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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
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report full hit names instead of short names? #302

Closed kevinkle closed 6 years ago

kevinkle commented 6 years ago 
would the full name being in `hit` and the shortname in `description` be the way to go?

chadlaing [11:18 AM]
to me, the longer of the two should be the description
kevinkle commented 6 years ago

note: having different long and short names is prob an edge case. ex:

[
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_1078 # 1156804 # 1158030 # -1 # ID=1_1078;partial=00;start_type=ATG;rbs_motif=GGA;rbs_spacer=5bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "mdtG", 
    "hitorientation": "-", 
    "hitstart": 1156804, 
    "hitstop": 1158030, 
    "longname": "mdtG"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_1090 # 1166658 # 1167866 # -1 # ID=1_1090;partial=00;start_type=ATG;rbs_motif=GGAGG;rbs_spacer=4bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "mdtH", 
    "hitorientation": "-", 
    "hitstart": 1166658, 
    "hitstop": 1167866, 
    "longname": "mdtH"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_1236 # 1319929 # 1320342 # -1 # ID=1_1236;partial=00;start_type=ATG;rbs_motif=GAG;rbs_spacer=9bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "H-NS", 
    "hitorientation": "-", 
    "hitstart": 1319929, 
    "hitstop": 1320342, 
    "longname": "H-NS"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_1506 # 1622774 # 1623208 # 1 # ID=1_1506;partial=00;start_type=GTG;rbs_motif=AGG;rbs_spacer=9bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "Escherichia coli marR mutant conferring antibiotic resistance", 
    "hitorientation": "+", 
    "hitstart": 1622774, 
    "hitstop": 1623208, 
    "longname": "Escherichia coli marR mutant conferring antibiotic resistance"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_1507 # 1623228 # 1623611 # 1 # ID=1_1507;partial=00;start_type=ATG;rbs_motif=GAGG;rbs_spacer=7bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "marA", 
    "hitorientation": "+", 
    "hitstart": 1623228, 
    "hitstop": 1623611, 
    "longname": "marA"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_1756 # 1865670 # 1866083 # -1 # ID=1_1756;partial=00;start_type=ATG;rbs_motif=GAG;rbs_spacer=10bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "msrB", 
    "hitorientation": "-", 
    "hitstart": 1865670, 
    "hitstop": 1866083, 
    "longname": "msrB"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_1991 # 2101383 # 2102549 # -1 # ID=1_1991;partial=00;start_type=ATG;rbs_motif=GAG;rbs_spacer=8bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "PmrE", 
    "hitorientation": "-", 
    "hitstart": 2101383, 
    "hitstop": 2102549, 
    "longname": "PmrE"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2039 # 2156952 # 2158199 # 1 # ID=1_2039;partial=00;start_type=ATG;rbs_motif=GAG;rbs_spacer=12bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "mdtA", 
    "hitorientation": "+", 
    "hitstart": 2156952, 
    "hitstop": 2158199, 
    "longname": "mdtA"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2040 # 2158199 # 2161321 # 1 # ID=1_2040;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=10bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "mdtB", 
    "hitorientation": "+", 
    "hitstart": 2158199, 
    "hitstop": 2161321, 
    "longname": "mdtB"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2041 # 2161322 # 2164399 # 1 # ID=1_2041;partial=00;start_type=GTG;rbs_motif=AGGAG;rbs_spacer=6bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "mdtC", 
    "hitorientation": "+", 
    "hitstart": 2161322, 
    "hitstop": 2164399, 
    "longname": "mdtC"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2043 # 2165812 # 2167215 # 1 # ID=1_2043;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=6bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "baeS", 
    "hitorientation": "+", 
    "hitstart": 2165812, 
    "hitstop": 2167215, 
    "longname": "baeS"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2044 # 2167212 # 2167934 # 1 # ID=1_2044;partial=00;start_type=ATG;rbs_motif=GAG;rbs_spacer=6bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "baeR", 
    "hitorientation": "+", 
    "hitstart": 2167212, 
    "hitstop": 2167934, 
    "longname": "baeR"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2174 # 2309848 # 2311491 # -1 # ID=1_2174;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "YojI", 
    "hitorientation": "-", 
    "hitstart": 2309848, 
    "hitstop": 2311491, 
    "longname": "YojI"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2218 # 2369947 # 2370915 # 1 # ID=1_2218;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=9bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "PmrF", 
    "hitorientation": "+", 
    "hitstart": 2369947, 
    "hitstop": 2370915, 
    "longname": "PmrF"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2219 # 2370915 # 2372897 # 1 # ID=1_2219;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=9bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "arnA", 
    "hitorientation": "+", 
    "hitstart": 2370915, 
    "hitstop": 2372897, 
    "longname": "arnA"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2332 # 2483514 # 2485052 # -1 # ID=1_2332;partial=00;start_type=ATG;rbs_motif=GGA;rbs_spacer=8bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 99.8, 
    "hitname": "emrY", 
    "hitorientation": "-", 
    "hitstart": 2483514, 
    "hitstop": 2485052, 
    "longname": "emrY"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2333 # 2485052 # 2486215 # -1 # ID=1_2333;partial=00;start_type=GTG;rbs_motif=GAG;rbs_spacer=8bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "emrK", 
    "hitorientation": "-", 
    "hitstart": 2485052, 
    "hitstop": 2486215, 
    "longname": "emrK"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2334 # 2486631 # 2487245 # 1 # ID=1_2334;partial=00;start_type=ATG;rbs_motif=GGA;rbs_spacer=7bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "evgA", 
    "hitorientation": "+", 
    "hitstart": 2486631, 
    "hitstop": 2487245, 
    "longname": "evgA"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2335 # 2487250 # 2490843 # 1 # ID=1_2335;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "evgS", 
    "hitorientation": "+", 
    "hitstart": 2487250, 
    "hitstop": 2490843, 
    "longname": "evgS"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2421 # 2583771 # 2586884 # 1 # ID=1_2421;partial=00;start_type=ATG;rbs_motif=GAGG;rbs_spacer=10bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "acrD", 
    "hitorientation": "+", 
    "hitstart": 2583771, 
    "hitstop": 2586884, 
    "longname": "acrD"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2627 # 2807074 # 2807604 # 1 # ID=1_2627;partial=00;start_type=ATG;rbs_motif=GAGG;rbs_spacer=10bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "emrR", 
    "hitorientation": "+", 
    "hitstart": 2807074, 
    "hitstop": 2807604, 
    "longname": "emrR"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2628 # 2807731 # 2808903 # 1 # ID=1_2628;partial=00;start_type=ATG;rbs_motif=GGAG;rbs_spacer=6bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "emrA", 
    "hitorientation": "+", 
    "hitstart": 2807731, 
    "hitstop": 2808903, 
    "longname": "emrA"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2629 # 2808920 # 2810458 # 1 # ID=1_2629;partial=00;start_type=ATG;rbs_motif=GAGG;rbs_spacer=8bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "emrB", 
    "hitorientation": "+", 
    "hitstart": 2808920, 
    "hitstop": 2810458, 
    "longname": "emrB"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2966 # 3174628 # 3176109 # 1 # ID=1_2966;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=6bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "TolC", 
    "hitorientation": "+", 
    "hitstart": 3174628, 
    "hitstop": 3176109, 
    "longname": "TolC"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_2988 # 3199823 # 3200644 # -1 # ID=1_2988;partial=00;start_type=ATG;rbs_motif=AGG;rbs_spacer=9bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "bacA", 
    "hitorientation": "-", 
    "hitstart": 3199823, 
    "hitstop": 3200644, 
    "longname": "bacA"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_3004 # 3215895 # 3217385 # 1 # ID=1_3004;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 99.78, 
    "hitname": "patA", 
    "hitorientation": "+", 
    "hitstart": 3215895, 
    "hitstop": 3217385, 
    "longname": "patA"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_3187 # 3409315 # 3409977 # -1 # ID=1_3187;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "AcrS", 
    "hitorientation": "-", 
    "hitstart": 3409315, 
    "hitstop": 3409977, 
    "longname": "AcrS"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_3188 # 3410376 # 3411533 # 1 # ID=1_3188;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=6bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "AcrE", 
    "hitorientation": "+", 
    "hitstart": 3410376, 
    "hitstop": 3411533, 
    "longname": "AcrE"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_3189 # 3411545 # 3414649 # 1 # ID=1_3189;partial=00;start_type=ATG;rbs_motif=AGG;rbs_spacer=9bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "AcrF", 
    "hitorientation": "+", 
    "hitstart": 3411545, 
    "hitstop": 3414649, 
    "longname": "AcrF"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_3278 # 3482632 # 3483264 # 1 # ID=1_3278;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=9bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 98.57, 
    "hitname": "CRP", 
    "hitorientation": "+", 
    "hitstart": 3482632, 
    "hitstop": 3483264, 
    "longname": "CRP"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_3434 # 3655745 # 3656902 # 1 # ID=1_3434;partial=00;start_type=ATG;rbs_motif=GGA;rbs_spacer=5bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "mdtE", 
    "hitorientation": "+", 
    "hitstart": 3655745, 
    "hitstop": 3656902, 
    "longname": "mdtE"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_3435 # 3656927 # 3660040 # 1 # ID=1_3435;partial=00;start_type=ATG;rbs_motif=GGA;rbs_spacer=5bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "mdtF", 
    "hitorientation": "+", 
    "hitstart": 3656927, 
    "hitstop": 3660040, 
    "longname": "mdtF"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_3436 # 3660403 # 3661131 # -1 # ID=1_3436;partial=00;start_type=ATG;rbs_motif=GGA;rbs_spacer=5bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 94.63, 
    "hitname": "gadW", 
    "hitorientation": "-", 
    "hitstart": 3660403, 
    "hitstop": 3661131, 
    "longname": "gadW"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_3437 # 3661499 # 3662323 # -1 # ID=1_3437;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "gadX", 
    "hitorientation": "-", 
    "hitstart": 3661499, 
    "hitstop": 3662323, 
    "longname": "gadX"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_3600 # 3850434 # 3851618 # 1 # ID=1_3600;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 99.49, 
    "hitname": "emrD", 
    "hitorientation": "+", 
    "hitstart": 3850434, 
    "hitstop": 3851618, 
    "longname": "emrD"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_3825 # 4100075 # 4101448 # -1 # ID=1_3825;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "cpxA", 
    "hitorientation": "-", 
    "hitstart": 4100075, 
    "hitstop": 4101448, 
    "longname": "cpxA"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_3972 # 4273533 # 4273856 # -1 # ID=1_3972;partial=00;start_type=ATG;rbs_motif=GAGG;rbs_spacer=7bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "Escherichia coli soxS with mutation conferring antibiotic resistance", 
    "hitorientation": "-", 
    "hitstart": 4273533, 
    "hitstop": 4273856, 
    "longname": "Escherichia coli soxS with mutation conferring antibiotic resistance"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_3973 # 4273942 # 4274406 # 1 # ID=1_3973;partial=00;start_type=ATG;rbs_motif=AGG;rbs_spacer=11bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "Escherichia coli soxR with mutation conferring antibiotic resistance", 
    "hitorientation": "+", 
    "hitstart": 4273942, 
    "hitstop": 4274406, 
    "longname": "Escherichia coli soxR with mutation conferring antibiotic resistance"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_3991 # 4296037 # 4297503 # -1 # ID=1_3991;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=7bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "mdtP", 
    "hitorientation": "-", 
    "hitstart": 4296037, 
    "hitstop": 4297503, 
    "longname": "mdtP"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_3992 # 4297500 # 4299551 # -1 # ID=1_3992;partial=00;start_type=ATG;rbs_motif=GAG;rbs_spacer=8bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "mdtO", 
    "hitorientation": "-", 
    "hitstart": 4297500, 
    "hitstop": 4299551, 
    "longname": "mdtO"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_3993 # 4299551 # 4300582 # -1 # ID=1_3993;partial=00;start_type=ATG;rbs_motif=GAG;rbs_spacer=8bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "mdtN", 
    "hitorientation": "-", 
    "hitstart": 4299551, 
    "hitstop": 4300582, 
    "longname": "mdtN"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_4026 # 4330420 # 4332063 # -1 # ID=1_4026;partial=00;start_type=ATG;rbs_motif=GGA;rbs_spacer=9bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "PmrC", 
    "hitorientation": "-", 
    "hitstart": 4330420, 
    "hitstop": 4332063, 
    "longname": "PmrC"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_4063 # 4374285 # 4375418 # -1 # ID=1_4063;partial=00;start_type=ATG;rbs_motif=GGA;rbs_spacer=11bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "Escherichia coli ampC beta-lactamase", 
    "hitorientation": "-", 
    "hitstart": 4374285, 
    "hitstop": 4375418, 
    "longname": "Escherichia coli ampC beta-lactamase"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_4248 # 4563761 # 4564993 # -1 # ID=1_4248;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=9bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "mdtM", 
    "hitorientation": "-", 
    "hitstart": 4563761, 
    "hitstop": 4564993, 
    "longname": "mdtM"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_449 # 480553 # 483702 # -1 # ID=1_449;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=10bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "acrB", 
    "hitorientation": "-", 
    "hitstart": 480553, 
    "hitstop": 483702, 
    "longname": "acrB"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_450 # 483725 # 484918 # -1 # ID=1_450;partial=00;start_type=ATG;rbs_motif=GAGG;rbs_spacer=7bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "Escherichia coli acrA", 
    "hitorientation": "-", 
    "hitstart": 483725, 
    "hitstop": 484918, 
    "longname": "Escherichia coli acrA"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_451 # 485060 # 485707 # 1 # ID=1_451;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "Escherichia coli acrR with mutation conferring multidrug antibiotic resistance", 
    "hitorientation": "+", 
    "hitstart": 485060, 
    "hitstop": 485707, 
    "longname": "Escherichia coli acrR with mutation conferring multidrug antibiotic resistance"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_526 # 567614 # 567946 # 1 # ID=1_526;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=11bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 100.0, 
    "hitname": "Escherichia coli emrE", 
    "hitorientation": "+", 
    "hitstart": 567614, 
    "hitstop": 567946, 
    "longname": "Escherichia coli emrE"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_670 # 717997 # 718674 # -1 # ID=1_670;partial=00;start_type=GTG;rbs_motif=GAGGA;rbs_spacer=3bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 99.56, 
    "hitname": "kdpE", 
    "hitorientation": "-", 
    "hitstart": 717997, 
    "hitstop": 718674, 
    "longname": "kdpE"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_762 # 814586 # 814786 # 1 # ID=1_762;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 29.41, 
    "hitname": "AAC(3)", 
    "hitorientation": "+", 
    "hitstart": 814586, 
    "hitstop": 814786, 
    "longname": "AAC(3)-IIb"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_82 # 91581 # 93347 # 1 # ID=1_82;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=12bp;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 53.11, 
    "hitname": "Haemophilus influenzae PBP3 conferring resistance to beta-lactam antibiotics", 
    "hitorientation": "+", 
    "hitstart": 91581, 
    "hitstop": 93347, 
    "longname": "Haemophilus influenzae PBP3 conferring resistance to beta-lactam antibiotics"
  }, 
  {
    "analysis": "Antimicrobial Resistance", 
    "contigid": "LT615373.1_870 # 926045 # 927277 # 1 # ID=1_870;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic.fna", 
    "hitcutoff": 97.07, 
    "hitname": "Escherichia coli mdfA", 
    "hitorientation": "+", 
    "hitstart": 926045, 
    "hitstop": 927277, 
    "longname": "Escherichia coli mdfA"
  }, 
  {
    "analysis": "Serotype", 
    "contigid": "n/a", 
    "filename": "GCA_900096815.1_Ecoli_AG100_Sample2_M9_Assembly_genomic", 
    "hitcutoff": "90", 
    "hitname": "O16:H48", 
    "hitorientation": "n/a", 
    "hitstart": "n/a", 
    "hitstop": "n/a", 
    "probability": "n/a"
  },
kevinkle commented 6 years ago

done in https://github.com/superphy/spfy/pull/306