hmm.out | 0
.../data}/hmm/pilM.res_hmm_extract | 0
.../data}/hmm/pilM.search_hmm.out | 0
.../data}/hmm/pilN.res_hmm_extract | 0
.../data}/hmm/pilN.search_hmm.out | 0
.../data}/hmm/pilO.res_hmm_extract | 0
.../data}/hmm/pilO.search_hmm.out | 0
.../data}/hmm/pilP.res_hmm_extract | 0
.../data}/hmm/pilP.search_hmm.out | 0
.../data}/hmm/pilQ.res_hmm_extract | 0
.../data}/hmm/pilQ.search_hmm.out | 0
.../data}/hmm/pilT_pilU.res_hmm_extract | 0
.../data}/hmm/pilT_pilU.search_hmm.out | 0
.../data}/hmm/rcpA.res_hmm_extract | 0
.../data}/hmm/rcpA.search_hmm.out | 0
.../data}/hmm/tadA.res_hmm_extract | 0
.../data}/hmm/tadA.search_hmm.out | 0
.../data}/hmm/tadB.res_hmm_extract | 0
.../data}/hmm/tadB.search_hmm.out | 0
.../data}/hmm/tadC.res_hmm_extract | 0
.../data}/hmm/tadC.search_hmm.out | 0
.../data}/hmm/tadD.res_hmm_extract | 0
.../data}/hmm/tadD.search_hmm.out | 0
.../data}/hmm/tadE.res_hmm_extract | 0
.../data}/hmm/tadE.search_hmm.out | 0
.../data}/hmm/tadF.res_hmm_extract | 0
.../data}/hmm/tadF.search_hmm.out | 0
.../data}/hmm/tadV.res_hmm_extract | 0
.../data}/hmm/tadV.search_hmm.out | 0
.../data}/hmm/tadZ.res_hmm_extract | 0
.../data}/hmm/tadZ.search_hmm.out | 0
.../data}/outputs_control/joint_res_file | 0
.../data}/outputs_control/joint_res_file.sel | 0
{test/datatest => tests/data}/profiles/abc.hmm | 0
{test/datatest => tests/data}/profiles/flgB.hmm | 0
{test/datatest => tests/data}/profiles/flgC.hmm | 0
{test/datatest => tests/data}/profiles/fliE.hmm | 0
{test/datatest => tests/data}/profiles/gspD.hmm | 0
{test/datatest => tests/data}/profiles/sctC.hmm | 0
{test/datatest => tests/data}/profiles/sctJ.hmm | 0
.../datatest => tests/data}/profiles/sctJ_FLG.hmm | 0
{test/datatest => tests/data}/profiles/sctN.hmm | 0
.../datatest => tests/data}/profiles/sctN_FLG.hmm | 0
{test/datatest => tests/data}/profiles/tadZ.hmm | 0
{test/datatest => tests/data}/profiles/toto.hmm | 0
{test/datatest => tests/data}/profiles/totote.hmm | 0
{macsypy => tests/functional}/__init__.py | 0
{test => tests/functional}/main.py | 38 +-
tests/functional/test_first_test.py | 141 +
{macsypy => tests/integration}/__init__.py | 0
{macsypy => tests/unit}/__init__.py | 0
{test => tests/unit}/main.py | 30 +-
tests/unit/test_Config.py | 659 +
{test => tests/unit}/test_Gene.py | 50 +-
{test => tests/unit}/test_GeneBank.py | 51 +-
tests/unit/test_Hit.py | 112 +
{test => tests/unit}/test_Homolog.py | 47 +-
{test => tests/unit}/test_Indexes.py | 117 +-
{test => tests/unit}/test_Profile.py | 52 +-
{test => tests/unit}/test_ProfileFactory.py | 7 +-
{test => tests/unit}/test_RepliconDB.py | 53 +-
{test => tests/unit}/test_Report.py | 92 +-
{test => tests/unit}/test_System.py | 44 +-
{test => tests/unit}/test_SystemBank.py | 45 +-
{test => tests/unit}/test_SystemParser.py | 81 +-
utils/setsid | Bin 0 -> 9140 bytes
294 files changed, 140820 insertions(+), 24549 deletions(-)
create mode 100644 .gitlab-ci.yml
rename CITATION => CITATION.yml (85%)
create mode 100644 CONTRIB
create mode 100644 Docker/coverage/Dockerfile
create mode 100644 Docker/pages/Dockerfile
create mode 100644 Docker/run_dep/Dockerfile
delete mode 100644 INSTALL
create mode 100644 INSTALL.md
delete mode 100644 data/sequence_data/datatest_gembase.fasta.idx
delete mode 100644 data/sequence_data/datatest_gembase.fasta.phr
delete mode 100644 data/sequence_data/datatest_gembase.fasta.pin
delete mode 100644 data/sequence_data/datatest_gembase.fasta.pog
delete mode 100644 data/sequence_data/datatest_gembase.fasta.psd
delete mode 100644 data/sequence_data/datatest_gembase.fasta.psi
delete mode 100644 data/sequence_data/datatest_gembase.fasta.psq
rename test/__init__.py => macsypy/utils.py (74%)
delete mode 100644 test/datatest/outputs_control/log_prru_psae
delete mode 100644 test/log_test
delete mode 100755 test/script_test.csh
delete mode 100644 test/test_Config.py
delete mode 100644 test/test_Hit.py
create mode 100644 tests.py
create mode 100644 tests/__init__.py
rename {test/datatest => tests/data}/DEF/bad_max_nb_genes.xml (100%)
rename {test/datatest => tests/data}/DEF/bad_min_genes_required.xml (100%)
rename {test/datatest => tests/data}/DEF/bad_min_mandatory_genes_required.xml (100%)
rename {test/datatest => tests/data}/DEF/bad_min_mandatory_genes_required_2.xml (100%)
rename {test/datatest => tests/data}/DEF/bad_sys_ref.xml (100%)
rename {test/datatest => tests/data}/DEF/fail_invalid_presence.xml (100%)
rename {test/datatest => tests/data}/DEF/fail_wo_presence.xml (100%)
rename {test/datatest => tests/data}/DEF/gene_no_name.xml (100%)
rename {test/datatest => tests/data}/DEF/invalid_aligned.xml (100%)
rename {test/datatest => tests/data}/DEF/invalid_homolog.xml (100%)
rename {test/datatest => tests/data}/DEF/system_1.xml (100%)
rename {test/datatest => tests/data}/DEF/system_2.xml (100%)
create mode 100644 tests/data/base/formatdb.err
rename {test/datatest => tests/data}/base/ordered_replicon_base (100%)
create mode 100644 tests/data/base/test_aesu.fa
create mode 100644 tests/data/base/test_aesu.fa.idx
create mode 100644 tests/data/base/test_aesu.fa.phr
create mode 100644 tests/data/base/test_aesu.fa.pin
create mode 100644 tests/data/base/test_aesu.fa.pog
create mode 100644 tests/data/base/test_aesu.fa.psd
create mode 100644 tests/data/base/test_aesu.fa.psi
create mode 100644 tests/data/base/test_aesu.fa.psq
rename {test/datatest => tests/data}/base/test_base.fa (93%)
create mode 100644 tests/data/data_set_1/basic_run_results/macsyfinder.conf
create mode 100644 tests/data/data_set_1/basic_run_results/macsyfinder.out
create mode 100644 tests/data/data_set_1/basic_run_results/macsyfinder.report
create mode 100644 tests/data/data_set_1/basic_run_results/macsyfinder.summary
create mode 100644 tests/data/data_set_1/basic_run_results/macsyfinder.tab
create mode 100644 tests/data/data_set_1/basic_run_results/results.macsyfinder.json
create mode 100644 tests/data/data_set_1/def/CONJ.xml
create mode 100644 tests/data/data_set_1/def/Flagellum.xml
create mode 100644 tests/data/data_set_1/def/T2SS.xml
create mode 100644 tests/data/data_set_1/def/T3SS.xml
create mode 100644 tests/data/data_set_1/def/T4P.xml
create mode 100644 tests/data/data_set_1/def/T4SS_typeF.xml
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create mode 100644 tests/data/data_set_1/def/Tad.xml
copy test/datatest/profiles/flgB.hmm => tests/data/data_set_1/profiles/Flg_flgB.hmm (100%)
copy test/datatest/profiles/flgC.hmm => tests/data/data_set_1/profiles/Flg_flgC.hmm (100%)
copy test/datatest/profiles/fliE.hmm => tests/data/data_set_1/profiles/Flg_fliE.hmm (100%)
copy test/datatest/profiles/sctJ_FLG.hmm => tests/data/data_set_1/profiles/Flg_sctJ_FLG.hmm (100%)
copy test/datatest/profiles/sctN_FLG.hmm => tests/data/data_set_1/profiles/Flg_sctN_FLG.hmm (100%)
create mode 100644 tests/data/data_set_1/profiles/Flg_sctQ_FLG.hmm
create mode 100644 tests/data/data_set_1/profiles/Flg_sctR_FLG.hmm
create mode 100644 tests/data/data_set_1/profiles/Flg_sctS_FLG.hmm
create mode 100644 tests/data/data_set_1/profiles/Flg_sctT_FLG.hmm
create mode 100644 tests/data/data_set_1/profiles/Flg_sctU_FLG.hmm
create mode 100644 tests/data/data_set_1/profiles/Flg_sctV_FLG.hmm
create mode 100644 tests/data/data_set_1/profiles/T2SS_gspC.hmm
copy test/datatest/profiles/gspD.hmm => tests/data/data_set_1/profiles/T2SS_gspD.hmm (100%)
create mode 100644 tests/data/data_set_1/profiles/T2SS_gspE.hmm
create mode 100644 tests/data/data_set_1/profiles/T2SS_gspF.hmm
create mode 100644 tests/data/data_set_1/profiles/T2SS_gspG.hmm
create mode 100644 tests/data/data_set_1/profiles/T2SS_gspH.hmm
create mode 100644 tests/data/data_set_1/profiles/T2SS_gspI.hmm
create mode 100644 tests/data/data_set_1/profiles/T2SS_gspJ.hmm
create mode 100644 tests/data/data_set_1/profiles/T2SS_gspK.hmm
create mode 100644 tests/data/data_set_1/profiles/T2SS_gspL.hmm
create mode 100644 tests/data/data_set_1/profiles/T2SS_gspM.hmm
create mode 100644 tests/data/data_set_1/profiles/T2SS_gspN.hmm
create mode 100644 tests/data/data_set_1/profiles/T2SS_gspO.hmm
copy test/datatest/profiles/sctC.hmm => tests/data/data_set_1/profiles/T3SS_sctC.hmm (100%)
copy test/datatest/profiles/sctJ.hmm => tests/data/data_set_1/profiles/T3SS_sctJ.hmm (100%)
copy test/datatest/profiles/sctN.hmm => tests/data/data_set_1/profiles/T3SS_sctN.hmm (100%)
create mode 100644 tests/data/data_set_1/profiles/T3SS_sctQ.hmm
create mode 100644 tests/data/data_set_1/profiles/T3SS_sctR.hmm
create mode 100644 tests/data/data_set_1/profiles/T3SS_sctS.hmm
create mode 100644 tests/data/data_set_1/profiles/T3SS_sctT.hmm
create mode 100644 tests/data/data_set_1/profiles/T3SS_sctU.hmm
create mode 100644 tests/data/data_set_1/profiles/T3SS_sctV.hmm
create mode 100644 tests/data/data_set_1/profiles/T4P_pilAE.hmm
create mode 100644 tests/data/data_set_1/profiles/T4P_pilB.hmm
create mode 100644 tests/data/data_set_1/profiles/T4P_pilC.hmm
create mode 100644 tests/data/data_set_1/profiles/T4P_pilD.hmm
create mode 100644 tests/data/data_set_1/profiles/T4P_pilI_pilV.hmm
create mode 100644 tests/data/data_set_1/profiles/T4P_pilM.hmm
create mode 100644 tests/data/data_set_1/profiles/T4P_pilN.hmm
create mode 100644 tests/data/data_set_1/profiles/T4P_pilO.hmm
copy test/datatest/profiles/flgC.hmm => tests/data/data_set_1/profiles/T4P_pilP.hmm (54%)
create mode 100644 tests/data/data_set_1/profiles/T4P_pilQ.hmm
create mode 100644 tests/data/data_set_1/profiles/T4P_pilT_pilU.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_F_traB.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_F_traE.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_F_traF.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_F_traG.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_F_traH.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_F_traK.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_F_traL.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_F_traN.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_F_traU.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_F_traV.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_F_traW.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_F_trbC.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_G_tfc7.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_I_traE.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_I_traI.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_I_traK.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_I_traL.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_I_traM.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_I_traN.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_I_traO.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_I_traP.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_I_traQ.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_I_traR.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_I_traT.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_I_traU.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_I_traW.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_I_traY.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_I_trbA.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_I_trbB.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_MOBB.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_MOBC.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_MOBF.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_MOBH.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_MOBP1.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_MOBP2.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_MOBP3.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_MOBQ.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_MOBT.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_MOBV.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_T_virB1.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_t4cp1.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_t4cp2.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_tcpA.hmm
create mode 100644 tests/data/data_set_1/profiles/T4SS_virb4.hmm
create mode 100644 tests/data/data_set_1/profiles/T9SS_gldJ_TIGR03524.hmm
create mode 100644 tests/data/data_set_1/profiles/T9SS_gldK_TIGR03525.hmm
create mode 100644 tests/data/data_set_1/profiles/T9SS_gldL_TIGR03513.hmm
create mode 100644 tests/data/data_set_1/profiles/T9SS_gldM_TIGR03517.hmm
create mode 100644 tests/data/data_set_1/profiles/T9SS_gldN_TIGR03523.hmm
create mode 100644 tests/data/data_set_1/profiles/T9SS_porQ.hmm
create mode 100644 tests/data/data_set_1/profiles/T9SS_porU.hmm
create mode 100644 tests/data/data_set_1/profiles/T9SS_porV.hmm
create mode 100644 tests/data/data_set_1/profiles/T9SS_sprA-2_PF12118.hmm
create mode 100644 tests/data/data_set_1/profiles/T9SS_sprA-3_TIGR04189.hmm
create mode 100644 tests/data/data_set_1/profiles/T9SS_sprA_PF14349.hmm
create mode 100644 tests/data/data_set_1/profiles/T9SS_sprE.hmm
create mode 100644 tests/data/data_set_1/profiles/T9SS_sprT.hmm
create mode 100644 tests/data/data_set_1/profiles/Tad_flp.hmm
create mode 100644 tests/data/data_set_1/profiles/Tad_rcpA.hmm
create mode 100644 tests/data/data_set_1/profiles/Tad_tadA.hmm
create mode 100644 tests/data/data_set_1/profiles/Tad_tadB.hmm
create mode 100644 tests/data/data_set_1/profiles/Tad_tadC.hmm
create mode 100644 tests/data/data_set_1/profiles/Tad_tadE.hmm
create mode 100644 tests/data/data_set_1/profiles/Tad_tadF.hmm
create mode 100644 tests/data/data_set_1/profiles/Tad_tadV.hmm
copy test/datatest/profiles/tadZ.hmm => tests/data/data_set_1/profiles/Tad_tadZ.hmm (100%)
rename {test/datatest => tests/data}/hmm/flp.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/flp.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/gspC.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/gspC.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/gspD.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/gspD.search_hmm.out (86%)
rename {test/datatest => tests/data}/hmm/gspE.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/gspE.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/gspF.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/gspF.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/gspG.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/gspG.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/gspH.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/gspH.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/gspI.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/gspI.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/gspJ.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/gspJ.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/gspK.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/gspK.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/gspL.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/gspL.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/gspM.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/gspM.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/gspO.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/gspO.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/pilAE.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/pilAE.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/pilB.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/pilB.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/pilC.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/pilC.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/pilD.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/pilD.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/pilI_pilV.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/pilI_pilV.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/pilM.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/pilM.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/pilN.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/pilN.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/pilO.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/pilO.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/pilP.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/pilP.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/pilQ.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/pilQ.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/pilT_pilU.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/pilT_pilU.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/rcpA.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/rcpA.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/tadA.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/tadA.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/tadB.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/tadB.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/tadC.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/tadC.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/tadD.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/tadD.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/tadE.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/tadE.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/tadF.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/tadF.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/tadV.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/tadV.search_hmm.out (100%)
rename {test/datatest => tests/data}/hmm/tadZ.res_hmm_extract (100%)
rename {test/datatest => tests/data}/hmm/tadZ.search_hmm.out (100%)
rename {test/datatest => tests/data}/outputs_control/joint_res_file (100%)
rename {test/datatest => tests/data}/outputs_control/joint_res_file.sel (100%)
rename {test/datatest => tests/data}/profiles/abc.hmm (100%)
rename {test/datatest => tests/data}/profiles/flgB.hmm (100%)
rename {test/datatest => tests/data}/profiles/flgC.hmm (100%)
rename {test/datatest => tests/data}/profiles/fliE.hmm (100%)
rename {test/datatest => tests/data}/profiles/gspD.hmm (100%)
rename {test/datatest => tests/data}/profiles/sctC.hmm (100%)
rename {test/datatest => tests/data}/profiles/sctJ.hmm (100%)
rename {test/datatest => tests/data}/profiles/sctJ_FLG.hmm (100%)
rename {test/datatest => tests/data}/profiles/sctN.hmm (100%)
rename {test/datatest => tests/data}/profiles/sctN_FLG.hmm (100%)
rename {test/datatest => tests/data}/profiles/tadZ.hmm (100%)
rename {test/datatest => tests/data}/profiles/toto.hmm (100%)
rename {test/datatest => tests/data}/profiles/totote.hmm (100%)
copy {macsypy => tests/functional}/__init__.py (100%)
copy {test => tests/functional}/main.py (70%)
create mode 100644 tests/functional/test_first_test.py
copy {macsypy => tests/integration}/__init__.py (100%)
copy {macsypy => tests/unit}/__init__.py (100%)
rename {test => tests/unit}/main.py (76%)
create mode 100644 tests/unit/test_Config.py
rename {test => tests/unit}/test_Gene.py (82%)
rename {test => tests/unit}/test_GeneBank.py (74%)
create mode 100644 tests/unit/test_Hit.py
rename {test => tests/unit}/test_Homolog.py (67%)
rename {test => tests/unit}/test_Indexes.py (68%)
rename {test => tests/unit}/test_Profile.py (71%)
rename {test => tests/unit}/test_ProfileFactory.py (96%)
rename {test => tests/unit}/test_RepliconDB.py (86%)
rename {test => tests/unit}/test_Report.py (53%)
rename {test => tests/unit}/test_System.py (88%)
rename {test => tests/unit}/test_SystemBank.py (73%)
rename {test => tests/unit}/test_SystemParser.py (63%)
create mode 100755 utils/setsid
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