This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository macsyfinder.
commit 7069f0d6a5be46045152b0affd49415575202991 Merge: bd835d1 e67d1ad Author: Andreas Tille <[email protected]> Date: Tue Feb 6 15:20:19 2018 +0100 Update upstream source from tag 'upstream/1.0.5' Update to upstream version '1.0.5' with Debian dir b2172c843d591f440d1a3d6f158a5e190dbcb72d .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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/macsyfinder.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
