[med-svn] [macsyfinder] branch master updated (bd835d1 -> 5b70ec5)
Andreas Tille
tille at debian.org
Tue Feb 6 16:15:43 UTC 2018
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository macsyfinder.
from bd835d1 Upload to unstable
new e67d1ad New upstream version 1.0.5
new 7069f0d Update upstream source from tag 'upstream/1.0.5'
new 3c1ebea New upstream version
new ec6cd98 cme fix dpkg-control
new c47c820 debhelper 11
new 262e8d2 Dir of test data changed
new 5b70ec5 Build-Depends: s/python-sphinx/python3-sphinx/, upload to unstable
The 7 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
debian/changelog | 10 +
debian/compat | 2 +-
debian/control | 6 +-
debian/copyright | 2 +-
debian/macsyfinder.examples | 2 +-
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
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.../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
299 files changed, 140836 insertions(+), 24555 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
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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
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delete mode 100644 test/test_Config.py
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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
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create mode 100644 tests/data/base/test_aesu.fa.pog
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rename {test/datatest => tests/data}/base/test_base.fa (93%)
create mode 100644 tests/data/data_set_1/basic_run_results/macsyfinder.conf
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create mode 100644 tests/data/data_set_1/def/CONJ.xml
create mode 100644 tests/data/data_set_1/def/Flagellum.xml
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create mode 100644 tests/data/data_set_1/def/T4SS_typeI.xml
create mode 100644 tests/data/data_set_1/def/T9SS.xml
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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