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superphy / spfy

Spfy: an integrated graph database for real-time prediction of Escherichia coli phenotypes and downstream comparative analyses
https://lfz.corefacility.ca/superphy/grouch/
Apache License 2.0
4 stars 2 forks source link

gene_dict empty? #317

Closed kevinkle closed 6 years ago

kevinkle commented 6 years ago 
ECI-2523.fsa with pi: 90 for Serotype VF
Submitted: ‎2018‎-‎06‎-‎22‎ ‎10‎:‎35‎:‎25‎ ‎AM, Status: FAILED
ERROR WITH JOB: pipelined1218b6d80d39bec9b17cb87257a24537a4e4e74
Traceback (most recent call last): File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/worker.py", line 700, in perform_job rv = job.perform() File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/job.py", line 500, in perform self._result = self.func(*self.args, **self.kwargs) File "./middleware/display/beautify.py", line 143, in display_subtyping list_return = beautify(gene_dict=result, args_dict=args_dict) File "./middleware/display/beautify.py", line 128, in beautify json_r = check_alleles(json_r) File "./middleware/display/find_widest.py", line 130, in check_alleles raise Exception('The Panadas DF from gene_dict is empty.') Exception: The Panadas DF from gene_dict is empty.
kevinkle commented 6 years ago 
webserver_1              | complete() checking status for: d1218b6d80d39bec9b17cb87257a24537a4e4e74 with 9 # of final jobs.
webserver_1              | model.Job.refetch(): job job_turtle was already determined to not be found.
webserver_1              | model.Job.refetch(): job job_ectyper_datastruct_serotype was already determined to not be found.
webserver_1              | model.Job.refetch(): job job_ectyper_serotype was already determined to not be found.
webserver_1              | model.Job.refetch(): job job_ectyper_vf was already determined to not be found.
webserver_1              | model.Job.refetch(): job job_ectyper_beautify_serotype was already determined to not be found.
webserver_1              | model.Job.refetch(): job job_ectyper_datastruct_vf was already determined to not be found.
webserver_1              | complete(): job job_turtle is finished but the result_ttl timed out.
webserver_1              | complete(): job job_ectyper_datastruct_serotype is finished but the result_ttl timed out.
webserver_1              | complete(): job job_ectyper_serotype is finished but the result_ttl timed out.
webserver_1              | complete(): job job_ectyper_vf is finished but the result_ttl timed out.
webserver_1              | complete(): job job_ectyper_beautify_serotype is finished but the result_ttl timed out.
webserver_1              | complete(): job job_ectyper_datastruct_vf is finished but the result_ttl timed out.
webserver_1              | complete(): job job_ectyper_beautify_vf is failed with exc_info Traceback (most recent call last):
webserver_1              |   File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/worker.py", line 700, in perform_job
webserver_1              |     rv = job.perform()
webserver_1              |   File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/job.py", line 500, in perform
webserver_1              |     self._result = self.func(*self.args, **self.kwargs)
webserver_1              |   File "./middleware/display/beautify.py", line 143, in display_subtyping
webserver_1              |     list_return = beautify(gene_dict=result, args_dict=args_dict)
webserver_1              |   File "./middleware/display/beautify.py", line 128, in beautify
webserver_1              |     json_r = check_alleles(json_r)
webserver_1              |   File "./middleware/display/find_widest.py", line 130, in check_alleles
webserver_1              |     raise Exception('The Panadas DF from gene_dict is empty.')
webserver_1              | Exception: The Panadas DF from gene_dict is empty.
webserver_1              | .
webserver_1              | store(): storing pipeline with id d1218b6d80d39bec9b17cb87257a24537a4e4e74 containing 1 # of files with 9 # of final jobs has finished.
webserver_1              | [pid: 23|app: 0|req: 2810/5986] 192.168.0.1 () {50 vars in 998 bytes} [Fri Jun 22 18:30:26 2018] GET /api/v0/results/pipelined1218b6d80d39bec9b17cb87257a24537a4e4e74 => generated 759 bytes in 57 msecs (HTTP/1.1 200) 3 headers in 104 bytes (2 switches on core 0)
webserver_1              | 192.168.0.1 - - [22/Jun/2018:18:30:26 +0000] "GET /api/v0/results/pipelined1218b6d80d39bec9b17cb87257a24537a4e4e74 HTTP/1.1" 200 759 "https://lfz.corefacility.ca/superphy/spfy/results?token=be6fb0b716b82cd1eb15b869a790f4a7f9ac34d1" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_12_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/67.0.3396.87 Safari/537.36"
kevinkle commented 6 years ago 
(backend) kevin@kevin-ThinkPad-T510:~/Desktop/backend/app$ python modules/ectyper/ecoli_serotyping/src/Tools_Controller/tools_controller.py -in tests/ecoli/ECI-2523.fsa -s 0 -vf 1 -pi 90
{'ECI-2523_contig234': {'Virulence Factors': {}}, 'ECI-2523_contig235': {'Virulence Factors': {'lcl|ECI-2523_contig235|': [{'START': 50620, 'STOP': 50653, 'ORIENTATION': '-', 'GENE_NAME': 'entD'}]}}, 'ECI-2523_contig236': {'Virulence Factors': {}}, 'ECI-2523_contig237': {'Virulence Factors': {}}, 'ECI-2523_contig128': {'Virulence Factors': {'lcl|ECI-2523_contig128|': [{'START': 20703, 'STOP': 24550, 'ORIENTATION': '+', 'GENE_NAME': 'entF'}, {'START': 16800, 'STOP': 19040, 'ORIENTATION': '-', 'GENE_NAME': 'fepA'}, {'START': 32430, 'STOP': 34040, 'ORIENTATION': '+', 'GENE_NAME': 'entE'}, {'START': 3150, 'STOP': 4532, 'ORIENTATION': '+', 'GENE_NAME': 'ibeB'}, {'START': 3146, 'STOP': 4532, 'ORIENTATION': '+', 'GENE_NAME': 'ibeB'}, {'START': 3150, 'STOP': 4522, 'ORIENTATION': '+', 'GENE_NAME': 'ibeB'}, {'START': 31233, 'STOP': 32420, 'ORIENTATION': '+', 'GENE_NAME': 'entC'}, {'START': 28846, 'STOP': 30096, 'ORIENTATION': '+', 'GENE_NAME': 'entS'}, {'START': 19283, 'STOP': 20485, 'ORIENTATION': '+', 'GENE_NAME': 'fes'}, {'START': 24800, 'STOP': 25933, 'ORIENTATION': '+', 'GENE_NAME': 'fepE'}, {'START': 27731, 'STOP': 28747, 'ORIENTATION': '-', 'GENE_NAME': 'fepD'}, {'START': 30100, 'STOP': 31056, 'ORIENTATION': '-', 'GENE_NAME': 'fepB'}, {'START': 26742, 'STOP': 27734, 'ORIENTATION': '-', 'GENE_NAME': 'fepG'}, {'START': 34054, 'STOP': 34911, 'ORIENTATION': '+', 'GENE_NAME': 'entB'}, {'START': 25930, 'STOP': 26745, 'ORIENTATION': '-', 'GENE_NAME': 'fepC'}, {'START': 34911, 'STOP': 35657, 'ORIENTATION': '+', 'GENE_NAME': 'entA'}, {'START': 16005, 'STOP': 16775, 'ORIENTATION': '-', 'GENE_NAME': 'entD'}, {'START': 1, 'STOP': 312, 'ORIENTATION': '-', 'GENE_NAME': 'aec15'}, {'START': 1, 'STOP': 278, 'ORIENTATION': '-', 'GENE_NAME': 'aec15'}, {'START': 1, 'STOP': 278, 'ORIENTATION': '-', 'GENE_NAME': 'vgrG'}]}}, 'ECI-2523_contig129': {'Virulence Factors': {}}, 'ECI-2523_contig232': {'Virulence Factors': {'lcl|ECI-2523_contig232|': [{'START': 699, 'STOP': 796, 'ORIENTATION': '-', 'GENE_NAME': 'espF'}, {'START': 699, 'STOP': 796, 'ORIENTATION': '-', 'GENE_NAME': 'tccP2'}, {'START': 699, 'STOP': 796, 'ORIENTATION': '-', 'GENE_NAME': 'tccP'}, {'START': 699, 'STOP': 794, 'ORIENTATION': '-', 'GENE_NAME': 'tccP2'}]}}, 'ECI-2523_contig233': {'Virulence Factors': {}}, 'ECI-2523_contig124': {'Virulence Factors': {}}, 'ECI-2523_contig125': {'Virulence Factors': {}}, 'ECI-2523_contig126': {'Virulence Factors': {'lcl|ECI-2523_contig126|': [{'START': 10921, 'STOP': 13938, 'ORIENTATION': '+', 'GENE_NAME': 'cah'}, {'START': 11089, 'STOP': 13938, 'ORIENTATION': '+', 'GENE_NAME': 'cah'}, {'START': 11089, 'STOP': 13938, 'ORIENTATION': '+', 'GENE_NAME': 'EC958_5138'}, {'START': 11017, 'STOP': 13938, 'ORIENTATION': '+', 'GENE_NAME': 'cah'}, {'START': 11089, 'STOP': 13938, 'ORIENTATION': '+', 'GENE_NAME': 'EC958_4121'}, {'START': 12767, 'STOP': 13938, 'ORIENTATION': '+', 'GENE_NAME': 'agn43'}, {'START': 12768, 'STOP': 13938, 'ORIENTATION': '+', 'GENE_NAME': 'flu'}, {'START': 12768, 'STOP': 13938, 'ORIENTATION': '+', 'GENE_NAME': 'agn43'}, {'START': 12773, 'STOP': 13938, 'ORIENTATION': '+', 'GENE_NAME': 'agn43'}, {'START': 12768, 'STOP': 13361, 'ORIENTATION': '+', 'GENE_NAME': 'agn43'}, {'START': 8265, 'STOP': 8500, 'ORIENTATION': '+', 'GENE_NAME': 'fimD'}, {'START': 1158, 'STOP': 1285, 'ORIENTATION': '+', 'GENE_NAME': 'EC55989_3315'}]}}, 'ECI-2523_contig127': {'Virulence Factors': {}}, 'ECI-2523_contig120': {'Virulence Factors': {'lcl|ECI-2523_contig120|': [{'START': 466, 'STOP': 701, 'ORIENTATION': '-', 'GENE_NAME': 'fimD'}]}}, 'ECI-2523_contig121': {'Virulence Factors': {}}, 'ECI-2523_contig122': {'Virulence Factors': {}}, 'ECI-2523_contig123': {'Virulence Factors': {}}, 'ECI-2523_contig193': {'Virulence Factors': {}}, 'ECI-2523_contig230': {'Virulence Factors': {}}, 'ECI-2523_contig231': {'Virulence Factors': {}}, 'ECI-2523_contig192': {'Virulence Factors': {}}, 'ECI-2523_contig55': {'Virulence Factors': {}}, 'ECI-2523_contig54': {'Virulence Factors': {'lcl|ECI-2523_contig54|': [{'START': 1, 'STOP': 819, 'ORIENTATION': '-', 'GENE_NAME': 'nleh1-2'}, {'START': 1, 'STOP': 819, 'ORIENTATION': '-', 'GENE_NAME': 'nleH2'}, {'START': 446, 'STOP': 819, 'ORIENTATION': '-', 'GENE_NAME': 'nleH1-1'}, {'START': 446, 'STOP': 819, 'ORIENTATION': '-', 'GENE_NAME': 'nleH1'}]}}, 'ECI-2523_contig57': {'Virulence Factors': {}}, 'ECI-2523_contig56': {'Virulence Factors': {}}, 'ECI-2523_contig51': {'Virulence Factors': {}}, 'ECI-2523_contig50': {'Virulence Factors': {}}, 'ECI-2523_contig53': {'Virulence Factors': {}}, 'ECI-2523_contig52': {'Virulence Factors': {}}, 'ECI-2523_contig59': {'Virulence Factors': {}}, 'ECI-2523_contig58': {'Virulence Factors': {}}, 'ECI-2523_contig9': {'Virulence Factors': {'lcl|ECI-2523_contig9|': [{'START': 5732, 'STOP': 7309, 'ORIENTATION': '-', 'GENE_NAME': 'vgrG'}]}}, 'ECI-2523_contig8': {'Virulence Factors': {}}, 'ECI-2523_contig229': {'Virulence Factors': {}}, 'ECI-2523_contig228': {'Virulence Factors': {}}, 'ECI-2523_contig1': {'Virulence Factors': {}}, 'ECI-2523_contig238': {'Virulence Factors': {}}, 'ECI-2523_contig3': {'Virulence Factors': {'lcl|ECI-2523_contig3|': [{'START': 11374, 'STOP': 13131, 'ORIENTATION': '-', 'GENE_NAME': 'fliC'}, {'START': 24708, 'STOP': 26366, 'ORIENTATION': '+', 'GENE_NAME': 'fliF'}, {'START': 13397, 'STOP': 14794, 'ORIENTATION': '+', 'GENE_NAME': 'fliD'}, {'START': 28095, 'STOP': 29468, 'ORIENTATION': '+', 'GENE_NAME': 'fliI'}, {'START': 29927, 'STOP': 31054, 'ORIENTATION': '+', 'GENE_NAME': 'fliK'}, {'START': 22691, 'STOP': 23830, 'ORIENTATION': '-', 'GENE_NAME': 'espR4'}, {'START': 20733, 'STOP': 21872, 'ORIENTATION': '-', 'GENE_NAME': 'espR3'}, {'START': 31628, 'STOP': 32632, 'ORIENTATION': '+', 'GENE_NAME': 'fliM'}, {'START': 26359, 'STOP': 27354, 'ORIENTATION': '+', 'GENE_NAME': 'fliG'}, {'START': 22796, 'STOP': 23830, 'ORIENTATION': '-', 'GENE_NAME': 'espR4'}, {'START': 8850, 'STOP': 9650, 'ORIENTATION': '-', 'GENE_NAME': 'fliY'}, {'START': 34434, 'STOP': 35219, 'ORIENTATION': '+', 'GENE_NAME': 'fliR'}, {'START': 33410, 'STOP': 34147, 'ORIENTATION': '+', 'GENE_NAME': 'fliP'}, {'START': 10335, 'STOP': 11054, 'ORIENTATION': '-', 'GENE_NAME': 'fliA'}, {'START': 27347, 'STOP': 28033, 'ORIENTATION': '+', 'GENE_NAME': 'fliH'}, {'START': 9738, 'STOP': 10325, 'ORIENTATION': '-', 'GENE_NAME': 'fliZ'}, {'START': 31159, 'STOP': 31623, 'ORIENTATION': '+', 'GENE_NAME': 'fliL'}, {'START': 29487, 'STOP': 29930, 'ORIENTATION': '+', 'GENE_NAME': 'fliJ'}, {'START': 32629, 'STOP': 33042, 'ORIENTATION': '+', 'GENE_NAME': 'fliN'}, {'START': 14819, 'STOP': 15229, 'ORIENTATION': '+', 'GENE_NAME': 'fliS'}, {'START': 33045, 'STOP': 33410, 'ORIENTATION': '+', 'GENE_NAME': 'fliO'}, {'START': 15229, 'STOP': 15594, 'ORIENTATION': '+', 'GENE_NAME': 'fliT'}, {'START': 24179, 'STOP': 24493, 'ORIENTATION': '-', 'GENE_NAME': 'fliE'}, {'START': 34157, 'STOP': 34426, 'ORIENTATION': '+', 'GENE_NAME': 'fliQ'}]}}, 'ECI-2523_contig2': {'Virulence Factors': {'lcl|ECI-2523_contig2|': [{'START': 74, 'STOP': 311, 'ORIENTATION': '+', 'GENE_NAME': 'fimD'}]}}, 'ECI-2523_contig5': {'Virulence Factors': {}}, 'ECI-2523_contig4': {'Virulence Factors': {'lcl|ECI-2523_contig4|': [{'START': 23399, 'STOP': 28165, 'ORIENTATION': '-', 'GENE_NAME': 'upaG/ehaG'}, {'START': 23399, 'STOP': 27514, 'ORIENTATION': '-', 'GENE_NAME': 'upaG/ehaG'}]}}, 'ECI-2523_contig7': {'Virulence Factors': {}}, 'ECI-2523_contig239': {'Virulence Factors': {}}, 'ECI-2523_contig133': {'Virulence Factors': {}}, 'ECI-2523_contig132': {'Virulence Factors': {'lcl|ECI-2523_contig132|': [{'START': 621, 'STOP': 1333, 'ORIENTATION': '-', 'GENE_NAME': 'nleG7'}, {'START': 621, 'STOP': 1271, 'ORIENTATION': '-', 'GENE_NAME': 'nleG7'}, {'START': 625, 'STOP': 1271, 'ORIENTATION': '-', 'GENE_NAME': 'nleG7'}, {'START': 1982, 'STOP': 2557, 'ORIENTATION': '-', 'GENE_NAME': 'nleG2-4'}, {'START': 1982, 'STOP': 2491, 'ORIENTATION': '-', 'GENE_NAME': 'nleG2-4'}, {'START': 1982, 'STOP': 2527, 'ORIENTATION': '-', 'GENE_NAME': 'nleG'}, {'START': 2019, 'STOP': 2512, 'ORIENTATION': '-', 'GENE_NAME': 'nleG2-4'}, {'START': 621, 'STOP': 992, 'ORIENTATION': '-', 'GENE_NAME': 'nleG7'}, {'START': 1563, 'STOP': 1691, 'ORIENTATION': '-', 'GENE_NAME': 'nleG-3'}, {'START': 1563, 'STOP': 1697, 'ORIENTATION': '-', 'GENE_NAME': 'nleG-2'}]}}, 'ECI-2523_contig131': {'Virulence Factors': {'lcl|ECI-2523_contig131|': [{'START': 404, 'STOP': 1462, 'ORIENTATION': '-', 'GENE_NAME': 'espW'}, {'START': 1541, 'STOP': 2191, 'ORIENTATION': '-', 'GENE_NAME': 'nleG8-2'}, {'START': 2374, 'STOP': 2964, 'ORIENTATION': '+', 'GENE_NAME': 'espM2'}, {'START': 1566, 'STOP': 2191, 'ORIENTATION': '-', 'GENE_NAME': 'nleG-1'}, {'START': 2380, 'STOP': 2964, 'ORIENTATION': '+', 'GENE_NAME': 'espM2'}, {'START': 2374, 'STOP': 2960, 'ORIENTATION': '+', 'GENE_NAME': 'espM1'}, {'START': 1630, 'STOP': 2191, 'ORIENTATION': '-', 'GENE_NAME': 'nleG8-2'}, {'START': 2374, 'STOP': 2959, 'ORIENTATION': '+', 'GENE_NAME': 'espM2'}, {'START': 1147, 'STOP': 1462, 'ORIENTATION': '-', 'GENE_NAME': 'espW'}, {'START': 1, 'STOP': 274, 'ORIENTATION': '+', 'GENE_NAME': 'nleG6-3'}, {'START': 1, 'STOP': 274, 'ORIENTATION': '+', 'GENE_NAME': 'nleG6-1'}, {'START': 1, 'STOP': 267, 'ORIENTATION': '+', 'GENE_NAME': 'nleG6-2'}, {'START': 3, 'STOP': 267, 'ORIENTATION': '+', 'GENE_NAME': 'nleG6-1'}]}}, 'ECI-2523_contig130': {'Virulence Factors': {}}, 'ECI-2523_contig137': {'Virulence Factors': {'lcl|ECI-2523_contig137|': [{'START': 1268, 'STOP': 2257, 'ORIENTATION': '+', 'GENE_NAME': 'nleB1'}, {'START': 1, 'STOP': 660, 'ORIENTATION': '+', 'GENE_NAME': 'espL2'}, {'START': 2306, 'STOP': 2838, 'ORIENTATION': '+', 'GENE_NAME': 'nleE'}, {'START': 2306, 'STOP': 2838, 'ORIENTATION': '+', 'GENE_NAME': 'nleE1'}, {'START': 2608, 'STOP': 2838, 'ORIENTATION': '+', 'GENE_NAME': 'nleE2'}]}}, 'ECI-2523_contig136': {'Virulence Factors': {'lcl|ECI-2523_contig136|': [{'START': 6809, 'STOP': 8995, 'ORIENTATION': '-', 'GENE_NAME': 'espL4'}, {'START': 43233, 'STOP': 44813, 'ORIENTATION': '+', 'GENE_NAME': 'espX4'}, {'START': 74275, 'STOP': 75567, 'ORIENTATION': '-', 'GENE_NAME': 'espX5'}, {'START': 7856, 'STOP': 8995, 'ORIENTATION': '-', 'GENE_NAME': 'espL4'}]}}, 'ECI-2523_contig135': {'Virulence Factors': {}}, 'ECI-2523_contig134': {'Virulence Factors': {'lcl|ECI-2523_contig134|': [{'START': 70458, 'STOP': 70496, 'ORIENTATION': '+', 'GENE_NAME': 'focD'}]}}, 'ECI-2523_contig139': {'Virulence Factors': {}}, 'ECI-2523_contig138': {'Virulence Factors': {'lcl|ECI-2523_contig138|': [{'START': 544, 'STOP': 1587, 'ORIENTATION': '+', 'GENE_NAME': 'nada'}]}}, 'ECI-2523_contig168': {'Virulence Factors': {'lcl|ECI-2523_contig168|': [{'START': 1, 'STOP': 98, 'ORIENTATION': '+', 'GENE_NAME': 'espF'}, {'START': 1, 'STOP': 98, 'ORIENTATION': '+', 'GENE_NAME': 'tccP2'}, {'START': 1, 'STOP': 98, 'ORIENTATION': '+', 'GENE_NAME': 'tccP'}, {'START': 3, 'STOP': 98, 'ORIENTATION': '+', 'GENE_NAME': 'tccP2'}]}}, 'ECI-2523_contig169': {'Virulence Factors': {}}, 'ECI-2523_contig46': {'Virulence Factors': {'lcl|ECI-2523_contig46|': [{'START': 122364, 'STOP': 124424, 'ORIENTATION': '+', 'GENE_NAME': 'eivA'}, {'START': 119518, 'STOP': 121221, 'ORIENTATION': '+', 'GENE_NAME': 'eivG'}, {'START': 124429, 'STOP': 125748, 'ORIENTATION': '+', 'GENE_NAME': 'eivC'}, {'START': 121226, 'STOP': 122371, 'ORIENTATION': '+', 'GENE_NAME': 'eivE'}, {'START': 129699, 'STOP': 130820, 'ORIENTATION': '+', 'GENE_NAME': 'epaS'}, {'START': 127009, 'STOP': 127995, 'ORIENTATION': '+', 'GENE_NAME': 'epaO'}, {'START': 17069, 'STOP': 18049, 'ORIENTATION': '+', 'GENE_NAME': 'yggr'}, {'START': 118772, 'STOP': 119521, 'ORIENTATION': '+', 'GENE_NAME': 'eivF'}, {'START': 133717, 'STOP': 134451, 'ORIENTATION': '+', 'GENE_NAME': 'eprK'}, {'START': 132381, 'STOP': 133115, 'ORIENTATION': '+', 'GENE_NAME': 'eprH'}, {'START': 127985, 'STOP': 128650, 'ORIENTATION': '+', 'GENE_NAME': 'epaP'}, {'START': 126432, 'STOP': 127049, 'ORIENTATION': '+', 'GENE_NAME': 'eivJ'}, {'START': 134467, 'STOP': 135048, 'ORIENTATION': '+', 'GENE_NAME': 'orgA'}, {'START': 131177, 'STOP': 131677, 'ORIENTATION': '-', 'GENE_NAME': 'etrA'}, {'START': 128908, 'STOP': 129375, 'ORIENTATION': '+', 'GENE_NAME': 'epaR'}, {'START': 135267, 'STOP': 135698, 'ORIENTATION': '+', 'GENE_NAME': 'orgB'}, {'START': 125861, 'STOP': 126196, 'ORIENTATION': '+', 'GENE_NAME': 'eivI'}, {'START': 133388, 'STOP': 133720, 'ORIENTATION': '+', 'GENE_NAME': 'eprJ'}, {'START': 128661, 'STOP': 128921, 'ORIENTATION': '+', 'GENE_NAME': 'epaQ'}, {'START': 133129, 'STOP': 133368, 'ORIENTATION': '+', 'GENE_NAME': 'eprI'}, {'START': 126174, 'STOP': 126407, 'ORIENTATION': '+', 'GENE_NAME': 'ECs3728'}, {'START': 118247, 'STOP': 118426, 'ORIENTATION': '+', 'GENE_NAME': 'pkgA'}]}}, 'ECI-2523_contig47': {'Virulence Factors': {}}, 'ECI-2523_contig44': {'Virulence Factors': {'lcl|ECI-2523_contig44|': [{'START': 39982, 'STOP': 42924, 'ORIENTATION': '+', 'GENE_NAME': 'ehaB'}, {'START': 90264, 'STOP': 91835, 'ORIENTATION': '-', 'GENE_NAME': 'espY3'}, {'START': 41052, 'STOP': 42924, 'ORIENTATION': '+', 'GENE_NAME': 'ehaB'}, {'START': 41470, 'STOP': 42924, 'ORIENTATION': '+', 'GENE_NAME': 'ehaB'}, {'START': 41470, 'STOP': 42924, 'ORIENTATION': '+', 'GENE_NAME': 'upaC'}, {'START': 41581, 'STOP': 42924, 'ORIENTATION': '+', 'GENE_NAME': 'ehaB'}]}}, 'ECI-2523_contig45': {'Virulence Factors': {'lcl|ECI-2523_contig45|': [{'START': 10, 'STOP': 585, 'ORIENTATION': '+', 'GENE_NAME': 'orf4'}, {'START': 10, 'STOP': 585, 'ORIENTATION': '+', 'GENE_NAME': 'ECO55CA74_21300'}, {'START': 10, 'STOP': 585, 'ORIENTATION': '+', 'GENE_NAME': 'G2583_4440'}, {'START': 10, 'STOP': 585, 'ORIENTATION': '+', 'GENE_NAME': 'ECO111_3769'}, {'START': 10, 'STOP': 585, 'ORIENTATION': '+', 'GENE_NAME': 'E2348C_3965'}, {'START': 10, 'STOP': 585, 'ORIENTATION': '+', 'GENE_NAME': 'ECO103_3635'}, {'START': 466, 'STOP': 585, 'ORIENTATION': '+', 'GENE_NAME': 'ECH74115_5077'}, {'START': 554, 'STOP': 585, 'ORIENTATION': '+', 'GENE_NAME': 'ECO26_5255'}, {'START': 554, 'STOP': 585, 'ORIENTATION': '+', 'GENE_NAME': 'ECO111_3768'}, {'START': 554, 'STOP': 585, 'ORIENTATION': '+', 'GENE_NAME': 'ECO103_3634'}, {'START': 554, 'STOP': 585, 'ORIENTATION': '+', 'GENE_NAME': 'E2348C_3964'}, {'START': 554, 'STOP': 585, 'ORIENTATION': '+', 'GENE_NAME': 'ECs4584'}]}}, 'ECI-2523_contig42': {'Virulence Factors': {'lcl|ECI-2523_contig42|': [{'START': 8175, 'STOP': 9614, 'ORIENTATION': '-', 'GENE_NAME': 'hlyD'}, {'START': 9618, 'STOP': 10288, 'ORIENTATION': '-', 'GENE_NAME': 'hlyB'}, {'START': 2189, 'STOP': 2493, 'ORIENTATION': '-', 'GENE_NAME': 'ccdb'}, {'START': 466, 'STOP': 701, 'ORIENTATION': '-', 'GENE_NAME': 'fimD'}]}}, 'ECI-2523_contig43': {'Virulence Factors': {}}, 'ECI-2523_contig40': {'Virulence Factors': {}}, 'ECI-2523_contig41': {'Virulence Factors': {}}, 'ECI-2523_contig48': {'Virulence Factors': {}}, 'ECI-2523_contig49': {'Virulence Factors': {'lcl|ECI-2523_contig49|': [{'START': 8106, 'STOP': 10910, 'ORIENTATION': '-', 'GENE_NAME': 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'ECI-2523_contig107': {'Virulence Factors': {}}, 'ECI-2523_contig104': {'Virulence Factors': {'lcl|ECI-2523_contig104|': [{'START': 1566, 'STOP': 2660, 'ORIENTATION': '+', 'GENE_NAME': 'rfbe'}]}}, 'ECI-2523_contig105': {'Virulence Factors': {'lcl|ECI-2523_contig105|': [{'START': 198513, 'STOP': 200495, 'ORIENTATION': '-', 'GENE_NAME': 'chuA'}, {'START': 198513, 'STOP': 200459, 'ORIENTATION': '-', 'GENE_NAME': 'chuA'}, {'START': 202112, 'STOP': 203449, 'ORIENTATION': '+', 'GENE_NAME': 'chuW'}, {'START': 40713, 'STOP': 41951, 'ORIENTATION': '-', 'GENE_NAME': 'hofq'}, {'START': 202190, 'STOP': 203449, 'ORIENTATION': '+', 'GENE_NAME': 'chuW'}, {'START': 197436, 'STOP': 198464, 'ORIENTATION': '-', 'GENE_NAME': 'chuS'}, {'START': 204628, 'STOP': 205620, 'ORIENTATION': '+', 'GENE_NAME': 'chuU'}, {'START': 201100, 'STOP': 202092, 'ORIENTATION': '+', 'GENE_NAME': 'chuT'}, {'START': 204664, 'STOP': 205620, 'ORIENTATION': '+', 'GENE_NAME': 'chuU'}, {'START': 204682, 'STOP': 205620, 'ORIENTATION': '+', 'GENE_NAME': 'chuU'}, {'START': 201178, 'STOP': 202092, 'ORIENTATION': '+', 'GENE_NAME': 'chuT'}, {'START': 201238, 'STOP': 202092, 'ORIENTATION': '+', 'GENE_NAME': 'chuT'}, {'START': 205587, 'STOP': 206387, 'ORIENTATION': '+', 'GENE_NAME': 'chuV'}, {'START': 201262, 'STOP': 202092, 'ORIENTATION': '+', 'GENE_NAME': 'chuT'}, {'START': 203956, 'STOP': 204579, 'ORIENTATION': '+', 'GENE_NAME': 'chuY'}, {'START': 216170, 'STOP': 216802, 'ORIENTATION': '-', 'GENE_NAME': 'gadX'}, {'START': 203462, 'STOP': 203956, 'ORIENTATION': '+', 'GENE_NAME': 'chuX'}]}}, 'ECI-2523_contig227': {'Virulence Factors': {}}, 'ECI-2523_contig191': {'Virulence Factors': {}}, 'ECI-2523_contig220': {'Virulence Factors': {}}, 'ECI-2523_contig39': {'Virulence Factors': {'lcl|ECI-2523_contig39|': [{'START': 2213, 'STOP': 4621, 'ORIENTATION': '+', 'GENE_NAME': 'espY4'}, {'START': 36059, 'STOP': 37936, 'ORIENTATION': '+', 'GENE_NAME': 'espL3'}, {'START': 68291, 'STOP': 69487, 'ORIENTATION': '-', 'GENE_NAME': 'espG'}, {'START': 730, 'STOP': 1912, 'ORIENTATION': '-', 'GENE_NAME': 'espX3'}, {'START': 68291, 'STOP': 69436, 'ORIENTATION': '-', 'GENE_NAME': 'espG'}, {'START': 68291, 'STOP': 69487, 'ORIENTATION': '-', 'GENE_NAME': 'espG1'}, {'START': 67345, 'STOP': 68163, 'ORIENTATION': '-', 'GENE_NAME': 'Z5143'}, {'START': 67345, 'STOP': 68163, 'ORIENTATION': '-', 'GENE_NAME': 'G2583_4445'}, {'START': 67345, 'STOP': 68163, 'ORIENTATION': '-', 'GENE_NAME': 'E2348C_3971'}, {'START': 67345, 'STOP': 68163, 'ORIENTATION': '-', 'GENE_NAME': 'ECO111_3730'}, {'START': 67345, 'STOP': 68163, 'ORIENTATION': '-', 'GENE_NAME': 'ECO103_3640'}, {'START': 67345, 'STOP': 68163, 'ORIENTATION': '-', 'GENE_NAME': 'ECO26_5249'}, {'START': 70732, 'STOP': 71121, 'ORIENTATION': '+', 'GENE_NAME': 'ler'}, {'START': 70750, 'STOP': 71121, 'ORIENTATION': '+', 'GENE_NAME': 'ler'}, {'START': 71358, 'STOP': 71660, 'ORIENTATION': '+', 'GENE_NAME': 'cesAB'}, {'START': 71367, 'STOP': 71660, 'ORIENTATION': '+', 'GENE_NAME': 'ECH74115_5078'}, {'START': 1, 'STOP': 256, 'ORIENTATION': '+', 'GENE_NAME': 'espY5'}, {'START': 71367, 'STOP': 71658, 'ORIENTATION': '+', 'GENE_NAME': 'ECO103_3636'}, {'START': 71136, 'STOP': 71354, 'ORIENTATION': '+', 'GENE_NAME': 'escE'}, {'START': 71136, 'STOP': 71354, 'ORIENTATION': '+', 'GENE_NAME': 'E2348C_3967'}, {'START': 71136, 'STOP': 71354, 'ORIENTATION': '+', 'GENE_NAME': 'ECs4587'}, {'START': 71136, 'STOP': 71354, 'ORIENTATION': '+', 'GENE_NAME': 'ECO111_3771'}, {'START': 71136, 'STOP': 71354, 'ORIENTATION': '+', 'GENE_NAME': 'ECO103_3637'}, {'START': 26990, 'STOP': 27097, 'ORIENTATION': '-', 'GENE_NAME': 'entD'}]}}, 'ECI-2523_contig38': {'Virulence Factors': {}}, 'ECI-2523_contig37': {'Virulence Factors': {'lcl|ECI-2523_contig37|': [{'START': 77820, 'STOP': 79832, 'ORIENTATION': '-', 'GENE_NAME': 'espX2'}, {'START': 108392, 'STOP': 109384, 'ORIENTATION': '-', 'GENE_NAME': 'nleC'}, {'START': 109445, 'STOP': 110425, 'ORIENTATION': '-', 'GENE_NAME': 'nleB'}, {'START': 109445, 'STOP': 110425, 'ORIENTATION': '-', 'GENE_NAME': 'nleB2'}, {'START': 109445, 'STOP': 110425, 'ORIENTATION': '-', 'GENE_NAME': 'nleB2-2'}, {'START': 106683, 'STOP': 107564, 'ORIENTATION': '-', 'GENE_NAME': 'nleH1'}, {'START': 106683, 'STOP': 107564, 'ORIENTATION': '-', 'GENE_NAME': 'nleH1-1'}, {'START': 108401, 'STOP': 109358, 'ORIENTATION': '-', 'GENE_NAME': 'nleC'}, {'START': 105754, 'STOP': 106452, 'ORIENTATION': '-', 'GENE_NAME': 'nleD'}, {'START': 5874, 'STOP': 6605, 'ORIENTATION': '+', 'GENE_NAME': 'artj'}, {'START': 107191, 'STOP': 107564, 'ORIENTATION': '-', 'GENE_NAME': 'nleh1-2'}, {'START': 107191, 'STOP': 107564, 'ORIENTATION': '-', 'GENE_NAME': 'nleH2'}, {'START': 106683, 'STOP': 106849, 'ORIENTATION': '-', 'GENE_NAME': 'nleH3'}]}}, 'ECI-2523_contig36': {'Virulence Factors': {}}, 'ECI-2523_contig35': {'Virulence Factors': {'lcl|ECI-2523_contig35|': [{'START': 2293, 'STOP': 3831, 'ORIENTATION': '+', 'GENE_NAME': 'escC'}, {'START': 1260, 'STOP': 1832, 'ORIENTATION': '+', 'GENE_NAME': 'escJ'}, {'START': 3845, 'STOP': 4300, 'ORIENTATION': '+', 'GENE_NAME': 'cesD'}, {'START': 1838, 'STOP': 2293, 'ORIENTATION': '+', 'GENE_NAME': 'sepD'}, {'START': 829, 'STOP': 1257, 'ORIENTATION': '+', 'GENE_NAME': 'escI'}, {'START': 4684, 'STOP': 5063, 'ORIENTATION': '-', 'GENE_NAME': 'glrA'}, {'START': 880, 'STOP': 1257, 'ORIENTATION': '+', 'GENE_NAME': 'ECO55CA74_21240'}, {'START': 4684, 'STOP': 5063, 'ORIENTATION': '-', 'GENE_NAME': 'grlA'}, {'START': 4685, 'STOP': 5063, 'ORIENTATION': '-', 'GENE_NAME': 'glrA'}, {'START': 829, 'STOP': 1257, 'ORIENTATION': '+', 'GENE_NAME': 'rorf8'}, {'START': 1, 'STOP': 312, 'ORIENTATION': '-', 'GENE_NAME': 'G2583_4425'}, {'START': 1, 'STOP': 312, 'ORIENTATION': '-', 'GENE_NAME': 'cesL'}, {'START': 2, 'STOP': 312, 'ORIENTATION': '-', 'GENE_NAME': 'mpc'}, {'START': 1, 'STOP': 312, 'ORIENTATION': '-', 'GENE_NAME': 'mpc'}, {'START': 497, 'STOP': 796, 'ORIENTATION': '+', 'GENE_NAME': 'sepZ'}, {'START': 2174, 'STOP': 2293, 'ORIENTATION': '+', 'GENE_NAME': 'ECH74115_5068'}]}}, 'ECI-2523_contig34': {'Virulence Factors': {}}, 'ECI-2523_contig33': {'Virulence Factors': {}}, 'ECI-2523_contig32': {'Virulence Factors': {'lcl|ECI-2523_contig32|': [{'START': 653, 'STOP': 945, 'ORIENTATION': '-', 'GENE_NAME': 'iss2'}]}}, 'ECI-2523_contig31': {'Virulence Factors': {}}, 'ECI-2523_contig30': {'Virulence Factors': {'lcl|ECI-2523_contig30|': [{'START': 2014, 'STOP': 2967, 'ORIENTATION': '-', 'GENE_NAME': 'ompt'}]}}, 'ECI-2523_contig182': {'Virulence Factors': {'lcl|ECI-2523_contig182|': [{'START': 144, 'STOP': 1689, 'ORIENTATION': '-', 'GENE_NAME': 'aec15'}, {'START': 144, 'STOP': 1687, 'ORIENTATION': '-', 'GENE_NAME': 'aec15'}]}}, 'ECI-2523_contig183': {'Virulence Factors': {'lcl|ECI-2523_contig183|': [{'START': 466, 'STOP': 701, 'ORIENTATION': '-', 'GENE_NAME': 'fimD'}]}}, 'ECI-2523_contig180': {'Virulence Factors': {}}, 'ECI-2523_contig181': {'Virulence Factors': {'lcl|ECI-2523_contig181|': [{'START': 34704, 'STOP': 36881, 'ORIENTATION': '-', 'GENE_NAME': 'espN'}, {'START': 30698, 'STOP': 32059, 'ORIENTATION': '+', 'GENE_NAME': 'espK'}, {'START': 32120, 'STOP': 32395, 'ORIENTATION': '+', 'GENE_NAME': 'espO1-1'}, {'START': 32475, 'STOP': 32588, 'ORIENTATION': '-', 'GENE_NAME': 'nleB2-2'}]}}, 'ECI-2523_contig186': {'Virulence Factors': {}}, 'ECI-2523_contig187': {'Virulence Factors': {}}, 'ECI-2523_contig184': {'Virulence Factors': {}}, 'ECI-2523_contig185': {'Virulence Factors': {}}, 'ECI-2523_contig195': {'Virulence Factors': {}}, 'ECI-2523_contig188': {'Virulence Factors': {}}, 'ECI-2523_contig189': {'Virulence Factors': {'lcl|ECI-2523_contig189|': [{'START': 37798, 'STOP': 39226, 'ORIENTATION': '-', 'GENE_NAME': 'aslA'}]}}, 'ECI-2523_contig221': {'Virulence Factors': {'lcl|ECI-2523_contig221|': [{'START': 27787, 'STOP': 31836, 'ORIENTATION': '-', 'GENE_NAME': 'ehaA'}, {'START': 27787, 'STOP': 31770, 'ORIENTATION': '-', 'GENE_NAME': 'ehaA'}, {'START': 20217, 'STOP': 20256, 'ORIENTATION': '-', 'GENE_NAME': 'entD'}]}}, 'ECI-2523_contig194': {'Virulence Factors': {'lcl|ECI-2523_contig194|': [{'START': 914, 'STOP': 2290, 'ORIENTATION': '+', 'GENE_NAME': 'ygeH'}, {'START': 3282, 'STOP': 3914, 'ORIENTATION': '-', 'GENE_NAME': 'ECs3712'}, {'START': 89, 'STOP': 580, 'ORIENTATION': '+', 'GENE_NAME': 'ygeG'}, {'START': 2862, 'STOP': 3263, 'ORIENTATION': '+', 'GENE_NAME': 'iagB'}, {'START': 2760, 'STOP': 3237, 'ORIENTATION': '+', 'GENE_NAME': 'b2854'}]}}, 'ECI-2523_contig119': {'Virulence Factors': {'lcl|ECI-2523_contig119|': [{'START': 17624, 'STOP': 20275, 'ORIENTATION': '-', 'GENE_NAME': 'Z2203'}, {'START': 17624, 'STOP': 20275, 'ORIENTATION': '-', 'GENE_NAME': 'fimD'}, {'START': 15590, 'STOP': 16504, 'ORIENTATION': '-', 'GENE_NAME': 'Z2206'}, {'START': 20317, 'STOP': 21036, 'ORIENTATION': '-', 'GENE_NAME': 'Z2201'}, {'START': 21388, 'STOP': 21951, 'ORIENTATION': '-', 'GENE_NAME': 'Z2200'}, {'START': 17080, 'STOP': 17610, 'ORIENTATION': '-', 'GENE_NAME': 'Z2204'}, {'START': 17080, 'STOP': 17610, 'ORIENTATION': '-', 'GENE_NAME': 'fimF'}, {'START': 16564, 'STOP': 17067, 'ORIENTATION': '-', 'GENE_NAME': 'Z2205'}, {'START': 16564, 'STOP': 17067, 'ORIENTATION': '-', 'GENE_NAME': 'fimG'}, {'START': 66507, 'STOP': 66621, 'ORIENTATION': '-', 'GENE_NAME': 'astA'}]}}, 'ECI-2523_contig200': {'Virulence Factors': {'lcl|ECI-2523_contig200|': [{'START': 61246, 'STOP': 61809, 'ORIENTATION': '-', 'GENE_NAME': 'ppdb'}, {'START': 61800, 'STOP': 62270, 'ORIENTATION': '-', 'GENE_NAME': 'ppda'}, {'START': 60842, 'STOP': 61249, 'ORIENTATION': '-', 'GENE_NAME': 'ygdb'}, {'START': 60534, 'STOP': 60857, 'ORIENTATION': '-', 'GENE_NAME': 'ppdc'}]}}, 'ECI-2523_contig203': {'Virulence Factors': {}}, 'ECI-2523_contig202': {'Virulence Factors': {'lcl|ECI-2523_contig202|': [{'START': 564, 'STOP': 1217, 'ORIENTATION': '+', 'GENE_NAME': 'espJ'}, {'START': 699, 'STOP': 1217, 'ORIENTATION': '+', 'GENE_NAME': 'espJ'}, {'START': 1542, 'STOP': 1983, 'ORIENTATION': '+', 'GENE_NAME': 'espF'}, {'START': 1542, 'STOP': 1983, 'ORIENTATION': '+', 'GENE_NAME': 'tccP'}, {'START': 1771, 'STOP': 1983, 'ORIENTATION': '+', 'GENE_NAME': 'tccP'}, {'START': 1767, 'STOP': 1983, 'ORIENTATION': '+', 'GENE_NAME': 'tccP2'}, {'START': 1771, 'STOP': 1983, 'ORIENTATION': '+', 'GENE_NAME': 'tccP2'}, {'START': 1806, 'STOP': 1983, 'ORIENTATION': '+', 'GENE_NAME': 'tccP2'}]}}, 'ECI-2523_contig205': {'Virulence Factors': {}}, 'ECI-2523_contig204': {'Virulence Factors': {}}, 'ECI-2523_contig207': {'Virulence Factors': {}}, 'ECI-2523_contig206': {'Virulence Factors': {}}, 'ECI-2523_contig111': {'Virulence Factors': {}}, 'ECI-2523_contig110': {'Virulence Factors': {'lcl|ECI-2523_contig110|': [{'START': 68783, 'STOP': 70958, 'ORIENTATION': '+', 'GENE_NAME': 'cadA'}]}}, 'ECI-2523_contig113': {'Virulence Factors': {}}, 'ECI-2523_contig112': {'Virulence Factors': {}}, 'ECI-2523_contig115': {'Virulence Factors': {}}, 'ECI-2523_contig114': {'Virulence Factors': {}}, 'ECI-2523_contig117': {'Virulence Factors': {}}, 'ECI-2523_contig116': {'Virulence Factors': {'lcl|ECI-2523_contig116|': [{'START': 1487, 'STOP': 4483, 'ORIENTATION': '-', 'GENE_NAME': 'hlyA'}, {'START': 18593, 'STOP': 21289, 'ORIENTATION': '-', 'GENE_NAME': 'stcE'}, {'START': 15663, 'STOP': 17591, 'ORIENTATION': '-', 'GENE_NAME': 'etpD'}, {'START': 14158, 'STOP': 15663, 'ORIENTATION': '-', 'GENE_NAME': 'etpE'}, {'START': 1, 'STOP': 1437, 'ORIENTATION': '-', 'GENE_NAME': 'hlyB'}, {'START': 8774, 'STOP': 10051, 'ORIENTATION': '-', 'GENE_NAME': 'etpL'}, {'START': 12933, 'STOP': 14156, 'ORIENTATION': '-', 'GENE_NAME': 'etpF'}, {'START': 9985, 'STOP': 10962, 'ORIENTATION': '-', 'GENE_NAME': 'etpK'}, {'START': 17631, 'STOP': 18506, 'ORIENTATION': '-', 'GENE_NAME': 'etpC'}, {'START': 7384, 'STOP': 8217, 'ORIENTATION': '-', 'GENE_NAME': 'etpN'}, {'START': 10959, 'STOP': 11558, 'ORIENTATION': '-', 'GENE_NAME': 'etpJ'}, {'START': 11917, 'STOP': 12471, 'ORIENTATION': '-', 'GENE_NAME': 'etpH'}, {'START': 4485, 'STOP': 5000, 'ORIENTATION': '-', 'GENE_NAME': 'hlyC'}, {'START': 8275, 'STOP': 8787, 'ORIENTATION': '-', 'GENE_NAME': 'etpM'}, {'START': 4485, 'STOP': 4976, 'ORIENTATION': '-', 'GENE_NAME': 'hlyC'}, {'START': 12468, 'STOP': 12902, 'ORIENTATION': '-', 'GENE_NAME': 'etpG'}, {'START': 6891, 'STOP': 7292, 'ORIENTATION': '-', 'GENE_NAME': 'etpO'}, {'START': 11555, 'STOP': 11920, 'ORIENTATION': '-', 'GENE_NAME': 'etpI'}, {'START': 6746, 'STOP': 6773, 'ORIENTATION': '+', 'GENE_NAME': 'agn43'}]}}, 'ECI-2523_contig199': {'Virulence Factors': {}}, 'ECI-2523_contig225': {'Virulence Factors': {}}, 'ECI-2523_contig198': {'Virulence Factors': {}}, 'ECI-2523_contig224': {'Virulence Factors': {'lcl|ECI-2523_contig224|': [{'START': 157601, 'STOP': 159679, 'ORIENTATION': '-', 'GENE_NAME': 'flhA'}, {'START': 167987, 'STOP': 169951, 'ORIENTATION': '-', 'GENE_NAME': 'cheA'}, {'START': 165659, 'STOP': 167320, 'ORIENTATION': '-', 'GENE_NAME': 'tar/cheM'}, {'START': 159672, 'STOP': 160820, 'ORIENTATION': '-', 'GENE_NAME': 'flhB'}, {'START': 162081, 'STOP': 163130, 'ORIENTATION': '-', 'GENE_NAME': 'cheB'}, {'START': 169956, 'STOP': 170882, 'ORIENTATION': '-', 'GENE_NAME': 'motB'}, {'START': 170879, 'STOP': 171766, 'ORIENTATION': '-', 'GENE_NAME': 'motA'}, {'START': 163133, 'STOP': 163993, 'ORIENTATION': '-', 'GENE_NAME': 'cheR'}, {'START': 161022, 'STOP': 161666, 'ORIENTATION': '-', 'GENE_NAME': 'cheZ'}, {'START': 171893, 'STOP': 172471, 'ORIENTATION': '-', 'GENE_NAME': 'flhC'}, {'START': 167463, 'STOP': 167966, 'ORIENTATION': '-', 'GENE_NAME': 'cheW'}, {'START': 157209, 'STOP': 157601, 'ORIENTATION': '-', 'GENE_NAME': 'flhE'}, {'START': 161677, 'STOP': 162066, 'ORIENTATION': '-', 'GENE_NAME': 'cheY'}, {'START': 172474, 'STOP': 172833, 'ORIENTATION': '-', 'GENE_NAME': 'flhD'}, {'START': 149057, 'STOP': 149171, 'ORIENTATION': '+', 'GENE_NAME': 'entD'}]}}, 'ECI-2523_contig226': {'Virulence Factors': {}}, 'ECI-2523_contig190': {'Virulence Factors': {'lcl|ECI-2523_contig190|': [{'START': 860, 'STOP': 2119, 'ORIENTATION': '+', 'GENE_NAME': 'espR1'}, {'START': 1051, 'STOP': 2112, 'ORIENTATION': '+', 'GENE_NAME': 'espR1'}, {'START': 1, 'STOP': 797, 'ORIENTATION': '+', 'GENE_NAME': 'espR2'}]}}, 'ECI-2523_contig20': {'Virulence Factors': {}}, 'ECI-2523_contig21': {'Virulence Factors': {}}, 'ECI-2523_contig22': {'Virulence Factors': {}}, 'ECI-2523_contig23': {'Virulence Factors': {}}, 'ECI-2523_contig24': {'Virulence Factors': {}}, 'ECI-2523_contig25': {'Virulence Factors': {}}, 'ECI-2523_contig26': {'Virulence Factors': {}}, 'ECI-2523_contig27': {'Virulence Factors': {'lcl|ECI-2523_contig27|': [{'START': 17816, 'STOP': 17850, 'ORIENTATION': '+', 'GENE_NAME': 'entD'}]}}, 'ECI-2523_contig28': {'Virulence Factors': {}}, 'ECI-2523_contig29': {'Virulence Factors': {}}, 'ECI-2523_contig63': {'Virulence Factors': {'lcl|ECI-2523_contig63|': [{'START': 24452, 'STOP': 24486, 'ORIENTATION': '-', 'GENE_NAME': 'entD'}]}}, 'ECI-2523_contig211': {'Virulence Factors': {}}}
kevinkle commented 6 years ago 
(backend) kevin@kevin-ThinkPad-T510:~/Desktop/backend/app$ python modules/ectyper/ecoli_serotyping/src/Tools_Controller/tools_controller.py -in tests/ecoli/GCA_900015695.1_ED647_contigs_genomic.fna -s 0 -vf 1 -pi 90
{'GCA_900015695.1_ED647_contigs_genomic': {'Virulence Factors': {'FAVS01000051.1': [{'START': 17044, 'STOP': 18024, 'ORIENTATION': '+', 'GENE_NAME': 'yggr'}, {'START': 10244, 'STOP': 10290, 'ORIENTATION': '-', 'GENE_NAME': 'entD'}], 'FAVS01000031.1': [{'START': 51862, 'STOP': 53290, 'ORIENTATION': '+', 'GENE_NAME': 'aslA'}, {'START': 7786, 'STOP': 7820, 'ORIENTATION': '+', 'GENE_NAME': 'entD'}], 'FAVS01000003.1': [{'START': 6997, 'STOP': 7992, 'ORIENTATION': '+', 'GENE_NAME': 'flk'}, {'START': 12845, 'STOP': 12879, 'ORIENTATION': '+', 'GENE_NAME': 'entD'}], 'FAVS01000064.1': [{'START': 6711, 'STOP': 8897, 'ORIENTATION': '-', 'GENE_NAME': 'espL4'}, {'START': 7758, 'STOP': 8897, 'ORIENTATION': '-', 'GENE_NAME': 'espL4'}], 'FAVS01000074.1': [{'START': 262, 'STOP': 297, 'ORIENTATION': '-', 'GENE_NAME': 'entD'}], 'FAVS01000135.1': [{'START': 6834, 'STOP': 6880, 'ORIENTATION': '+', 'GENE_NAME': 'fimD'}], 'FAVS01000037.1': [{'START': 9, 'STOP': 45, 'ORIENTATION': '+', 'GENE_NAME': 'entD'}], 'FAVS01000059.1': [{'START': 8100, 'STOP': 12149, 'ORIENTATION': '+', 'GENE_NAME': 'ehaA'}, {'START': 8166, 'STOP': 12149, 'ORIENTATION': '+', 'GENE_NAME': 'ehaA'}, {'START': 19680, 'STOP': 19719, 'ORIENTATION': '+', 'GENE_NAME': 'entD'}], 'FAVS01000260.1': [{'START': 188, 'STOP': 1194, 'ORIENTATION': '-', 'GENE_NAME': 'espR3'}, {'START': 188, 'STOP': 1194, 'ORIENTATION': '-', 'GENE_NAME': 'espR4'}, {'START': 293, 'STOP': 1194, 'ORIENTATION': '-', 'GENE_NAME': 'espR4'}], 'FAVS01000088.1': [{'START': 18395, 'STOP': 20485, 'ORIENTATION': '-', 'GENE_NAME': 'c3610'}, {'START': 18395, 'STOP': 20485, 'ORIENTATION': '-', 'GENE_NAME': 'iha'}, {'START': 17495, 'STOP': 17803, 'ORIENTATION': '-', 'GENE_NAME': 'tlra'}], 'FAVS01000109.1': [{'START': 12805, 'STOP': 14178, 'ORIENTATION': '-', 'GENE_NAME': 'fliI'}, {'START': 11219, 'STOP': 12346, 'ORIENTATION': '-', 'GENE_NAME': 'fliK'}, {'START': 9641, 'STOP': 10645, 'ORIENTATION': '-', 'GENE_NAME': 'fliM'}, {'START': 7054, 'STOP': 7839, 'ORIENTATION': '-', 'GENE_NAME': 'fliR'}, {'START': 8126, 'STOP': 8863, 'ORIENTATION': '-', 'GENE_NAME': 'fliP'}, {'START': 10650, 'STOP': 11114, 'ORIENTATION': '-', 'GENE_NAME': 'fliL'}, {'START': 12343, 'STOP': 12786, 'ORIENTATION': '-', 'GENE_NAME': 'fliJ'}, {'START': 9231, 'STOP': 9644, 'ORIENTATION': '-', 'GENE_NAME': 'fliN'}, {'START': 8863, 'STOP': 9228, 'ORIENTATION': '-', 'GENE_NAME': 'fliO'}, {'START': 7847, 'STOP': 8116, 'ORIENTATION': '-', 'GENE_NAME': 'fliQ'}, {'START': 14178, 'STOP': 14225, 'ORIENTATION': '-', 'GENE_NAME': 'fliH'}], 'FAVS01000091.1': [{'START': 1, 'STOP': 2429, 'ORIENTATION': '-', 'GENE_NAME': 'entF'}, {'START': 4092, 'STOP': 6332, 'ORIENTATION': '+', 'GENE_NAME': 'fepA'}, {'START': 18600, 'STOP': 19982, 'ORIENTATION': '-', 'GENE_NAME': 'ibeB'}, {'START': 18600, 'STOP': 19986, 'ORIENTATION': '-', 'GENE_NAME': 'ibeB'}, {'START': 18610, 'STOP': 19982, 'ORIENTATION': '-', 'GENE_NAME': 'ibeB'}, {'START': 2647, 'STOP': 3849, 'ORIENTATION': '-', 'GENE_NAME': 'fes'}, {'START': 6357, 'STOP': 7127, 'ORIENTATION': '+', 'GENE_NAME': 'entD'}, {'START': 22820, 'STOP': 23137, 'ORIENTATION': '+', 'GENE_NAME': 'aec15'}, {'START': 22854, 'STOP': 23137, 'ORIENTATION': '+', 'GENE_NAME': 'aec15'}, {'START': 22854, 'STOP': 23137, 'ORIENTATION': '+', 'GENE_NAME': 'vgrG'}], 'FAVS01000174.1': [{'START': 2094, 'STOP': 3152, 'ORIENTATION': '+', 'GENE_NAME': 'espW'}, {'START': 1365, 'STOP': 2015, 'ORIENTATION': '+', 'GENE_NAME': 'nleG8-2'}, {'START': 592, 'STOP': 1182, 'ORIENTATION': '-', 'GENE_NAME': 'espM2'}, {'START': 1365, 'STOP': 1990, 'ORIENTATION': '+', 'GENE_NAME': 'nleG-1'}, {'START': 592, 'STOP': 1176, 'ORIENTATION': '-', 'GENE_NAME': 'espM2'}, {'START': 596, 'STOP': 1182, 'ORIENTATION': '-', 'GENE_NAME': 'espM1'}, {'START': 1365, 'STOP': 1926, 'ORIENTATION': '+', 'GENE_NAME': 'nleG8-2'}, {'START': 597, 'STOP': 1182, 'ORIENTATION': '-', 'GENE_NAME': 'espM2'}, {'START': 3282, 'STOP': 3761, 'ORIENTATION': '-', 'GENE_NAME': 'nleG6-3'}, {'START': 3282, 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'FAVS01000001.1': [{'START': 15735, 'STOP': 17357, 'ORIENTATION': '-', 'GENE_NAME': 'nadb'}, {'START': 53844, 'STOP': 53875, 'ORIENTATION': '-', 'GENE_NAME': 'entD'}], 'FAVS01000081.1': [{'START': 12411, 'STOP': 12445, 'ORIENTATION': '-', 'GENE_NAME': 'entD'}], 'FAVS01000161.1': [{'START': 1257, 'STOP': 2210, 'ORIENTATION': '+', 'GENE_NAME': 'ompt'}], 'FAVS01000025.1': [{'START': 36597, 'STOP': 37802, 'ORIENTATION': '+', 'GENE_NAME': 'flgE'}, {'START': 4870, 'STOP': 5703, 'ORIENTATION': '-', 'GENE_NAME': 'csgG'}, {'START': 37822, 'STOP': 38577, 'ORIENTATION': '+', 'GENE_NAME': 'flgF'}, {'START': 35877, 'STOP': 36572, 'ORIENTATION': '+', 'GENE_NAME': 'flgD'}, {'START': 34227, 'STOP': 34886, 'ORIENTATION': '-', 'GENE_NAME': 'flgA'}, {'START': 6565, 'STOP': 7215, 'ORIENTATION': '-', 'GENE_NAME': 'csgD'}, {'START': 7942, 'STOP': 8424, 'ORIENTATION': '+', 'GENE_NAME': 'csgB'}, {'START': 8465, 'STOP': 8923, 'ORIENTATION': '+', 'GENE_NAME': 'csgA'}, {'START': 7969, 'STOP': 8424, 'ORIENTATION': '+', 'GENE_NAME': 'csgB'}, {'START': 35041, 'STOP': 35457, 'ORIENTATION': '+', 'GENE_NAME': 'flgB'}, {'START': 33437, 'STOP': 33853, 'ORIENTATION': '-', 'GENE_NAME': 'flgN'}, {'START': 5730, 'STOP': 6146, 'ORIENTATION': '-', 'GENE_NAME': 'csgF'}, {'START': 35461, 'STOP': 35865, 'ORIENTATION': '+', 'GENE_NAME': 'flgC'}, {'START': 6171, 'STOP': 6560, 'ORIENTATION': '-', 'GENE_NAME': 'csgE'}, {'START': 8982, 'STOP': 9314, 'ORIENTATION': '+', 'GENE_NAME': 'csgC'}], 'FAVS01000052.1': [{'START': 1611, 'STOP': 1649, 'ORIENTATION': '-', 'GENE_NAME': 'focD'}], 'FAVS01000036.1': [{'START': 32397, 'STOP': 34350, 'ORIENTATION': '-', 'GENE_NAME': 'ecpC'}, {'START': 32397, 'STOP': 34349, 'ORIENTATION': '-', 'GENE_NAME': 'ecpC'}, {'START': 30764, 'STOP': 32407, 'ORIENTATION': '-', 'GENE_NAME': 'ecpD'}, {'START': 30764, 'STOP': 32383, 'ORIENTATION': '-', 'GENE_NAME': 'ecpD'}, {'START': 30085, 'STOP': 30840, 'ORIENTATION': '-', 'GENE_NAME': 'ecpE'}, {'START': 30087, 'STOP': 30840, 'ORIENTATION': '-', 'GENE_NAME': 'ecpE'}, {'START': 30085, 'STOP': 30795, 'ORIENTATION': '-', 'GENE_NAME': 'ecpE'}, {'START': 30087, 'STOP': 30840, 'ORIENTATION': '-', 'GENE_NAME': 'matF'}, {'START': 30087, 'STOP': 30795, 'ORIENTATION': '-', 'GENE_NAME': 'ecpE'}, {'START': 30087, 'STOP': 30748, 'ORIENTATION': '-', 'GENE_NAME': 'ecpE'}], 'FAVS01000019.1': [{'START': 45485, 'STOP': 45722, 'ORIENTATION': '+', 'GENE_NAME': 'fimD'}], 'FAVS01000071.1': [{'START': 9334, 'STOP': 10518, 'ORIENTATION': '-', 'GENE_NAME': 'wzy'}, {'START': 6144, 'STOP': 7238, 'ORIENTATION': '-', 'GENE_NAME': 'rfbe'}], 'FAVS01000027.1': [{'START': 40815, 'STOP': 41402, 'ORIENTATION': '+', 'GENE_NAME': 'tccP2'}, {'START': 41069, 'STOP': 41402, 'ORIENTATION': '+', 'GENE_NAME': 'espF'}, {'START': 41069, 'STOP': 41402, 'ORIENTATION': '+', 'GENE_NAME': 'tccP'}, {'START': 41069, 'STOP': 41402, 'ORIENTATION': '+', 'GENE_NAME': 'tccP2'}, {'START': 40317, 'STOP': 40499, 'ORIENTATION': '+', 'GENE_NAME': 'espV'}], 'FAVS01000034.1': [{'START': 13736, 'STOP': 14620, 'ORIENTATION': '-', 'GENE_NAME': 'ECS88_3547'}], 'FAVS01000138.1': [{'START': 12334, 'STOP': 12410, 'ORIENTATION': '-', 'GENE_NAME': 'nleG5-1'}, {'START': 12334, 'STOP': 12410, 'ORIENTATION': '-', 'GENE_NAME': 'nleG5-2'}], 'FAVS01000087.1': [{'START': 3275, 'STOP': 6676, 'ORIENTATION': '+', 'GENE_NAME': 'espN'}, {'START': 3350, 'STOP': 6676, 'ORIENTATION': '+', 'GENE_NAME': 'espN'}, {'START': 3863, 'STOP': 6676, 'ORIENTATION': '+', 'GENE_NAME': 'espN'}, {'START': 336, 'STOP': 2684, 'ORIENTATION': '+', 'GENE_NAME': 'espX7'}, {'START': 735, 'STOP': 2684, 'ORIENTATION': '+', 'GENE_NAME': 'espX7'}, {'START': 735, 'STOP': 2684, 'ORIENTATION': '+', 'GENE_NAME': 'nleL'}, {'START': 9321, 'STOP': 10682, 'ORIENTATION': '-', 'GENE_NAME': 'espK'}, {'START': 8985, 'STOP': 9260, 'ORIENTATION': '-', 'GENE_NAME': 'espO1-1'}, {'START': 8792, 'STOP': 8905, 'ORIENTATION': '+', 'GENE_NAME': 'nleB2-2'}], 'FAVS01000112.1': [{'START': 354, 'STOP': 3050, 'ORIENTATION': '+', 'GENE_NAME': 'stcE'}, {'START': 4052, 'STOP': 5980, 'ORIENTATION': '+', 'GENE_NAME': 'etpD'}, {'START': 5980, 'STOP': 7485, 'ORIENTATION': '+', 'GENE_NAME': 'etpE'}, {'START': 7487, 'STOP': 8710, 'ORIENTATION': '+', 'GENE_NAME': 'etpF'}, {'START': 3137, 'STOP': 4012, 'ORIENTATION': '+', 'GENE_NAME': 'etpC'}, {'START': 10085, 'STOP': 10684, 'ORIENTATION': '+', 'GENE_NAME': 'etpJ'}, {'START': 9172, 'STOP': 9726, 'ORIENTATION': '+', 'GENE_NAME': 'etpH'}, {'START': 8741, 'STOP': 9175, 'ORIENTATION': '+', 'GENE_NAME': 'etpG'}, {'START': 9723, 'STOP': 10088, 'ORIENTATION': '+', 'GENE_NAME': 'etpI'}], 'FAVS01000106.1': [{'START': 188, 'STOP': 4090, 'ORIENTATION': '+', 'GENE_NAME': 'espP'}, {'START': 8286, 'STOP': 10007, 'ORIENTATION': '+', 'GENE_NAME': 'ibeC'}, {'START': 8463, 'STOP': 10007, 'ORIENTATION': '+', 'GENE_NAME': 'ibeC'}, {'START': 3248, 'STOP': 4090, 'ORIENTATION': '+', 'GENE_NAME': 'epeA'}, {'START': 1, 'STOP': 49, 'ORIENTATION': '-', 'GENE_NAME': 'fimD'}], 'FAVS01000259.1': [{'START': 188, 'STOP': 1140, 'ORIENTATION': '-', 'GENE_NAME': 'espR4'}, {'START': 293, 'STOP': 1140, 'ORIENTATION': '-', 'GENE_NAME': 'espR4'}, {'START': 188, 'STOP': 1140, 'ORIENTATION': '-', 'GENE_NAME': 'espR3'}], 'FAVS01000041.1': [{'START': 3731, 'STOP': 3760, 'ORIENTATION': '+', 'GENE_NAME': 'entD'}], 'FAVS01000126.1': [{'START': 1168, 'STOP': 1295, 'ORIENTATION': '+', 'GENE_NAME': 'EC55989_3315'}, {'START': 8275, 'STOP': 8319, 'ORIENTATION': '+', 'GENE_NAME': 'fimD'}], 'FAVS01000008.1': [{'START': 148987, 'STOP': 150969, 'ORIENTATION': '-', 'GENE_NAME': 'chuA'}, {'START': 148987, 'STOP': 150933, 'ORIENTATION': '-', 'GENE_NAME': 'chuA'}, {'START': 152586, 'STOP': 153923, 'ORIENTATION': '+', 'GENE_NAME': 'chuW'}, {'START': 152664, 'STOP': 153923, 'ORIENTATION': '+', 'GENE_NAME': 'chuW'}, {'START': 147910, 'STOP': 148938, 'ORIENTATION': '-', 'GENE_NAME': 'chuS'}, {'START': 155102, 'STOP': 156094, 'ORIENTATION': '+', 'GENE_NAME': 'chuU'}, {'START': 151574, 'STOP': 152566, 'ORIENTATION': '+', 'GENE_NAME': 'chuT'}, {'START': 155138, 'STOP': 156094, 'ORIENTATION': '+', 'GENE_NAME': 'chuU'}, {'START': 155156, 'STOP': 156094, 'ORIENTATION': '+', 'GENE_NAME': 'chuU'}, {'START': 151652, 'STOP': 152566, 'ORIENTATION': '+', 'GENE_NAME': 'chuT'}, {'START': 151712, 'STOP': 152566, 'ORIENTATION': '+', 'GENE_NAME': 'chuT'}, {'START': 156061, 'STOP': 156861, 'ORIENTATION': '+', 'GENE_NAME': 'chuV'}, {'START': 151736, 'STOP': 152566, 'ORIENTATION': '+', 'GENE_NAME': 'chuT'}, {'START': 154430, 'STOP': 155053, 'ORIENTATION': '+', 'GENE_NAME': 'chuY'}, {'START': 166644, 'STOP': 167276, 'ORIENTATION': '-', 'GENE_NAME': 'gadX'}, {'START': 153936, 'STOP': 154430, 'ORIENTATION': '+', 'GENE_NAME': 'chuX'}], 'FAVS01000098.1': [{'START': 1, 'STOP': 203, 'ORIENTATION': '-', 'GENE_NAME': 'flhD'}], 'FAVS01000095.1': [{'START': 13677, 'STOP': 14732, 'ORIENTATION': '+', 'GENE_NAME': 'hlyE'}, {'START': 13815, 'STOP': 14732, 'ORIENTATION': '+', 'GENE_NAME': 'hlyE'}, {'START': 13821, 'STOP': 14732, 'ORIENTATION': '+', 'GENE_NAME': 'hlyE'}, {'START': 13815, 'STOP': 14732, 'ORIENTATION': '+', 'GENE_NAME': 'hlye'}, {'START': 13821, 'STOP': 14668, 'ORIENTATION': '+', 'GENE_NAME': 'hlyE'}, {'START': 13821, 'STOP': 14331, 'ORIENTATION': '+', 'GENE_NAME': 'hlyE'}, {'START': 14451, 'STOP': 14732, 'ORIENTATION': '+', 'GENE_NAME': 'hlyE'}, {'START': 14472, 'STOP': 14732, 'ORIENTATION': '+', 'GENE_NAME': 'EC958_1421'}, {'START': 2, 'STOP': 237, 'ORIENTATION': '-', 'GENE_NAME': 'fimD'}, {'START': 14451, 'STOP': 14668, 'ORIENTATION': '+', 'GENE_NAME': 'hlyE'}], 'FAVS01000148.1': [{'START': 190, 'STOP': 1833, 'ORIENTATION': '-', 'GENE_NAME': 'flgK'}, {'START': 2840, 'STOP': 3937, 'ORIENTATION': '-', 'GENE_NAME': 'flgI'}, {'START': 1899, 'STOP': 2840, 'ORIENTATION': '-', 'GENE_NAME': 'flgJ'}, {'START': 4700, 'STOP': 5482, 'ORIENTATION': '-', 'GENE_NAME': 'flgG'}, {'START': 3949, 'STOP': 4647, 'ORIENTATION': '-', 'GENE_NAME': 'flgH'}, {'START': 1, 'STOP': 178, 'ORIENTATION': '-', 'GENE_NAME': 'flgL'}]}}}
kevinkle commented 6 years ago 
>>> a.keys()
['ECI-2523_contig234', 'ECI-2523_contig235', 'ECI-2523_contig236', 'ECI-2523_contig237', 'ECI-2523_contig128', 'ECI-2523_contig129', 'ECI-2523_contig232', 'ECI-2523_contig233', 'ECI-2523_contig124', 'ECI-2523_contig125', 'ECI-2523_contig126', 'ECI-2523_contig127', 'ECI-2523_contig120', 'ECI-2523_contig121', 'ECI-2523_contig122', 'ECI-2523_contig123', 'ECI-2523_contig230', 'ECI-2523_contig179', 'ECI-2523_contig231', 'ECI-2523_contig183', 'ECI-2523_contig55', 'ECI-2523_contig54', 'ECI-2523_contig57', 'ECI-2523_contig56', 'ECI-2523_contig51', 'ECI-2523_contig50', 'ECI-2523_contig53', 'ECI-2523_contig52', 'ECI-2523_contig59', 'ECI-2523_contig58', 'ECI-2523_contig9', 'ECI-2523_contig8', 'ECI-2523_contig229', 'ECI-2523_contig228', 'ECI-2523_contig27', 'ECI-2523_contig1', 'ECI-2523_contig238', 'ECI-2523_contig3', 'ECI-2523_contig2', 'ECI-2523_contig5', 'ECI-2523_contig4', 'ECI-2523_contig7', 'ECI-2523_contig239', 'ECI-2523_contig133', 'ECI-2523_contig132', 'ECI-2523_contig131', 'ECI-2523_contig130', 'ECI-2523_contig137', 'ECI-2523_contig136', 'ECI-2523_contig135', 'ECI-2523_contig134', 'ECI-2523_contig139', 'ECI-2523_contig138', 'ECI-2523_contig82', 'ECI-2523_contig83', 'ECI-2523_contig46', 'ECI-2523_contig47', 'ECI-2523_contig44', 'ECI-2523_contig45', 'ECI-2523_contig42', 'ECI-2523_contig43', 'ECI-2523_contig40', 'ECI-2523_contig41', 'ECI-2523_contig26', 'ECI-2523_contig48', 'ECI-2523_contig49', 'ECI-2523_contig119', 'ECI-2523_contig258', 'ECI-2523_contig259', 'ECI-2523_contig256', 'ECI-2523_contig257', 'ECI-2523_contig254', 'ECI-2523_contig252', 'ECI-2523_contig253', 'ECI-2523_contig250', 'ECI-2523_contig251', 'ECI-2523_contig146', 'ECI-2523_contig147', 'ECI-2523_contig144', 'ECI-2523_contig145', 'ECI-2523_contig142', 'ECI-2523_contig143', 'ECI-2523_contig140', 'ECI-2523_contig141', 'ECI-2523_contig88', 'ECI-2523_contig148', 'ECI-2523_contig149', 'ECI-2523_contig89', 'ECI-2523_contig111', 'ECI-2523_contig79', 'ECI-2523_contig78', 'ECI-2523_contig110', 'ECI-2523_contig73', 'ECI-2523_contig72', 'ECI-2523_contig71', 'ECI-2523_contig70', 'ECI-2523_contig77', 'ECI-2523_contig76', 'ECI-2523_contig75', 'ECI-2523_contig74', 'ECI-2523_contig249', 'ECI-2523_contig248', 'ECI-2523_contig185', 'ECI-2523_contig245', 'ECI-2523_contig244', 'ECI-2523_contig247', 'ECI-2523_contig246', 'ECI-2523_contig241', 'ECI-2523_contig240', 'ECI-2523_contig243', 'ECI-2523_contig242', 'ECI-2523_contig91', 'ECI-2523_contig90', 'ECI-2523_contig93', 'ECI-2523_contig92', 'ECI-2523_contig95', 'ECI-2523_contig150', 'ECI-2523_contig97', 'ECI-2523_contig96', 'ECI-2523_contig99', 'ECI-2523_contig98', 'ECI-2523_contig159', 'ECI-2523_contig158', 'ECI-2523_contig155', 'ECI-2523_contig178', 'ECI-2523_contig154', 'ECI-2523_contig157', 'ECI-2523_contig156', 'ECI-2523_contig68', 'ECI-2523_contig69', 'ECI-2523_contig64', 'ECI-2523_contig65', 'ECI-2523_contig66', 'ECI-2523_contig67', 'ECI-2523_contig60', 'ECI-2523_contig61', 'ECI-2523_contig62', 'ECI-2523_contig94', 'ECI-2523_contig22', 'ECI-2523_contig153', 'ECI-2523_contig152', 'ECI-2523_contig108', 'ECI-2523_contig168', 'ECI-2523_contig169', 'ECI-2523_contig80', 'ECI-2523_contig81', 'ECI-2523_contig86', 'ECI-2523_contig87', 'ECI-2523_contig84', 'ECI-2523_contig85', 'ECI-2523_contig160', 'ECI-2523_contig161', 'ECI-2523_contig162', 'ECI-2523_contig163', 'ECI-2523_contig164', 'ECI-2523_contig165', 'ECI-2523_contig166', 'ECI-2523_contig167', 'ECI-2523_contig19', 'ECI-2523_contig18', 'ECI-2523_contig11', 'ECI-2523_contig10', 'ECI-2523_contig13', 'ECI-2523_contig12', 'ECI-2523_contig15', 'ECI-2523_contig14', 'ECI-2523_contig17', 'ECI-2523_contig16', 'ECI-2523_contig100', 'ECI-2523_contig224', 'ECI-2523_contig101', 'ECI-2523_contig200', 'ECI-2523_contig262', 'ECI-2523_contig261', 'ECI-2523_contig260', 'ECI-2523_contig177', 'ECI-2523_contig176', 'ECI-2523_contig175', 'ECI-2523_contig174', 'ECI-2523_contig173', 'ECI-2523_contig172', 'ECI-2523_contig171', 'ECI-2523_contig170', 'ECI-2523_contig151', 'ECI-2523_contig212', 'ECI-2523_contig213', 'ECI-2523_contig210', 'ECI-2523_contig109', 'ECI-2523_contig216', 'ECI-2523_contig217', 'ECI-2523_contig214', 'ECI-2523_contig215', 'ECI-2523_contig102', 'ECI-2523_contig103', 'ECI-2523_contig218', 'ECI-2523_contig219', 'ECI-2523_contig106', 'ECI-2523_contig107', 'ECI-2523_contig104', 'ECI-2523_contig105', 'ECI-2523_contig227', 'ECI-2523_contig23', 'ECI-2523_contig20', 'ECI-2523_contig39', 'ECI-2523_contig38', 'ECI-2523_contig37', 'ECI-2523_contig36', 'ECI-2523_contig35', 'ECI-2523_contig34', 'ECI-2523_contig33', 'ECI-2523_contig32', 'ECI-2523_contig31', 'ECI-2523_contig30', 'ECI-2523_contig182', 'ECI-2523_contig223', 'ECI-2523_contig180', 'ECI-2523_contig181', 'ECI-2523_contig186', 'ECI-2523_contig187', 'ECI-2523_contig184', 'ECI-2523_contig222', 'ECI-2523_contig24', 'ECI-2523_contig188', 'ECI-2523_contig189', 'ECI-2523_contig202', 'ECI-2523_contig221', 'ECI-2523_contig25', 'ECI-2523_contig201', 'ECI-2523_contig118', 'ECI-2523_contig203', 'ECI-2523_contig220', 'ECI-2523_contig205', 'ECI-2523_contig204', 'ECI-2523_contig207', 'ECI-2523_contig206', 'ECI-2523_contig209', 'ECI-2523_contig208', 'ECI-2523_contig113', 'ECI-2523_contig112', 'ECI-2523_contig115', 'ECI-2523_contig114', 'ECI-2523_contig117', 'ECI-2523_contig116', 'ECI-2523_contig28', 'ECI-2523_contig225', 'ECI-2523_contig29', 'ECI-2523_contig6', 'ECI-2523_contig226', 'ECI-2523_contig21', 'ECI-2523_contig191', 'ECI-2523_contig190', 'ECI-2523_contig193', 'ECI-2523_contig192', 'ECI-2523_contig195', 'ECI-2523_contig194', 'ECI-2523_contig197', 'ECI-2523_contig196', 'ECI-2523_contig199', 'ECI-2523_contig198', 'ECI-2523_contig63', 'ECI-2523_contig211']
>>> b.keys()
['GCA_900015695.1_ED647_contigs_genomic']
kevinkle commented 6 years ago 
>>> a['ECI-2523_contig29']
{'Virulence Factors': {}}
>>> a['ECI-2523_contig244']
{'Virulence Factors': {}}
>>> a['ECI-2523_contig235']
{'Virulence Factors': {'lcl|ECI-2523_contig235|': [{'START': 50620, 'STOP': 50653, 'ORIENTATION': '-', 'GENE_NAME': 'entD'}]}}
kevinkle commented 6 years ago

expected behaviour:

>>> d['Virulence Factors']['FAVS01000095.1']
[{'START': 13677, 'STOP': 14732, 'ORIENTATION': '+', 'GENE_NAME': 'hlyE'}, {'START': 13815, 'STOP': 14732, 'ORIENTATION': '+', 'GENE_NAME': 'hlyE'}, {'START': 13821, 'STOP': 14732, 'ORIENTATION': '+', 'GENE_NAME': 'hlyE'}, {'START': 13815, 'STOP': 14732, 'ORIENTATION': '+', 'GENE_NAME': 'hlye'}, {'START': 13821, 'STOP': 14668, 'ORIENTATION': '+', 'GENE_NAME': 'hlyE'}, {'START': 13821, 'STOP': 14331, 'ORIENTATION': '+', 'GENE_NAME': 'hlyE'}, {'START': 14451, 'STOP': 14732, 'ORIENTATION': '+', 'GENE_NAME': 'hlyE'}, {'START': 14472, 'STOP': 14732, 'ORIENTATION': '+', 'GENE_NAME': 'EC958_1421'}, {'START': 2, 'STOP': 237, 'ORIENTATION': '-', 'GENE_NAME': 'fimD'}, {'START': 14451, 'STOP': 14668, 'ORIENTATION': '+', 'GENE_NAME': 'hlyE'}]
kevinkle commented 6 years ago

Fixed in https://github.com/superphy/spfy/pull/320