In [1]:
from om import base
from om.components import *
from om.data import *
from unittest import TestCase, TestLoader, TextTestRunner
ome = base.Session()
In [3]:
cpge = ChIPPeakGeneExpression
ome.query(cpge).filter(and_(cpge.expression_value < 0, cpge.pval < .05,
cpge.carbon_source.in_(['fructose','glycerol']))).all()
Out[3]:
[TF: Crp, Gene: yaiY, b0379, -1.67, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 398681-398882 value:9968.70,
TF: Crp, Gene: yaiY, b0379, -1.67, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 398711-398912 value:38234.30,
TF: Crp, Gene: entC, b0593, -4.21, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 628991-629192 value:5808.00,
TF: Crp, Gene: insH1, b0552, -inf, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 575989-576190 value:9718.00,
TF: Crp, Gene: entE, b0594, -4.39, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 628991-629192 value:5808.00,
TF: Crp, Gene: tam, b1519, -1.77, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 1608651-1608852 value:4410.00,
TF: Crp, Gene: mdtB, b2075, -0.70, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 2165034-2165235 value:14879.00,
TF: Crp, Gene: mdtB, b2075, -0.70, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 2165022-2165223 value:10754.40,
TF: Crp, Gene: mdtB, b2075, -0.70, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 2165042-2165243 value:17703.60,
TF: Crp, Gene: mdtB, b2075, -0.70, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 2151571-2151772 value:8320.00,
TF: Crp, Gene: cdd, b2143, -0.65, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 2229675-2229876 value:8384.00,
TF: Crp, Gene: bcp, b2480, -0.69, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 2598914-2599115 value:6163.00,
TF: Crp, Gene: guaB, b2508, -1.38, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2632105-2632306 value:9194.50,
TF: Crp, Gene: guaB, b2508, -1.38, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2632129-2632330 value:4874.50,
TF: Crp, Gene: glnB, b2553, -0.73, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2685353-2685554 value:4657.00,
TF: Crp, Gene: nlpD, b2742, -0.83, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2866029-2866230 value:6459.00,
TF: Crp, Gene: fbaA, b2925, -0.71, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3071738-3071939 value:5903.00,
TF: Crp, Gene: mutY, b2961, -0.75, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3103505-3103706 value:10829.90,
TF: Crp, Gene: mutY, b2961, -0.75, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3103580-3103781 value:3839.10,
TF: Crp, Gene: mltC, b2963, -0.69, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3103505-3103706 value:10829.90,
TF: Crp, Gene: mltC, b2963, -0.69, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3103580-3103781 value:3839.10,
TF: Crp, Gene: exbB, b3006, -1.53, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3151460-3151661 value:5551.00,
TF: Crp, Gene: rpoS, b2741, -1.23, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2866029-2866230 value:6459.00,
TF: Crp, Gene: exbD, b3005, -1.49, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3151460-3151661 value:5551.00,
TF: Crp, Gene: deaD, b3162, -0.47, 0.02 Condition: glycerol, NH4Cl, O2 Peak: 3305905-3306106 value:5864.00,
TF: Crp, Gene: hslR, b3400, -0.82, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3530722-3530923 value:7161.00,
TF: Crp, Gene: glpR, b3423, -0.56, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 3559902-3560103 value:5143.00,
TF: Crp, Gene: panM, b3459, -1.11, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3598766-3598967 value:10877.50,
TF: Crp, Gene: panM, b3459, -1.11, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3598786-3598987 value:5475.50,
TF: Crp, Gene: rpoH, b3461, -0.73, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3598766-3598967 value:10877.50,
TF: Crp, Gene: rpoH, b3461, -0.73, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3598786-3598987 value:5475.50,
TF: Crp, Gene: treF, b3519, -3.01, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3667366-3667567 value:4329.00,
TF: Crp, Gene: hpf, b3203, -1.49, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3348506-3348707 value:13355.00,
TF: Crp, Gene: hslO, b3401, -1.03, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3530722-3530923 value:7161.00,
TF: Crp, Gene: udp, b3831, -0.50, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 4014322-4014523 value:5458.20,
TF: Crp, Gene: udp, b3831, -0.50, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 4014246-4014447 value:16854.80,
TF: Crp, Gene: ilvM, b3769, -1.56, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3948329-3948530 value:6923.00,
TF: Crp, Gene: ilvD, b3771, -1.16, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3948329-3948530 value:6923.00,
TF: Crp, Gene: ytfB, b4206, -0.86, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 4427527-4427728 value:5120.00,
TF: Crp, Gene: osmY, b4376, -4.49, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 4609227-4609428 value:10399.00,
TF: Crp, Gene: deoC, b4381, -1.92, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 4615165-4615366 value:5679.40,
TF: Crp, Gene: deoC, b4381, -1.92, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 4615133-4615334 value:8743.60,
TF: Crp, Gene: deoB, b4383, -1.50, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 4615165-4615366 value:5679.40,
TF: Crp, Gene: deoB, b4383, -1.50, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 4615133-4615334 value:8743.60,
TF: Crp, Gene: yibT, b4554, -1.94, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 3775247-3775448 value:5468.00,
TF: Crp, Gene: metN, b0199, -0.64, 0.01 Condition: fructose, NH4Cl, O2 Peak: 223356-223557 value:9664.00,
TF: Crp, Gene: nrdR, b0413, -0.66, 0.00 Condition: fructose, NH4Cl, O2 Peak: 431272-431473 value:9414.00,
TF: Crp, Gene: yaiY, b0379, -2.89, 0.00 Condition: fructose, NH4Cl, O2 Peak: 398680-398881 value:19020.80,
TF: Crp, Gene: yaiY, b0379, -2.89, 0.00 Condition: fructose, NH4Cl, O2 Peak: 398709-398910 value:67414.20,
TF: Crp, Gene: ddlA, b0381, -0.57, 0.01 Condition: fructose, NH4Cl, O2 Peak: 400227-400428 value:4497.70,
TF: Crp, Gene: ddlA, b0381, -0.57, 0.01 Condition: fructose, NH4Cl, O2 Peak: 398680-398881 value:19020.80,
TF: Crp, Gene: ddlA, b0381, -0.57, 0.01 Condition: fructose, NH4Cl, O2 Peak: 400185-400386 value:5584.30,
TF: Crp, Gene: ddlA, b0381, -0.57, 0.01 Condition: fructose, NH4Cl, O2 Peak: 398709-398910 value:67414.20,
TF: Crp, Gene: insH1, b0552, -inf, 0.00 Condition: fructose, NH4Cl, O2 Peak: 575988-576189 value:11681.00,
TF: Crp, Gene: entE, b0594, -0.45, 0.03 Condition: fructose, NH4Cl, O2 Peak: 628990-629191 value:6455.00,
TF: Crp, Gene: lsrF, b1517, -0.99, 0.00 Condition: fructose, NH4Cl, O2 Peak: 1608651-1608852 value:5234.00,
TF: Crp, Gene: tam, b1519, -1.07, 0.00 Condition: fructose, NH4Cl, O2 Peak: 1608651-1608852 value:5234.00,
TF: Crp, Gene: mdtB, b2075, -0.72, 0.01 Condition: fructose, NH4Cl, O2 Peak: 2165034-2165235 value:11287.90,
TF: Crp, Gene: mdtB, b2075, -0.72, 0.01 Condition: fructose, NH4Cl, O2 Peak: 2165022-2165223 value:10145.00,
TF: Crp, Gene: mdtB, b2075, -0.72, 0.01 Condition: fructose, NH4Cl, O2 Peak: 2165042-2165243 value:17084.00,
TF: Crp, Gene: mdtB, b2075, -0.72, 0.01 Condition: fructose, NH4Cl, O2 Peak: 2151570-2151771 value:7302.00,
TF: Crp, Gene: cdd, b2143, -1.32, 0.00 Condition: fructose, NH4Cl, O2 Peak: 2229675-2229876 value:11425.00,
TF: Crp, Gene: nlpD, b2742, -1.40, 0.00 Condition: fructose, NH4Cl, O2 Peak: 2866030-2866231 value:6731.00,
TF: Crp, Gene: guaB, b2508, -1.41, 0.00 Condition: fructose, NH4Cl, O2 Peak: 2632105-2632306 value:12036.00,
TF: Crp, Gene: rpoS, b2741, -1.49, 0.00 Condition: fructose, NH4Cl, O2 Peak: 2866030-2866231 value:6731.00,
TF: Crp, Gene: mutY, b2961, -0.53, 0.01 Condition: fructose, NH4Cl, O2 Peak: 3103505-3103706 value:16925.00,
TF: Crp, Gene: mltC, b2963, -0.49, 0.02 Condition: fructose, NH4Cl, O2 Peak: 3103505-3103706 value:16925.00,
TF: Crp, Gene: hpf, b3203, -1.21, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3348507-3348708 value:8274.00,
TF: Crp, Gene: livJ, b3460, -0.74, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3598829-3599030 value:4175.70,
TF: Crp, Gene: livJ, b3460, -0.74, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3598786-3598987 value:6495.80,
TF: Crp, Gene: livJ, b3460, -0.74, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3598760-3598961 value:12763.50,
TF: Crp, Gene: ilvD, b3771, -0.91, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3948328-3948529 value:8686.00,
TF: Crp, Gene: glpK, b3926, -2.39, 0.00 Condition: fructose, NH4Cl, O2 Peak: 4115765-4115966 value:13025.00,
TF: Crp, Gene: ytfH, b4212, -0.87, 0.02 Condition: fructose, NH4Cl, O2 Peak: 4434544-4434745 value:6503.00,
TF: Crp, Gene: deoC, b4381, -1.72, 0.00 Condition: fructose, NH4Cl, O2 Peak: 4615165-4615366 value:7955.30,
TF: Crp, Gene: deoC, b4381, -1.72, 0.00 Condition: fructose, NH4Cl, O2 Peak: 4615133-4615334 value:14764.70,
TF: Crp, Gene: deoB, b4383, -1.72, 0.00 Condition: fructose, NH4Cl, O2 Peak: 4615165-4615366 value:7955.30,
TF: Crp, Gene: deoB, b4383, -1.72, 0.00 Condition: fructose, NH4Cl, O2 Peak: 4615133-4615334 value:14764.70,
TF: Crp, Gene: osmY, b4376, -3.44, 0.00 Condition: fructose, NH4Cl, O2 Peak: 4609228-4609429 value:15395.00,
TF: Crp, Gene: thrB, b0003, -0.52, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 70-271 value:5668.50,
TF: Crp, Gene: thrB, b0003, -0.52, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 170-371 value:3400.50,
TF: Crp, Gene: psiF, b0384, -2.36, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 400185-400386 value:7335.00,
TF: Crp, Gene: thrA, b0002, -0.65, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 70-271 value:5668.50,
TF: Crp, Gene: thrA, b0002, -0.65, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 170-371 value:3400.50,
TF: Crp, Gene: yaiW, b0378, -0.83, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 398681-398882 value:9968.70,
TF: Crp, Gene: yaiW, b0378, -0.83, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 398711-398912 value:38234.30,
TF: Crp, Gene: entB, b0595, -4.65, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 628991-629192 value:5808.00,
TF: Crp, Gene: entH, b0597, -4.21, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 628991-629192 value:5808.00,
TF: Crp, Gene: aroG, b0754, -0.86, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 784636-784837 value:12668.00,
TF: Crp, Gene: entA, b0596, -4.43, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 628991-629192 value:5808.00,
TF: Crp, Gene: pagP, b0622, -1.19, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 656341-656542 value:10022.40,
TF: Crp, Gene: pagP, b0622, -1.19, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 656382-656583 value:25806.40,
TF: Crp, Gene: pagP, b0622, -1.19, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 656494-656695 value:7505.20,
TF: Crp, Gene: fldA, b0684, -0.77, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 709834-710035 value:6641.00,
TF: Crp, Gene: ldtB, b0819, -1.05, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 855060-855261 value:7996.00,
TF: Crp, Gene: clpA, b0882, -1.14, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 921962-922163 value:7964.00,
TF: Crp, Gene: tonB, b1252, -1.51, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 1311925-1312126 value:4794.00,
TF: Crp, Gene: ynfE, b1587, -0.54, 0.02 Condition: glycerol, NH4Cl, O2 Peak: 1665330-1665531 value:5461.40,
TF: Crp, Gene: ynfE, b1587, -0.54, 0.02 Condition: glycerol, NH4Cl, O2 Peak: 1665304-1665505 value:6801.60,
TF: Crp, Gene: spy, b1743, -1.35, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 1823069-1823270 value:3008.00,
TF: Crp, Gene: ynfG, b1589, -0.82, 0.03 Condition: glycerol, NH4Cl, O2 Peak: 1665330-1665531 value:5461.40,
TF: Crp, Gene: ynfG, b1589, -0.82, 0.03 Condition: glycerol, NH4Cl, O2 Peak: 1665304-1665505 value:6801.60,
TF: Crp, Gene: pfkB, b1723, -1.83, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 1805704-1805905 value:2840.00,
TF: Crp, Gene: gapA, b1779, -0.60, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 1860382-1860583 value:4451.60,
TF: Crp, Gene: gapA, b1779, -0.60, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 1860538-1860739 value:10124.30,
TF: Crp, Gene: gapA, b1779, -0.60, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 1860525-1860726 value:14053.10,
TF: Crp, Gene: mdtD, b2077, -1.29, 0.02 Condition: glycerol, NH4Cl, O2 Peak: 2165034-2165235 value:14879.00,
TF: Crp, Gene: mdtD, b2077, -1.29, 0.02 Condition: glycerol, NH4Cl, O2 Peak: 2165022-2165223 value:10754.40,
TF: Crp, Gene: mdtD, b2077, -1.29, 0.02 Condition: glycerol, NH4Cl, O2 Peak: 2151571-2151772 value:8320.00,
TF: Crp, Gene: mdtD, b2077, -1.29, 0.02 Condition: glycerol, NH4Cl, O2 Peak: 2165042-2165243 value:17703.60,
TF: Crp, Gene: baeR, b2079, -1.18, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2165034-2165235 value:14879.00,
TF: Crp, Gene: baeR, b2079, -1.18, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2165022-2165223 value:10754.40,
TF: Crp, Gene: baeR, b2079, -1.18, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2151571-2151772 value:8320.00,
TF: Crp, Gene: baeR, b2079, -1.18, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2165042-2165243 value:17703.60,
TF: Crp, Gene: mdtA, b2074, -1.24, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2165034-2165235 value:14879.00,
TF: Crp, Gene: mdtA, b2074, -1.24, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2165022-2165223 value:10754.40,
TF: Crp, Gene: mdtA, b2074, -1.24, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2151571-2151772 value:8320.00,
TF: Crp, Gene: mdtA, b2074, -1.24, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2165042-2165243 value:17703.60,
TF: Crp, Gene: mdtC, b2076, -0.74, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2165034-2165235 value:14879.00,
TF: Crp, Gene: mdtC, b2076, -0.74, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2165022-2165223 value:10754.40,
TF: Crp, Gene: mdtC, b2076, -0.74, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2151571-2151772 value:8320.00,
TF: Crp, Gene: mdtC, b2076, -0.74, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2165042-2165243 value:17703.60,
TF: Crp, Gene: baeS, b2078, -1.25, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2165034-2165235 value:14879.00,
TF: Crp, Gene: baeS, b2078, -1.25, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2165022-2165223 value:10754.40,
TF: Crp, Gene: baeS, b2078, -1.25, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2151571-2151772 value:8320.00,
TF: Crp, Gene: baeS, b2078, -1.25, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2165042-2165243 value:17703.60,
TF: Crp, Gene: gcvR, b2479, -1.11, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2598914-2599115 value:6163.00,
TF: Crp, Gene: hyfI, b2489, -0.77, 0.04 Condition: glycerol, NH4Cl, O2 Peak: 2598914-2599115 value:6163.00,
TF: Crp, Gene: guaA, b2507, -1.04, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2632105-2632306 value:9194.50,
TF: Crp, Gene: guaA, b2507, -1.04, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2632129-2632330 value:4874.50,
TF: Crp, Gene: xseA, b2509, -1.11, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2632105-2632306 value:9194.50,
TF: Crp, Gene: xseA, b2509, -1.11, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2632129-2632330 value:4874.50,
TF: Crp, Gene: hmp, b2552, -1.25, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2685353-2685554 value:4657.00,
TF: Crp, Gene: yfiF, b2581, -0.57, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2717860-2718061 value:9748.00,
TF: Crp, Gene: mntH, b2392, -2.32, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2510864-2511065 value:3072.70,
TF: Crp, Gene: mntH, b2392, -2.32, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2510919-2511120 value:4154.30,
TF: Crp, Gene: crr, b2417, -0.93, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2531429-2531630 value:15632.10,
TF: Crp, Gene: crr, b2417, -0.93, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2531298-2531499 value:10995.30,
TF: Crp, Gene: crr, b2417, -0.93, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2531388-2531589 value:8695.30,
TF: Crp, Gene: crr, b2417, -0.93, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2531467-2531668 value:10556.30,
TF: Crp, Gene: yffP, b2447, -1.07, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 2561314-2561515 value:3185.70,
TF: Crp, Gene: yffP, b2447, -1.07, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 2561335-2561536 value:6335.30,
TF: Crp, Gene: pheA, b2599, -0.66, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2734887-2735088 value:8117.90,
TF: Crp, Gene: pheA, b2599, -0.66, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2735054-2735255 value:34869.10,
TF: Crp, Gene: pheA, b2599, -0.66, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 2735031-2735232 value:14952.00,
TF: Crp, Gene: yggN, b2958, -0.67, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3098843-3099044 value:6534.00,
TF: Crp, Gene: zupT, b3040, -1.13, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3182628-3182829 value:5611.00,
TF: Crp, Gene: yggX, b2962, -0.62, 0.02 Condition: glycerol, NH4Cl, O2 Peak: 3103580-3103781 value:3839.10,
TF: Crp, Gene: yggX, b2962, -0.62, 0.02 Condition: glycerol, NH4Cl, O2 Peak: 3103505-3103706 value:10829.90,
TF: Crp, Gene: rpoN, b3202, -0.50, 0.01 Condition: glycerol, NH4Cl, O2 Peak: 3348506-3348707 value:13355.00,
TF: Crp, Gene: ptsN, b3204, -1.04, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3348506-3348707 value:13355.00,
TF: Crp, Gene: yrbL, b3207, -0.86, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3348506-3348707 value:13355.00,
TF: Crp, Gene: fic, b3361, -2.41, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3490445-3490646 value:3937.60,
TF: Crp, Gene: fic, b3361, -2.41, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3490395-3490596 value:10038.60,
TF: Crp, Gene: fic, b3361, -2.41, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3490383-3490584 value:15508.30,
TF: Crp, Gene: fic, b3361, -2.41, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3490508-3490709 value:6215.50,
TF: Crp, Gene: lptB, b3201, -0.67, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3348506-3348707 value:13355.00,
TF: Crp, Gene: yhbJ, b3205, -0.73, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3348506-3348707 value:13355.00,
TF: Crp, Gene: pabA, b3360, -0.79, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3490445-3490646 value:3937.60,
TF: Crp, Gene: pabA, b3360, -0.79, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3490395-3490596 value:10038.60,
TF: Crp, Gene: pabA, b3360, -0.79, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3490383-3490584 value:15508.30,
TF: Crp, Gene: pabA, b3360, -0.79, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3490508-3490709 value:6215.50,
TF: Crp, Gene: yifE, b3764, -0.42, 0.04 Condition: glycerol, NH4Cl, O2 Peak: 3948329-3948530 value:6923.00,
TF: Crp, Gene: ilvE, b3770, -1.09, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3948329-3948530 value:6923.00,
TF: Crp, Gene: ilvA, b3772, -0.94, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3948329-3948530 value:6923.00,
TF: Crp, Gene: tufB, b3980, -5.39, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 4173309-4173510 value:7655.00,
TF: Crp, Gene: nepI, b3662, -1.89, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 3839688-3839889 value:7657.00,
TF: Crp, Gene: ysgA, b3830, -1.04, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 4014246-4014447 value:16854.80,
TF: Crp, Gene: ysgA, b3830, -1.04, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 4014322-4014523 value:5458.20,
TF: Crp, Gene: tyrB, b4054, -0.82, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 4267312-4267513 value:10862.00,
TF: Crp, Gene: deoA, b4382, -1.89, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 4615133-4615334 value:8743.60,
TF: Crp, Gene: deoA, b4382, -1.89, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 4615165-4615366 value:5679.40,
TF: Crp, Gene: deoD, b4384, -0.59, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 4615133-4615334 value:8743.60,
TF: Crp, Gene: deoD, b4384, -0.59, 0.00 Condition: glycerol, NH4Cl, O2 Peak: 4615165-4615366 value:5679.40,
TF: Crp, Gene: yjiR, b4340, -0.53, 0.02 Condition: glycerol, NH4Cl, O2 Peak: 4570068-4570269 value:4234.80,
TF: Crp, Gene: yjiR, b4340, -0.53, 0.02 Condition: glycerol, NH4Cl, O2 Peak: 4570093-4570294 value:3190.20,
TF: Crp, Gene: yicS, b4555, -1.66, 0.04 Condition: glycerol, NH4Cl, O2 Peak: 3839688-3839889 value:7657.00,
TF: Crp, Gene: thrB, b0003, -0.62, 0.00 Condition: fructose, NH4Cl, O2 Peak: 69-270 value:10116.00,
TF: Crp, Gene: thrA, b0002, -0.86, 0.00 Condition: fructose, NH4Cl, O2 Peak: 69-270 value:10116.00,
TF: Crp, Gene: caiB, b0038, -0.93, 0.00 Condition: fructose, NH4Cl, O2 Peak: 42217-42418 value:8746.20,
TF: Crp, Gene: caiB, b0038, -0.93, 0.00 Condition: fructose, NH4Cl, O2 Peak: 42101-42302 value:12967.70,
TF: Crp, Gene: caiB, b0038, -0.93, 0.00 Condition: fructose, NH4Cl, O2 Peak: 42085-42286 value:7966.50,
TF: Crp, Gene: caiB, b0038, -0.93, 0.00 Condition: fructose, NH4Cl, O2 Peak: 42004-42205 value:8780.00,
TF: Crp, Gene: caiB, b0038, -0.93, 0.00 Condition: fructose, NH4Cl, O2 Peak: 41967-42168 value:10815.00,
TF: Crp, Gene: caiB, b0038, -0.93, 0.00 Condition: fructose, NH4Cl, O2 Peak: 41931-42132 value:13650.90,
TF: Crp, Gene: caiB, b0038, -0.93, 0.00 Condition: fructose, NH4Cl, O2 Peak: 41843-42044 value:9514.50,
TF: Crp, Gene: caiB, b0038, -0.93, 0.00 Condition: fructose, NH4Cl, O2 Peak: 42140-42341 value:8614.20,
TF: Crp, Gene: dnaQ, b0215, -0.74, 0.00 Condition: fructose, NH4Cl, O2 Peak: 236817-237018 value:7904.00,
TF: Crp, Gene: yaiW, b0378, -0.82, 0.00 Condition: fructose, NH4Cl, O2 Peak: 398680-398881 value:19020.80,
TF: Crp, Gene: yaiW, b0378, -0.82, 0.00 Condition: fructose, NH4Cl, O2 Peak: 398709-398910 value:67414.20,
TF: Crp, Gene: psiF, b0384, -2.21, 0.00 Condition: fructose, NH4Cl, O2 Peak: 400227-400428 value:4497.70,
TF: Crp, Gene: psiF, b0384, -2.21, 0.00 Condition: fructose, NH4Cl, O2 Peak: 400185-400386 value:5584.30,
TF: Crp, Gene: pgpA, b0418, -0.81, 0.01 Condition: fructose, NH4Cl, O2 Peak: 431272-431473 value:9414.00,
TF: Crp, Gene: entB, b0595, -0.86, 0.01 Condition: fructose, NH4Cl, O2 Peak: 628990-629191 value:6455.00,
TF: Crp, Gene: pagP, b0622, -1.95, 0.00 Condition: fructose, NH4Cl, O2 Peak: 656341-656542 value:6916.70,
TF: Crp, Gene: pagP, b0622, -1.95, 0.00 Condition: fructose, NH4Cl, O2 Peak: 656382-656583 value:25477.30,
TF: Crp, Gene: flc, b0624, -1.02, 0.00 Condition: fructose, NH4Cl, O2 Peak: 656341-656542 value:6916.70,
TF: Crp, Gene: flc, b0624, -1.02, 0.00 Condition: fructose, NH4Cl, O2 Peak: 656382-656583 value:25477.30,
TF: Crp, Gene: sbmA, b0377, -0.89, 0.00 Condition: fructose, NH4Cl, O2 Peak: 398680-398881 value:19020.80,
TF: Crp, Gene: sbmA, b0377, -0.89, 0.00 Condition: fructose, NH4Cl, O2 Peak: 398709-398910 value:67414.20,
TF: Crp, Gene: thiL, b0417, -0.97, 0.01 Condition: fructose, NH4Cl, O2 Peak: 431272-431473 value:9414.00,
TF: Crp, Gene: entA, b0596, -0.78, 0.02 Condition: fructose, NH4Cl, O2 Peak: 628990-629191 value:6455.00,
TF: Crp, Gene: ybeZ, b0660, -0.88, 0.00 Condition: fructose, NH4Cl, O2 Peak: 688285-688486 value:3478.00,
TF: Crp, Gene: ldtB, b0819, -0.78, 0.00 Condition: fructose, NH4Cl, O2 Peak: 855044-855245 value:6469.00,
TF: Crp, Gene: macB, b0879, -0.66, 0.03 Condition: fructose, NH4Cl, O2 Peak: 921963-922164 value:5576.00,
TF: Crp, Gene: clpA, b0882, -1.68, 0.00 Condition: fructose, NH4Cl, O2 Peak: 921963-922164 value:5576.00,
TF: Crp, Gene: lsrG, b1518, -1.56, 0.01 Condition: fructose, NH4Cl, O2 Peak: 1608651-1608852 value:5234.00,
TF: Crp, Gene: ynfE, b1587, -0.52, 0.04 Condition: fructose, NH4Cl, O2 Peak: 1665330-1665531 value:12193.10,
TF: Crp, Gene: ynfE, b1587, -0.52, 0.04 Condition: fructose, NH4Cl, O2 Peak: 1665303-1665504 value:6329.90,
TF: Crp, Gene: ynfF, b1588, -0.70, 0.00 Condition: fructose, NH4Cl, O2 Peak: 1665330-1665531 value:12193.10,
TF: Crp, Gene: ynfF, b1588, -0.70, 0.00 Condition: fructose, NH4Cl, O2 Peak: 1665303-1665504 value:6329.90,
TF: Crp, Gene: mdtD, b2077, -1.07, 0.02 Condition: fructose, NH4Cl, O2 Peak: 2165034-2165235 value:11287.90,
TF: Crp, Gene: mdtD, b2077, -1.07, 0.02 Condition: fructose, NH4Cl, O2 Peak: 2165022-2165223 value:10145.00,
TF: Crp, Gene: mdtD, b2077, -1.07, 0.02 Condition: fructose, NH4Cl, O2 Peak: 2151570-2151771 value:7302.00,
TF: Crp, Gene: mdtD, b2077, -1.07, 0.02 Condition: fructose, NH4Cl, O2 Peak: 2165042-2165243 value:17084.00,
TF: Crp, Gene: baeR, b2079, -1.35, 0.00 Condition: fructose, NH4Cl, O2 Peak: 2165034-2165235 value:11287.90,
TF: Crp, Gene: baeR, b2079, -1.35, 0.00 Condition: fructose, NH4Cl, O2 Peak: 2165022-2165223 value:10145.00,
TF: Crp, Gene: baeR, b2079, -1.35, 0.00 Condition: fructose, NH4Cl, O2 Peak: 2151570-2151771 value:7302.00,
TF: Crp, Gene: baeR, b2079, -1.35, 0.00 Condition: fructose, NH4Cl, O2 Peak: 2165042-2165243 value:17084.00,
TF: Crp, Gene: mdtA, b2074, -0.99, 0.01 Condition: fructose, NH4Cl, O2 Peak: 2165034-2165235 value:11287.90,
TF: Crp, Gene: mdtA, b2074, -0.99, 0.01 Condition: fructose, NH4Cl, O2 Peak: 2165022-2165223 value:10145.00,
TF: Crp, Gene: mdtA, b2074, -0.99, 0.01 Condition: fructose, NH4Cl, O2 Peak: 2151570-2151771 value:7302.00,
TF: Crp, Gene: mdtA, b2074, -0.99, 0.01 Condition: fructose, NH4Cl, O2 Peak: 2165042-2165243 value:17084.00,
TF: Crp, Gene: mdtC, b2076, -0.53, 0.02 Condition: fructose, NH4Cl, O2 Peak: 2165034-2165235 value:11287.90,
TF: Crp, Gene: mdtC, b2076, -0.53, 0.02 Condition: fructose, NH4Cl, O2 Peak: 2165022-2165223 value:10145.00,
TF: Crp, Gene: mdtC, b2076, -0.53, 0.02 Condition: fructose, NH4Cl, O2 Peak: 2151570-2151771 value:7302.00,
TF: Crp, Gene: mdtC, b2076, -0.53, 0.02 Condition: fructose, NH4Cl, O2 Peak: 2165042-2165243 value:17084.00,
TF: Crp, Gene: baeS, b2078, -1.28, 0.00 Condition: fructose, NH4Cl, O2 Peak: 2165034-2165235 value:11287.90,
TF: Crp, Gene: baeS, b2078, -1.28, 0.00 Condition: fructose, NH4Cl, O2 Peak: 2165022-2165223 value:10145.00,
TF: Crp, Gene: baeS, b2078, -1.28, 0.00 Condition: fructose, NH4Cl, O2 Peak: 2151570-2151771 value:7302.00,
TF: Crp, Gene: baeS, b2078, -1.28, 0.00 Condition: fructose, NH4Cl, O2 Peak: 2165042-2165243 value:17084.00,
TF: Crp, Gene: mntH, b2392, -1.64, 0.00 Condition: fructose, NH4Cl, O2 Peak: 2510918-2511119 value:8403.00,
TF: Crp, Gene: cysK, b2414, -0.58, 0.01 Condition: fructose, NH4Cl, O2 Peak: 2531208-2531409 value:4376.00,
TF: Crp, Gene: cysK, b2414, -0.58, 0.01 Condition: fructose, NH4Cl, O2 Peak: 2531298-2531499 value:9836.60,
TF: Crp, Gene: cysK, b2414, -0.58, 0.01 Condition: fructose, NH4Cl, O2 Peak: 2531388-2531589 value:9176.80,
TF: Crp, Gene: cysK, b2414, -0.58, 0.01 Condition: fructose, NH4Cl, O2 Peak: 2531430-2531631 value:14989.50,
TF: Crp, Gene: yffP, b2447, -0.86, 0.02 Condition: fructose, NH4Cl, O2 Peak: 2561314-2561515 value:4909.90,
TF: Crp, Gene: yffP, b2447, -0.86, 0.02 Condition: fructose, NH4Cl, O2 Peak: 2561335-2561536 value:6928.10,
TF: Crp, Gene: hyfJ, b2490, -2.40, 0.04 Condition: fructose, NH4Cl, O2 Peak: 2598929-2599130 value:5701.00,
TF: Crp, Gene: guaA, b2507, -0.82, 0.00 Condition: fructose, NH4Cl, O2 Peak: 2632105-2632306 value:12036.00,
TF: Crp, Gene: xseA, b2509, -0.44, 0.03 Condition: fructose, NH4Cl, O2 Peak: 2632105-2632306 value:12036.00,
TF: Crp, Gene: ssrS, b2911, -1.03, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3056462-3056663 value:7417.00,
TF: Crp, Gene: ansB, b2957, -0.86, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3098837-3099038 value:6531.00,
TF: Crp, Gene: yggX, b2962, -0.64, 0.01 Condition: fructose, NH4Cl, O2 Peak: 3103505-3103706 value:16925.00,
TF: Crp, Gene: hyfI, b2489, -0.97, 0.01 Condition: fructose, NH4Cl, O2 Peak: 2598929-2599130 value:5701.00,
TF: Crp, Gene: pheA, b2599, -0.50, 0.01 Condition: fructose, NH4Cl, O2 Peak: 2734886-2735087 value:5334.80,
TF: Crp, Gene: pheA, b2599, -0.50, 0.01 Condition: fructose, NH4Cl, O2 Peak: 2735055-2735256 value:20368.10,
TF: Crp, Gene: pheA, b2599, -0.50, 0.01 Condition: fructose, NH4Cl, O2 Peak: 2735031-2735232 value:9363.10,
TF: Crp, Gene: serA, b2913, -1.36, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3056462-3056663 value:7417.00,
TF: Crp, Gene: yggN, b2958, -0.99, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3098837-3099038 value:6531.00,
TF: Crp, Gene: zupT, b3040, -1.17, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3182627-3182828 value:4973.00,
TF: Crp, Gene: lptB, b3201, -0.50, 0.01 Condition: fructose, NH4Cl, O2 Peak: 3348507-3348708 value:8274.00,
TF: Crp, Gene: yhbJ, b3205, -0.61, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3348507-3348708 value:8274.00,
TF: Crp, Gene: pabA, b3360, -1.49, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3490445-3490646 value:6541.40,
TF: Crp, Gene: pabA, b3360, -1.49, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3490388-3490589 value:19980.00,
TF: Crp, Gene: pabA, b3360, -1.49, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3490541-3490742 value:8576.60,
TF: Crp, Gene: pabA, b3360, -1.49, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3490383-3490584 value:15987.70,
TF: Crp, Gene: pabA, b3360, -1.49, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3490396-3490597 value:15430.80,
TF: Crp, Gene: pabA, b3360, -1.49, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3490495-3490696 value:6003.50,
TF: Crp, Gene: infB, b3168, -0.66, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3316272-3316473 value:6893.00,
TF: Crp, Gene: ptsN, b3204, -1.16, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3348507-3348708 value:8274.00,
TF: Crp, Gene: yrbL, b3207, -1.09, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3348507-3348708 value:8274.00,
TF: Crp, Gene: fic, b3361, -2.73, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3490445-3490646 value:6541.40,
TF: Crp, Gene: fic, b3361, -2.73, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3490388-3490589 value:19980.00,
TF: Crp, Gene: fic, b3361, -2.73, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3490541-3490742 value:8576.60,
TF: Crp, Gene: fic, b3361, -2.73, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3490383-3490584 value:15987.70,
TF: Crp, Gene: fic, b3361, -2.73, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3490396-3490597 value:15430.80,
TF: Crp, Gene: fic, b3361, -2.73, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3490495-3490696 value:6003.50,
TF: Crp, Gene: ysgA, b3830, -1.23, 0.00 Condition: fructose, NH4Cl, O2 Peak: 4014246-4014447 value:25459.10,
TF: Crp, Gene: ysgA, b3830, -1.23, 0.00 Condition: fructose, NH4Cl, O2 Peak: 4014322-4014523 value:6084.90,
TF: Crp, Gene: zapB, b3928, -0.97, 0.00 Condition: fructose, NH4Cl, O2 Peak: 4115765-4115966 value:13025.00,
TF: Crp, Gene: tufB, b3980, -5.33, 0.00 Condition: fructose, NH4Cl, O2 Peak: 4173311-4173512 value:11982.00,
TF: Crp, Gene: nepI, b3662, -0.82, 0.00 Condition: fructose, NH4Cl, O2 Peak: 3839691-3839892 value:9691.00,
TF: Crp, Gene: ilvA, b3772, -0.49, 0.02 Condition: fructose, NH4Cl, O2 Peak: 3948328-3948529 value:8686.00,
TF: Crp, Gene: metE, b3829, -0.49, 0.04 Condition: fructose, NH4Cl, O2 Peak: 4014322-4014523 value:6084.90,
TF: Crp, Gene: glpF, b3927, -1.95, 0.00 Condition: fructose, NH4Cl, O2 Peak: 4115765-4115966 value:13025.00,
TF: Crp, Gene: tyrB, b4054, -1.47, 0.00 Condition: fructose, NH4Cl, O2 Peak: 4267313-4267514 value:13482.00,
TF: Crp, Gene: yjiR, b4340, -0.70, 0.00 Condition: fructose, NH4Cl, O2 Peak: 4570068-4570269 value:6135.00,
TF: Crp, Gene: deoA, b4382, -1.77, 0.00 Condition: fructose, NH4Cl, O2 Peak: 4615133-4615334 value:14764.70,
TF: Crp, Gene: deoA, b4382, -1.77, 0.00 Condition: fructose, NH4Cl, O2 Peak: 4615165-4615366 value:7955.30,
TF: Crp, Gene: deoD, b4384, -0.54, 0.01 Condition: fructose, NH4Cl, O2 Peak: 4615133-4615334 value:14764.70,
TF: Crp, Gene: deoD, b4384, -0.54, 0.01 Condition: fructose, NH4Cl, O2 Peak: 4615165-4615366 value:7955.30]
In [2]:
ome.query(Protein).limit(20).all()
Out[2]:
[Protein (#1, leader; Amino acid biosynthesis: Threonine),
Protein (#2, ThrA),
Protein (#3, ThrB),
Protein (#4, enzyme; Amino acid biosynthesis: Threonine),
Protein (#5, predicted protein),
Protein (#6, protein that reduces intracellular iron levels under peroxide stress),
Protein (#7, inner membrane protein YaaJ),
Protein (#8, transaldolase B),
Protein (#9, MogA),
Protein (#10, acetate / succinate:H<sup>+</sup> symporter),
Protein (#11, conserved protein),
Protein (#12, predicted protein),
Protein (#13, chaperone protein DnaK),
Protein (#14, chaperone protein DnaJ),
Protein (#15, IS186/IS421 transposase),
Protein (#16, regulatory peptide whose translation enables hokC (gef) expression),
Protein (#17, HokC, Gef toxin; interferes with membrane function when in excess),
Protein (#18, NhaA),
Protein (#19, NhaR transcriptional activator),
Protein (#20, IS1 protein InsB)]
In [2]:
a = ome.query(Gene).filter(Gene.locus_id == 'b4028').first()
In [10]:
from trnlib.model_utility import *
In [13]:
model = load_model()
model.reactions.PGK.reaction
Out[13]:
'1.0 atp_c + 1.0 3pg_c <=> 1.0 adp_c + 1.0 13dpg_c'
In [2]:
class TestGenomeRegion(TestCase):
def setUp(self):
self.test_genome_region = components.GenomeRegion(10000,10200,'+')
def testAdd(self):
ome.add(self.test_genome_region)
ome.commit()
queried_genome_region = ome.query(components.GenomeRegion).first()
self.assertEqual(self.test_genome_region, queried_genome_region)
def testDelete(self):
ome.delete(components.GenomeRegion(10000,10200,'+'))
ome.commit()
queried_genome_region = ome.query(components.GenomeRegion).first()
self.assertEqual(queried_genome_region, None)
suite = TestLoader().loadTestsFromTestCase(TestGenomeRegion)
TextTestRunner(verbosity=2).run(suite)
Out[2]:
<unittest.runner.TextTestResult run=2 errors=1 failures=0>
In [2]:
ome.add(components.DNA('test2','gene',10000,10200,'+'))
ome.commit()
In [3]:
ome.add(components.DNA('test2','gene',10000,10200,'+'))
ome.commit()
In [4]:
ome.add(components.DNA('test2','gene',10000,10200,'+'))
ome.commit()
In [6]:
a = components.GenomeRegion(10000,10200,'+')
In [6]:
a = ome.query(components.DNA).first()
In [9]:
a.type
Out[9]:
u'DNA'
In [7]:
ome.query(components.GenomeRegion).filter_by(leftpos=a.leftpos,rightpos=a.rightpos, strand=a.strand).delete()
Out[7]:
1
In [8]:
ome.query(components.GenomeRegion).all()
Out[8]:
[]
In [6]:
#component = base.get_or_create(ome, components.Component, name='crp_gene', component_type_id=1)
#genome_region = base.get_or_create(ome, components.GenomeRegion, leftpos=1000, rightpos=1800, strand='+')
#dna = base.get_or_create(ome, components.DNA, component_id=component.id, component_type_id=1, dna_type_id=2, genome_region_id=genome_region.id)
#crp = base.get_or_create(ome, components.Gene, name='crp', locus_id='b1234', dna_id=dna.id, dna_type_id=2)
#base.get_or_create(ome, components.Protein, name='Crp')
---------------------------------------------------------------------------
InvalidRequestError Traceback (most recent call last)
<ipython-input-6-0c35b12c31fb> in <module>()
----> 1 component = base.get_or_create(ome, components.Component, name='crp_gene', component_type_id=1)
2 genome_region = base.get_or_create(ome, components.GenomeRegion, leftpos=1000, rightpos=1800, strand='+')
3 dna = base.get_or_create(ome, components.DNA, component_id=component.id, component_type_id=1, dna_type_id=2, genome_region_id=genome_region.id)
4 #crp = base.get_or_create(ome, components.Gene, name='crp', locus_id='b1234', dna_id=dna.id, dna_type_id=2)
5 #base.get_or_create(ome, components.Protein, name='Crp')
/Users/sfederow/ome/PrototypeDB/orm/base.pyc in get_or_create(session, class_type, **kwargs)
62 is found in the database, a new one will be created which satisfies
63 these constraints"""
---> 64 result = session.query(class_type).filter_by(**kwargs).first()
65 if result is None:
66 result = class_type()
/Library/Python/2.7/site-packages/sqlalchemy/orm/query.pyc in filter_by(self, **kwargs)
1243
1244 clauses = [_entity_descriptor(self._joinpoint_zero(), key) == value
-> 1245 for key, value in kwargs.iteritems()]
1246 return self.filter(sql.and_(*clauses))
1247
/Library/Python/2.7/site-packages/sqlalchemy/orm/util.pyc in _entity_descriptor(entity, key)
1188 raise sa_exc.InvalidRequestError(
1189 "Entity '%s' has no property '%s'" %
-> 1190 (description, key)
1191 )
1192
InvalidRequestError: Entity '<class 'PrototypeDB.orm.components.Component'>' has no property 'component_type_id'
In [21]:
ome.query(components.GenomeRegion).all()
Out[21]:
[<PrototypeDB.orm.components.GenomeRegion at 0x11187e2d0>]
In [19]:
a = crp.genome_region
In [20]:
a.leftpos
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-20-b9bbd17a80c9> in <module>()
----> 1 a.leftpos
AttributeError: 'NoneType' object has no attribute 'leftpos'
In [6]:
base.get_or_create(ome, components.DnaBindingSite, name='gapA_promoter')
---------------------------------------------------------------------------
IntegrityError Traceback (most recent call last)
<ipython-input-6-06454ac5f73d> in <module>()
----> 1 base.get_or_create(ome, components.DnaBindingSite, name='gapA_promoter')
/Users/sfederow/ome/ome/orm/base.pyc in get_or_create(session, class_type, **kwargs)
68 setattr(result, key, value)
69 session.add(result)
---> 70 session.commit()
71 return result
72
/Library/Python/2.7/site-packages/sqlalchemy/orm/session.pyc in commit(self)
719 raise sa_exc.InvalidRequestError("No transaction is begun.")
720
--> 721 self.transaction.commit()
722
723 def prepare(self):
/Library/Python/2.7/site-packages/sqlalchemy/orm/session.pyc in commit(self)
352 self._assert_active(prepared_ok=True)
353 if self._state is not PREPARED:
--> 354 self._prepare_impl()
355
356 if self._parent is None or self.nested:
/Library/Python/2.7/site-packages/sqlalchemy/orm/session.pyc in _prepare_impl(self)
332 if self.session._is_clean():
333 break
--> 334 self.session.flush()
335 else:
336 raise exc.FlushError(
/Library/Python/2.7/site-packages/sqlalchemy/orm/session.pyc in flush(self, objects)
1816 try:
1817 self._flushing = True
-> 1818 self._flush(objects)
1819 finally:
1820 self._flushing = False
/Library/Python/2.7/site-packages/sqlalchemy/orm/session.pyc in _flush(self, objects)
1934 except:
1935 with util.safe_reraise():
-> 1936 transaction.rollback(_capture_exception=True)
1937
1938 def is_modified(self, instance, include_collections=True,
/Library/Python/2.7/site-packages/sqlalchemy/util/langhelpers.pyc in __exit__(self, type_, value, traceback)
56 exc_type, exc_value, exc_tb = self._exc_info
57 self._exc_info = None # remove potential circular references
---> 58 compat.reraise(exc_type, exc_value, exc_tb)
59 else:
60 self._exc_info = None # remove potential circular references
/Library/Python/2.7/site-packages/sqlalchemy/orm/session.pyc in _flush(self, objects)
1898 self._warn_on_events = True
1899 try:
-> 1900 flush_context.execute()
1901 finally:
1902 self._warn_on_events = False
/Library/Python/2.7/site-packages/sqlalchemy/orm/unitofwork.pyc in execute(self)
370 self.dependencies,
371 postsort_actions):
--> 372 rec.execute(self)
373
374 def finalize_flush_changes(self):
/Library/Python/2.7/site-packages/sqlalchemy/orm/unitofwork.pyc in execute(self, uow)
523 persistence.save_obj(self.mapper,
524 uow.states_for_mapper_hierarchy(self.mapper, False, False),
--> 525 uow
526 )
527
/Library/Python/2.7/site-packages/sqlalchemy/orm/persistence.pyc in save_obj(base_mapper, states, uowtransaction, single)
62 _emit_insert_statements(base_mapper, uowtransaction,
63 cached_connections,
---> 64 table, insert)
65
66 _finalize_insert_update_commands(base_mapper, uowtransaction,
/Library/Python/2.7/site-packages/sqlalchemy/orm/persistence.pyc in _emit_insert_statements(base_mapper, uowtransaction, cached_connections, table, insert)
567 else:
568 result = cached_connections[connection].\
--> 569 execute(statement, params)
570
571 primary_key = result.context.inserted_primary_key
/Library/Python/2.7/site-packages/sqlalchemy/engine/base.pyc in execute(self, object, *multiparams, **params)
660 object,
661 multiparams,
--> 662 params)
663 else:
664 raise exc.InvalidRequestError(
/Library/Python/2.7/site-packages/sqlalchemy/engine/base.pyc in _execute_clauseelement(self, elem, multiparams, params)
759 compiled_sql,
760 distilled_params,
--> 761 compiled_sql, distilled_params
762 )
763 if self._has_events:
/Library/Python/2.7/site-packages/sqlalchemy/engine/base.pyc in _execute_context(self, dialect, constructor, statement, parameters, *args)
872 parameters,
873 cursor,
--> 874 context)
875
876 if self._has_events:
/Library/Python/2.7/site-packages/sqlalchemy/engine/base.pyc in _handle_dbapi_exception(self, e, statement, parameters, cursor, context)
1022 self.dialect.dbapi.Error,
1023 connection_invalidated=self._is_disconnect),
-> 1024 exc_info
1025 )
1026
/Library/Python/2.7/site-packages/sqlalchemy/util/compat.pyc in raise_from_cause(exception, exc_info)
193 # the code line where the issue occurred
194 exc_type, exc_value, exc_tb = exc_info
--> 195 reraise(type(exception), exception, tb=exc_tb)
196
197
/Library/Python/2.7/site-packages/sqlalchemy/engine/base.pyc in _execute_context(self, dialect, constructor, statement, parameters, *args)
865 statement,
866 parameters,
--> 867 context)
868 except Exception, e:
869 self._handle_dbapi_exception(
/Library/Python/2.7/site-packages/sqlalchemy/engine/default.pyc in do_execute(self, cursor, statement, parameters, context)
322
323 def do_execute(self, cursor, statement, parameters, context=None):
--> 324 cursor.execute(statement, parameters)
325
326 def do_execute_no_params(self, cursor, statement, context=None):
IntegrityError: (IntegrityError) null value in column "bound_component_id" violates not-null constraint
'INSERT INTO ecoli.dna_binding_site (dna_id, dna_type_id) VALUES (%(dna_id)s, %(dna_type_id)s) RETURNING ecoli.dna_binding_site.bound_component_id' {'dna_type_id': 1, 'dna_id': 3}
In [6]:
ome.query(components.DNA).all()
Out[6]:
[DNA (#1, None), DNA (#2, thrA_promoter)]
In [7]:
components.DNA_binding_site
Out[7]:
ome.orm.components.DNA_binding_site
In [ ]:
Content source: steve-federowicz/om
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