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@bneron
bneron committed May 5, 2023
2 parents 9c3bc54 + a3388d2 commit c4faebc
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Showing 12 changed files with 587 additions and 45,995 deletions.
11 changes: 10 additions & 1 deletion macsypy/scripts/macsyfinder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -744,6 +744,8 @@ def systems_to_tsv(models_fam_name, models_version, systems, hit_system_tracker,
:return: None
"""
print(_outfile_header(models_fam_name, models_version, skipped_replicons=skipped_replicons), file=sys_file)
if skipped_replicons:
systems = [s for s in systems if s.replicon_name not in skipped_replicons]
if systems:
print("# Systems found:", file=sys_file)
print(TsvSystemSerializer.header, file=sys_file)
Expand Down Expand Up @@ -773,6 +775,8 @@ def systems_to_txt(models_fam_name, models_version, systems, hit_system_tracker,
"""

print(_outfile_header(models_fam_name, models_version, skipped_replicons=skipped_replicons), file=sys_file)
if skipped_replicons:
systems = [s for s in systems if s.replicon_name not in skipped_replicons]
if systems:
print("# Systems found:\n", file=sys_file)
for system in systems:
Expand Down Expand Up @@ -991,6 +995,8 @@ def rejected_candidates_to_txt(models_fam_name, models_version, rejected_candida
:return: None
"""
print(_outfile_header(models_fam_name, models_version, skipped_replicons=skipped_replicons), file=cand_file)
if skipped_replicons:
rejected_candidates = [rc for rc in rejected_candidates if rc.replicon_name not in skipped_replicons]
if rejected_candidates:
print("# Rejected candidates:\n", file=cand_file)
for rej_cand in rejected_candidates:
Expand All @@ -1014,6 +1020,8 @@ def rejected_candidates_to_tsv(models_fam_name, models_version, rejected_candida
:return: None
"""
print(_outfile_header(models_fam_name, models_version, skipped_replicons=skipped_replicons), file=cand_file)
if skipped_replicons:
rejected_candidates = [rc for rc in rejected_candidates if rc.replicon_name not in skipped_replicons]
if rejected_candidates:
serializer = TsvRejectedCandidatesSerializer()
rej_candidates = serializer.serialize(rejected_candidates)
Expand Down Expand Up @@ -1253,7 +1261,8 @@ def main(args=None, loglevel=None):
cluster_filename = os.path.join(config.working_dir(), "rejected_candidates.txt")
with open(cluster_filename, "w") as clst_file:
rejected_candidates.sort(key=lambda clst: (clst.replicon_name, clst.model, clst.hits))
rejected_candidates_to_txt(models_fam_name, models_version, rejected_candidates, clst_file)
rejected_candidates_to_txt(models_fam_name, models_version, rejected_candidates, clst_file,
skipped_replicons=skipped_replicons)
if not (all_systems or rejected_candidates):
logger.info("No Systems found in this dataset.")

Expand Down
150 changes: 75 additions & 75 deletions tests/data/functional_test_timeout/all_best_solutions.tsv
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14,447 changes: 315 additions & 14,132 deletions tests/data/functional_test_timeout/all_systems.tsv
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28,777 changes: 46 additions & 28,731 deletions tests/data/functional_test_timeout/all_systems.txt
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70 changes: 35 additions & 35 deletions tests/data/functional_test_timeout/best_solution.tsv
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# macsyfinder 20230118.dev
# macsyfinder 20230505.dev
# models : TFF-SF-0.0b2
# /home/bneron/Projects/GEM/macsyfinder/py311/bin/macsyfinder --db-type gembase --models-dir tests/data/models/ --models TFF-SF all -w 5 --sequence-db tests/data/base/gembase_w_slow_genome.fa --timeout 2 --out-dir functional_test_timeout --index-dir .
# /home/bneron/Projects/GEM/MacSyFinder/MacSyFinder/py311/bin/macsyfinder --db-type gembase --models-dir tests/data/models/ --models TFF-SF all -w 5 --sequence-db tests/data/base/gembase_w_slow_genome.fa --timeout 2 --out-dir functional_test_timeout --index-dir .
#
# WARNING: The replicon 'THHY002.0321.00001.C001' has been SKIPPED. Cannot be solved before timeout.
#
Expand Down Expand Up @@ -49,40 +49,40 @@ PSAV001.0321.00001.C001 PSAV001.0321.00001.C001_04761 Tad_tadB 4450 TFF-SF/Tad P
PSAV001.0321.00001.C001 PSAV001.0321.00001.C001_04762 Tad_tadC 4451 TFF-SF/Tad PSAV001.0321.00001.C001_Tad_14 2 2 0.833 8.500 1 Tad_tadC mandatory 294 5.4e-34 116.800 1.000 0.524 130 283
PSAV001.0321.00001.C001 PSAV001.0321.00001.C001_04763 Tad_tadD 4452 TFF-SF/Tad PSAV001.0321.00001.C001_Tad_14 2 2 0.833 8.500 1 Tad_tadD accessory 250 5.4e-14 51.500 0.751 0.596 38 186

XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00037 Tad_tadD 7362 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_860 2 1 0.857 8.000 1 Tad_tadD accessory 568 4.3e-05 22.500 0.571 0.206 11 127
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00040 Tad_tadD 7365 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_860 2 1 0.857 8.000 1 Tad_tadD accessory 562 2.5e-08 33.000 0.717 0.270 321 472
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03012 T2SS_gspD 9820 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_860 2 2 0.857 8.000 1 T2SS_gspD mandatory 768 2.7e-56 189.100 0.989 0.255 559 754
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03013 T2SS_gspN 9821 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_860 2 2 0.857 8.000 1 T2SS_gspN accessory 267 4.1e-20 71.400 0.991 0.479 21 148
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03014 T2SS_gspM 9822 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_860 2 2 0.857 8.000 1 T2SS_gspM accessory 217 1.3e-30 105.800 1.000 0.742 7 167
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03015 T2SS_gspL 9823 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_860 2 2 0.857 8.000 1 T2SS_gspL accessory 373 1.7e-26 92.100 0.965 0.370 49 186
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03016 T2SS_gspK 9824 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_860 2 2 0.857 8.000 1 T2SS_gspK accessory 284 2.4e-14 52.500 0.983 0.204 5 62
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03017 T2SS_gspJ 9825 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_860 2 2 0.857 8.000 1 T2SS_gspJ accessory 211 3.3e-13 49.200 0.946 0.412 7 93
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03018 T2SS_gspI 9826 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_860 2 2 0.857 8.000 1 T2SS_gspI accessory 138 2.2e-13 49.800 0.964 0.391 5 58
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03019 T2SS_gspH 9827 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_860 2 2 0.857 8.000 1 T2SS_gspH accessory 169 6.6e-16 57.900 1.000 0.391 23 88
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03020 T2SS_gspG 9828 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_860 2 2 0.857 8.000 1 T2SS_gspG mandatory 143 1.7e-19 69.100 0.977 0.552 17 95
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03021 T2SS_gspF 9829 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_860 2 2 0.857 8.000 1 T2SS_gspF mandatory 405 6.2e-115 383.000 0.997 0.825 68 401
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03023 T2SS_gspE 9831 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_860 2 2 0.857 8.000 1 T2SS_gspE mandatory 575 1.6e-175 583.000 0.941 0.694 172 570
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00037 Tad_tadD 7362 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_520 2 1 0.857 8.000 1 Tad_tadD accessory 568 4.3e-05 22.500 0.571 0.206 11 127
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00040 Tad_tadD 7365 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_520 2 1 0.857 8.000 1 Tad_tadD accessory 562 2.5e-08 33.000 0.717 0.270 321 472
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03012 T2SS_gspD 9820 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_520 2 2 0.857 8.000 1 T2SS_gspD mandatory 768 2.7e-56 189.100 0.989 0.255 559 754
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03013 T2SS_gspN 9821 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_520 2 2 0.857 8.000 1 T2SS_gspN accessory 267 4.1e-20 71.400 0.991 0.479 21 148
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03014 T2SS_gspM 9822 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_520 2 2 0.857 8.000 1 T2SS_gspM accessory 217 1.3e-30 105.800 1.000 0.742 7 167
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03015 T2SS_gspL 9823 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_520 2 2 0.857 8.000 1 T2SS_gspL accessory 373 1.7e-26 92.100 0.965 0.370 49 186
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03016 T2SS_gspK 9824 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_520 2 2 0.857 8.000 1 T2SS_gspK accessory 284 2.4e-14 52.500 0.983 0.204 5 62
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03017 T2SS_gspJ 9825 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_520 2 2 0.857 8.000 1 T2SS_gspJ accessory 211 3.3e-13 49.200 0.946 0.412 7 93
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03018 T2SS_gspI 9826 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_520 2 2 0.857 8.000 1 T2SS_gspI accessory 138 2.2e-13 49.800 0.964 0.391 5 58
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03019 T2SS_gspH 9827 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_520 2 2 0.857 8.000 1 T2SS_gspH accessory 169 6.6e-16 57.900 1.000 0.391 23 88
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03020 T2SS_gspG 9828 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_520 2 2 0.857 8.000 1 T2SS_gspG mandatory 143 1.7e-19 69.100 0.977 0.552 17 95
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03021 T2SS_gspF 9829 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_520 2 2 0.857 8.000 1 T2SS_gspF mandatory 405 6.2e-115 383.000 0.997 0.825 68 401
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03023 T2SS_gspE 9831 TFF-SF/T2SS XAOR001.0321.00001.C001_T2SS_520 2 2 0.857 8.000 1 T2SS_gspE mandatory 575 1.6e-175 583.000 0.941 0.694 172 570

XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00240 T4P_pilM 7530 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_875 2 1 0.611 7.350 1 T4P_pilM accessory 360 3.2e-46 156.600 1.000 0.453 20 182
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00241 T4P_pilN 7531 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_875 2 1 0.611 7.350 1 T4P_pilN mandatory 260 1.8e-39 134.500 0.993 0.546 4 145
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00242 T4P_pilO 7532 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_875 2 1 0.611 7.350 1 T4P_pilO mandatory 221 7.9e-32 109.600 0.980 0.683 24 174
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00243 T4P_pilP 7533 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_875 2 1 0.611 7.350 1 T4P_pilP accessory 177 1.6e-19 70.200 0.971 0.763 20 154
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00244 T4P_pilQ 7534 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_875 2 1 0.611 7.350 1 T4P_pilQ mandatory 652 5.3e-54 181.500 0.930 0.268 475 649
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00872 T4P_fimT 8028 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_875 2 2 0.611 7.350 1 T4P_fimT accessory 171 2.6e-18 65.400 0.939 0.363 7 68
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00873 T4P_pilV 8029 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_875 2 2 0.611 7.350 1 T4P_pilV accessory 158 5e-18 64.300 1.000 0.354 14 69
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00874 T4P_pilW 8030 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_875 2 2 0.611 7.350 1 T4P_pilW accessory 388 1e-14 54.100 0.633 0.196 12 87
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00876 T4P_pilY 8032 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_875 2 2 0.611 7.350 1 T4P_pilY accessory 1003 1.8e-125 418.900 1.000 0.601 285 887
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00877 T4P_pilE 8033 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_875 2 2 0.611 7.350 1 T4P_pilE mandatory 149 2.3e-21 75.400 0.833 0.389 21 78
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00879 T4P_fimT 8034 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_875 2 2 0.611 7.350 1 T4P_fimT accessory 180 5.6e-12 45.100 1.000 0.367 10 75
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03253 T4P_pilA 10027 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_875 2 -1 0.611 7.350 1 T4P_pilA accessory 240 5.7e-06 25.900 0.718 0.233 114 169
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00240 T4P_pilM 7530 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_535 2 1 0.611 7.350 1 T4P_pilM accessory 360 3.2e-46 156.600 1.000 0.453 20 182
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00241 T4P_pilN 7531 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_535 2 1 0.611 7.350 1 T4P_pilN mandatory 260 1.8e-39 134.500 0.993 0.546 4 145
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00242 T4P_pilO 7532 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_535 2 1 0.611 7.350 1 T4P_pilO mandatory 221 7.9e-32 109.600 0.980 0.683 24 174
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00243 T4P_pilP 7533 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_535 2 1 0.611 7.350 1 T4P_pilP accessory 177 1.6e-19 70.200 0.971 0.763 20 154
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00244 T4P_pilQ 7534 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_535 2 1 0.611 7.350 1 T4P_pilQ mandatory 652 5.3e-54 181.500 0.930 0.268 475 649
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00872 T4P_fimT 8028 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_535 2 2 0.611 7.350 1 T4P_fimT accessory 171 2.6e-18 65.400 0.939 0.363 7 68
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00873 T4P_pilV 8029 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_535 2 2 0.611 7.350 1 T4P_pilV accessory 158 5e-18 64.300 1.000 0.354 14 69
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00874 T4P_pilW 8030 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_535 2 2 0.611 7.350 1 T4P_pilW accessory 388 1e-14 54.100 0.633 0.196 12 87
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00876 T4P_pilY 8032 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_535 2 2 0.611 7.350 1 T4P_pilY accessory 1003 1.8e-125 418.900 1.000 0.601 285 887
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00877 T4P_pilE 8033 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_535 2 2 0.611 7.350 1 T4P_pilE mandatory 149 2.3e-21 75.400 0.833 0.389 21 78
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00879 T4P_fimT 8034 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_535 2 2 0.611 7.350 1 T4P_fimT accessory 180 5.6e-12 45.100 1.000 0.367 10 75
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03253 T4P_pilA 10027 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_535 2 -1 0.611 7.350 1 T4P_pilA accessory 240 5.7e-06 25.900 0.718 0.233 114 169

XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00601 T4P_pilU 7819 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_877 2 1 0.389 5.850 1 T4P_pilU accessory 376 4.4e-178 590.500 0.994 0.904 7 346
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00602 T4P_pilT 7820 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_877 2 1 0.389 5.850 1 T4P_pilT mandatory 345 2.3e-178 591.700 0.994 0.983 2 340
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_02929 T4P_pilB 9754 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_877 2 2 0.389 5.850 1 T4P_pilB mandatory 577 4.4e-178 591.300 0.924 0.672 186 573
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_02933 T4P_pilE 9758 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_877 2 2 0.389 5.850 1 T4P_pilE mandatory 137 1.4e-19 69.700 0.909 0.431 5 63
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_02934 T4P_pilC 9759 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_877 2 2 0.389 5.850 1 T4P_pilC mandatory 419 5.3e-122 406.300 0.997 0.800 81 415
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_02935 T4P_pilD 9760 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_877 2 2 0.389 5.850 1 T4P_pilD mandatory 287 4.4e-81 270.900 1.000 0.836 28 267 XAOR001.0321.00001.C001_T2SS_861,XAOR001.0321.00001.C001_T2SS_862
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03253 T4P_pilA 10027 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_877 2 -1 0.389 5.850 1 T4P_pilA accessory 240 5.7e-06 25.900 0.718 0.233 114 169
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00601 T4P_pilU 7819 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_537 2 1 0.389 5.850 1 T4P_pilU accessory 376 4.4e-178 590.500 0.994 0.904 7 346
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_00602 T4P_pilT 7820 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_537 2 1 0.389 5.850 1 T4P_pilT mandatory 345 2.3e-178 591.700 0.994 0.983 2 340
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_02929 T4P_pilB 9754 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_537 2 2 0.389 5.850 1 T4P_pilB mandatory 577 4.4e-178 591.300 0.924 0.672 186 573
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_02933 T4P_pilE 9758 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_537 2 2 0.389 5.850 1 T4P_pilE mandatory 137 1.4e-19 69.700 0.909 0.431 5 63
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_02934 T4P_pilC 9759 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_537 2 2 0.389 5.850 1 T4P_pilC mandatory 419 5.3e-122 406.300 0.997 0.800 81 415
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_02935 T4P_pilD 9760 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_537 2 2 0.389 5.850 1 T4P_pilD mandatory 287 4.4e-81 270.900 1.000 0.836 28 267 XAOR001.0321.00001.C001_T2SS_521,XAOR001.0321.00001.C001_T2SS_522
XAOR001.0321.00001.C001 XAOR001.0321.00001.C001_03253 T4P_pilA 10027 TFF-SF/T4P XAOR001.0321.00001.C001_T4P_537 2 -1 0.389 5.850 1 T4P_pilA accessory 240 5.7e-06 25.900 0.718 0.233 114 169

# WARNING Loner: there is only 1 occurrence(s) of loner 'T4P_pilT' and 2 potential systems [PSAV001.0321.00001.C001_T4P_10, PSAV001.0321.00001.C001_T4P_7]
# WARNING Loner: there is only 1 occurrence(s) of loner 'T4P_pilA' and 2 potential systems [XAOR001.0321.00001.C001_T4P_875, XAOR001.0321.00001.C001_T4P_877]
# WARNING Loner: there is only 1 occurrence(s) of loner 'T4P_pilA' and 2 potential systems [XAOR001.0321.00001.C001_T4P_535, XAOR001.0321.00001.C001_T4P_537]
4 changes: 2 additions & 2 deletions tests/data/functional_test_timeout/best_solution_loners.tsv
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# macsyfinder 20230118.dev
# macsyfinder 20230505.dev
# models : TFF-SF-0.0b2
# /home/bneron/Projects/GEM/macsyfinder/py311/bin/macsyfinder --db-type gembase --models-dir tests/data/models/ --models TFF-SF all -w 5 --sequence-db tests/data/base/gembase_w_slow_genome.fa --timeout 2 --out-dir functional_test_timeout --index-dir .
# /home/bneron/Projects/GEM/MacSyFinder/MacSyFinder/py311/bin/macsyfinder --db-type gembase --models-dir tests/data/models/ --models TFF-SF all -w 5 --sequence-db tests/data/base/gembase_w_slow_genome.fa --timeout 2 --out-dir functional_test_timeout --index-dir .
# Loners found:
replicon model_fqn function gene_name hit_id hit_pos hit_status hit_seq_len hit_i_eval hit_score hit_profile_cov hit_seq_cov hit_begin_match hit_end_match
PSAV001.0321.00001.C001 TFF-SF/T4P T4P_pilT T4P_pilT PSAV001.0321.00001.C001_04959 4643 mandatory 344 3.100e-179 594.500 1.000 0.991 2 342
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4 changes: 2 additions & 2 deletions tests/data/functional_test_timeout/best_solution_multisystems.tsv
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@@ -1,4 +1,4 @@
# macsyfinder 20230118.dev
# macsyfinder 20230505.dev
# models : TFF-SF-0.0b2
# /home/bneron/Projects/GEM/macsyfinder/py311/bin/macsyfinder --db-type gembase --models-dir tests/data/models/ --models TFF-SF all -w 5 --sequence-db tests/data/base/gembase_w_slow_genome.fa --timeout 2 --out-dir functional_test_timeout --index-dir .
# /home/bneron/Projects/GEM/MacSyFinder/MacSyFinder/py311/bin/macsyfinder --db-type gembase --models-dir tests/data/models/ --models TFF-SF all -w 5 --sequence-db tests/data/base/gembase_w_slow_genome.fa --timeout 2 --out-dir functional_test_timeout --index-dir .
# No Multisystems found
4 changes: 2 additions & 2 deletions tests/data/functional_test_timeout/best_solution_summary.tsv
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@@ -1,6 +1,6 @@
# macsyfinder 20230118.dev
# macsyfinder 20230505.dev
# models : TFF-SF-0.0b2
# /home/bneron/Projects/GEM/macsyfinder/py311/bin/macsyfinder --db-type gembase --models-dir tests/data/models/ --models TFF-SF all -w 5 --sequence-db tests/data/base/gembase_w_slow_genome.fa --timeout 2 --out-dir functional_test_timeout --index-dir .
# /home/bneron/Projects/GEM/MacSyFinder/MacSyFinder/py311/bin/macsyfinder --db-type gembase --models-dir tests/data/models/ --models TFF-SF all -w 5 --sequence-db tests/data/base/gembase_w_slow_genome.fa --timeout 2 --out-dir functional_test_timeout --index-dir .
#
# WARNING: The replicon 'THHY002.0321.00001.C001' has been SKIPPED. Cannot be solved before timeout.
#
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5 changes: 3 additions & 2 deletions tests/data/functional_test_timeout/macsyfinder.conf
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ coverage_profile = 0.5
e_value_search = 0.1
cut_ga = False
i_evalue_sel = 0.001
hmmer = /home/bneron/Sys/bin/hmmsearch
hmmer = /usr/bin/hmmsearch
[score_opt]
mandatory_weight = 1.0
accessory_weight = 0.5
Expand All @@ -22,7 +22,7 @@ redundancy_penalty = 1.5
out_of_cluster_weight = 0.7
[directories]
models_dir = tests/data/models/
system_models_dir = /home/bneron/Projects/GEM/macsyfinder/py311/share/macsyfinder/models, /home/bneron/.macsyfinder/models
system_models_dir = /home/bneron/Projects/GEM/MacSyFinder/MacSyFinder/py311/share/macsyfinder/models, /home/bneron/.macsyfinder/models
out_dir = functional_test_timeout
profile_suffix = .hmm
res_search_dir = .
Expand All @@ -38,4 +38,5 @@ quiet = 0
mute = False
worker = 5
timeout = 2
force_run = False

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