In [1]:
from om.orm import base
from om.orm import data
from om.orm import components
from om.orm.components import *
from om.lib import settings
from om.loading import load_components
from sqlalchemy import func
import simplejson as json
import numpy as np
import os
import math
import shutil
import subprocess
ome = base.Session()
In [ ]:
base.omics_database.genome_data.count()
In [4]:
#base.Base.metadata.drop_all()
#base.omics_database.genome_data.drop()
#base.Base.metadata.create_all()
In [5]:
load_components.load_genes(base, components)
load_genes(<module 'om.orm.base' from '/Users/sfederow/om/orm/base.pyc'>, <module 'om.orm.components' from '/Users/sfederow/om/orm/components.pyc'>) complete (44.10 sec)
In [3]:
load_components.load_transcription_units(base, components)
load_transcription_units(<module 'om_dev.orm.base' from '/Volumes/extra/Dropbox/om_dev/orm/base.pyc'>, <module 'om_dev.orm.components' from '/Volumes/extra/Dropbox/om_dev/orm/components.pyc'>) complete (74.50 sec)
In [4]:
load_components.load_proteins(base, components)
load_proteins(<module 'om_dev.orm.base' from '/Volumes/extra/Dropbox/om_dev/orm/base.pyc'>, <module 'om_dev.orm.components' from '/Volumes/extra/Dropbox/om_dev/orm/components.pyc'>) complete (57.87 sec)
In [5]:
load_components.load_bindsites(base, components)
load_bindsites(<module 'om_dev.orm.base' from '/Volumes/extra/Dropbox/om_dev/orm/base.pyc'>, <module 'om_dev.orm.components' from '/Volumes/extra/Dropbox/om_dev/orm/components.pyc'>) complete (136.71 sec)
In [3]:
ome.query(Complex).join(ComplexComposition).join(Protein).filter(Protein.name.ilike('Ace%')).limit(10).all()
Out[3]:
[Complex (#114): acetylglutamate kinase,
Complex (#780): acetylornithine aminotransferase / <i>N</i>-succinyldiaminopimelate aminotransferase]
In [6]:
ome.query(DnaBindingSite).limit(10).all()
Out[6]:
[DNA (#6452, BS0-2550) 786853-786853 +,
DNA (#6453, BS0-1342) 3681627-3681627 +,
DNA (#6454, BS00207) 4630726-4630726 +,
DNA (#6455, BS0-8130) 1102827-1102827 +,
DNA (#6456, BS0-8133) 2585498-2585514 +,
DNA (#6457, BS0-8134) 2585468-2585480 +,
DNA (#6458, BS0-8135) 2585435-2585453 +,
DNA (#6459, BS0-8136) 2151929-2151943 +,
DNA (#6460, BS0-8137) 3037213-3037213 +,
DNA (#6461, BS0-8138) 3865415-3865431 +]
In [3]:
ComplexComposition2 = aliased(ComplexComposition)
ome.query(Protein, DnaBindingSite).join(Gene).\
join(ComplexComposition, ComplexComposition.component_id == Protein.id).\
join(ComplexComposition2, ComplexComposition2.complex_id == ComplexComposition.complex_id).\
join(DnaBindingSite, DnaBindingSite.id == ComplexComposition2.component_id).\
filter(Gene.name.ilike('c%')).limit(10).all()
Out[3]:
[(Protein (#3750, Cbl DNA-binding transcriptional activator),
DNA (#6751, BS-7081) 996840-996840 +),
(Protein (#4507, CsgD DNA-binding transcriptional dual regulator),
DNA (#6969, BS00593) 1103044-1103044 +),
(Protein (#5473, CspA DNA-binding transcriptional activator),
DNA (#7079, BS00717) 2337567-2337567 +),
(Protein (#5473, CspA DNA-binding transcriptional activator),
DNA (#7088, BS00718) 2337587-2337587 +),
(Protein (#2390, ChbR DNA-binding transcriptional dual regulator),
DNA (#7451, BS0-3562) 1819788-1819788 +),
(Protein (#2390, ChbR DNA-binding transcriptional dual regulator),
DNA (#7452, BS0-3563) 1819811-1819811 +),
(Protein (#3750, Cbl DNA-binding transcriptional activator),
DNA (#7639, BS166) 384338-384338 +),
(Protein (#4507, CsgD DNA-binding transcriptional dual regulator),
DNA (#7733, BS0-8049) 1027095-1027109 +),
(Protein (#4507, CsgD DNA-binding transcriptional dual regulator),
DNA (#7737, BS0-8046) 3299328-3299342 +),
(Protein (#4507, CsgD DNA-binding transcriptional dual regulator),
DNA (#7732, BS0-8048) 2011077-2011091 +)]
In [6]:
ome.query(Complex).filter(Complex.long_name.ilike('Crp-cAMP%')).one()
Out[6]:
Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator
In [7]:
ComplexComposition2 = aliased(ComplexComposition)
ome.query(Complex, DnaBindingSite).join(ComplexComposition, ComplexComposition.component_id == Complex.id).\
join(ComplexComposition2, ComplexComposition2.complex_id == ComplexComposition.complex_id).\
join(DnaBindingSite, ComplexComposition2.component_id == DnaBindingSite.id).\
filter(Complex.long_name.ilike('Crp-cAMP%')).all()
Out[7]:
[(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6880, BS0-5842) 347752-347774 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8146, BS0-8087) 1168208-1168230 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8144, BS0-8085) 118697-118719 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8295, BS0-8091) 2583587-2583609 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8241, BS-7097) 1617064-1617064 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7866, BS00563) 3575736-3575736 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8252, BS-7098) 794222-794222 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7453, BS0-3561) 1819833-1819833 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7056, BS00663) 3103580-3103580 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7057, BS00664) 3103728-3103728 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7058, BS00665) 3103632-3103632 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8662, BS0-3303) 703001-703001 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8680, BS0-6561) 703035-703035 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7060, BS00667) 431355-431355 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6832, BS0-7610) 2231953-2231953 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6744, BS0-2181) 1451830-1451830 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8546, BS00090) 2350604-2350604 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8712, BS00081) 2350564-2350564 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6470, BS65) 3770152-3770152 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6472, BS63) 3769991-3769991 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6474, BS61) 3770108-3770108 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8140, BS0-8089) 3387504-3387526 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8139, BS0-8088) 2263383-2263405 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8296, BS0-8090) 855061-855083 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8005, BS0-1842) 367647-367647 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7055, BS00662) 431377-431399 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7942, BS0-6582) 1570159-1570159 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7799, BS0-7269) 3352465-3352465 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8470, BS00089) 2350514-2350514 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6669, BS0-5524) 4538012-4538012 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6974, BS0-5501) 628988-628988 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7396, BS0-8156) 656400-656422 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6471, BS64) 3769949-3769949 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6473, BS62) 3770035-3770035 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8179, BS0-5024) 3963646-3963646 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8145, BS0-8086) 214195-214217 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6500, BS0-7975) 1608838-1608838 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6935, BS00073) 791345-791345 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8288, BS0-8300) 1099416-1099438 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6478, BS0-7809) 1986043-1986043 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8620, BS0-7811) 312539-312561 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7443, BS0-7397) 1257919-1257919 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8246, BS-7092) 2175296-2175296 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6786, BS0-8203) 3048928-3048950 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8182, BS424) 1236754-1236754 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7894, BS0-1202) 4095641-4095641 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7906, BS0-8295) 1684775-1684797 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7090, BS0-8172) 2717860-2717882 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8750, BS00624) 3190074-3190074 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8410, BS-7088) 1102737-1102737 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8079, BS00682) 4116221-4116221 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6568, BS00321) 2238629-2238629 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8619, BS0-7810) 1986073-1986073 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7438, BS0-7398) 4348645-4348645 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6785, BS0-8202) 3049096-3049118 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8184, BS423) 1236677-1236699 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6646, BS0-8126) 4398135-4398157 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7623, BS0-4601) 4095622-4095622 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7907, BS0-8294) 1686390-1686412 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8342, BS00699) 3490459-3490459 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8081, BS00681) 4116244-4116244 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8721, BS00317) 3265158-3265158 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7524, BS154) 3534782-3534782 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7030, BS0-3944) 1694265-1694265 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7398, BS00738) 4014320-4014320 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7885, BS00691) 4464293-4464293 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8373, BS00555) 4095587-4095587 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8502, BS622) 4346893-4346893 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8243, BS-7095) 2749012-2749012 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6765, BS0-7593) 365556-365556 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7111, BS0-8005) 367800-367800 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7924, BS0-8180) 651251-651251 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7946, BS0-7215) 1445444-1445444 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7780, BS0-4602) 4095617-4095617 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7888, BS00692) 4464222-4464222 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8431, BS0-1321) 3681602-3681602 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8665, BS-7103) 2714585-2714585 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8354, BS0-3812) 3544355-3544355 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7165, BS821) 2229798-2229798 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6566, BS00327) 3845324-3845324 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8181, BS0-5022) 1327326-1327326 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8056, BS-7093) 3126209-3126209 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8334, BS523) 2632246-2632246 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8054, BS-7094) 4549377-4549377 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8722, BS00319) 754097-754097 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8411, BS-7089) 451068-451068 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6997, BS00340) 3754618-3754618 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8251, BS-7099) 2342640-2342640 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8180, BS0-5021) 1327326-1327326 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7743, BS0-8289) 1686500-1686522 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8723, BS476) 460472-460472 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7002, BS0-7114) 1697235-1697235 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6465, BS0-4126) 4492549-4492549 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6522, BS0-4121) 4492499-4492499 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7980, BS145) 4549483-4549483 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6861, BS322) 576124-576124 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6749, BS00337) 1976490-1976490 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6599, BS146) 1078388-1078388 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7582, BS147) 1078356-1078356 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6882, BS81) 2510990-2510990 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7250, BS00654) 2866084-2866084 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6833, BS00653) 2866202-2866202 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7249, BS00655) 3071915-3071915 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8183, BS422) 1236751-1236751 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7961, BS541) 3559930-3559930 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8014, BS0-6622) 3665692-3665692 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8032, BS321) 576166-576166 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6475, BS60) 3382395-3382395 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8274, BS0-3681) 2599032-2599032 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7580, BS148) 1078327-1078327 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6988, BS0-4901) 4122596-4122596 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8436, BS82) 2510941-2510941 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8061, BS0-7684) 3242862-3242862 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7180, BS0-7638) 2079368-2079368 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7448, BS0-4623) 4339828-4339828 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8161, BS0-6959) 841029-841029 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8450, BS0-7824) 1599341-1599341 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7486, BS0-6957) 611932-611932 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6723, BS00720) 1697295-1697295 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7911, BS0-8290) 1686573-1686573 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7387, BS0-1703) 141294-141294 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7385, BS00115) 4244563-4244563 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6627, BS00052) 4615260-4615260 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7192, BS0-7708) 117685-117685 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7447, BS0-4622) 4339714-4339714 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7040, BS0-7221) 1840299-1840299 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8037, BS0-5103) 4244658-4244658 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7910, BS0-8291) 1686581-1686581 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6573, BS463) 4198135-4198135 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7555, BS0-5481) 3371702-3371702 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7725, BS00117) 4244626-4244626 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7377, BS00051) 4615207-4615207 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7193, BS0-7709) 3521030-3521030 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7411, BS0-7710) 3520949-3520949 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7391, BS00005) 70168-70168 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8151, BS0-6954) 623786-623786 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8152, BS0-6955) 624024-624024 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7709, BS00754) 3483915-3483915 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8417, BS00798) 754614-754614 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6970, BS0-8365) 1359127-1359149 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6878, BS00047) 3989020-3989020 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8077, BS00684) 4328308-4328308 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7166, BS822) 2229748-2229748 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8247, BS-7091) 1887890-1887890 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8720, BS00313) 710016-710016 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7006, BS125) 34176-34176 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7503, BS0-3354) 4056185-4056185 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7682, BS00241) 3886374-3886374 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8656, BS0-6966) 121971-121971 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6567, BS00326) 3103630-3103630 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8652, BS-7105) 3408100-3408100 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8613, BS00637) 3598913-3598913 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7371, BS00267) 3550975-3550975 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7502, BS0-3355) 4056187-4056187 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6532, BS0-3001) 2786880-2786880 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8655, BS0-6967) 121983-121983 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8583, BS0-1661) 3408205-3408205 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7545, BS-7104) 3408015-3408015 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8486, BS0-7311) 3656348-3656348 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8419, BS00794) 127698-127698 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8601, BS00638) 3598966-3598966 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7659, BS0-1821) 3056651-3056651 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7873, BS0-8204) 1403816-1403838 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6947, BS00701) 3490512-3490512 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6898, BS0-7619) 2165095-2165095 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8028, BS327) 3740591-3740591 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6962, BS0-3841) 4549398-4549398 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6604, BS00613) 2475755-2475755 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7919, BS00760) 2531459-2531459 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7708, BS00753) 3484015-3484015 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8300, BS0-7238) 2912359-2912359 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7297, BS0-5701) 3086234-3086234 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7510, BS755) 1666685-1666685 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6571, BS00322) 1984304-1984304 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6564, BS00325) 411843-411843 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7724, BS0-2745) 4285483-4285483 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8209, BS0-5201) 4453713-4453713 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6606, BS00614) 2475725-2475725 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7706, BS00758) 2531587-2531587 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8044, BS-7096) 4199704-4199704 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7035, BS00702) 411698-411720 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7470, BS0-2746) 4285536-4285536 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6939, BS00076) 4056316-4056316 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7444, BS0-7396) 3217191-3217191 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8221, BS00585) 2459058-2459080 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7069, BS00067) 2239774-2239774 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7915, BS00764) 4098682-4098682 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6758, BS00196) 3598920-3598920 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7905, BS0-8298) 1099467-1099489 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6482, BS0-7806) 1490410-1490410 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8408, BS-7087) 1102609-1102609 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7414, BS00648) 1899916-1899916 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7227, BS00721) 1899864-1899864 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7707, BS-7110) 989844-989844 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8672, BS-7109) 989674-989674 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7512, BS759) 1333764-1333764 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7667, BS762) 131481-131481 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8015, BS0-6623) 1599412-1599412 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7922, BS0-3622) 365628-365628 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6748, BS00332) 4014372-4014372 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7650, BS0-7648) 2543683-2543683 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8438, BS84) 3931282-3931282 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6662, BS0-2847) 4609163-4609163 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8572, BS0-1062) 1156948-1156948 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8185, BS00219) 2980324-2980324 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8187, BS00215) 3098864-3098864 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8668, BS-7102) 2823471-2823471 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7548, BS-7101) 2823771-2823771 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6818, BS41) 1486154-1486154 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8376, BS0-7233) 956732-956732 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8380, BS00153) 1019453-1019453 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8166, BS0-3721) 1156894-1156894 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7929, BS0-2821) 3740758-3740758 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6883, BS0-4102) 4417889-4417889 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8565, BS0-6044) 3242973-3242995 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8674, BS-7108) 3491712-3491712 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7628, BS563) 1229750-1229750 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6563, BS0-6761) 1860579-1860579 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8069, BS-7090) 450914-450914 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7804, BS0-6937) 4328307-4328307 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7167, BS823) 2229746-2229746 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8763, BS0-5321) 3728911-3728911 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7520, BS0-3883) 3542647-3542647 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8150, BS0-4881) 2932060-2932060 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6746, BS00338) 3735261-3735261 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7546, BS-7107) 3491967-3491967 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6565, BS00324) 2932100-2932100 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8124, BS0-6960) 1686866-1686866 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7344, BS741) 4366545-4366545 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7848, BS00586) 42078-42078 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8071, BS0-4341) 3316416-3316416 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7089, BS0-8171) 2717900-2717922 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8098, BS0-3745) 3904781-3904781 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7823, BS773) 4047837-4047837 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7909, BS0-8296) 1685206-1685228 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7808, BS0-6083) 1064538-1064560 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7125, BS0-7932) 3229584-3229584 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8156, BS0-6953) 4213394-4213394 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8548, BS00096) 3851110-3851110 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8660, BS0-6962) 986407-986407 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8245, BS0-8277) 4589511-4589533 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8663, BS-7106) 3084538-3084538 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8480, BS0-6972) 1733399-1733421 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6872, BS0-4664) 4244592-4244592 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8657, BS0-6961) 986436-986436 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8659, BS0-6963) 986367-986367 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8070, BS00579) 953756-953756 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6767, BS0-7591) 161569-161591 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6661, BS0-2846) 4609187-4609187 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8007, BS0-1681) 4238298-4238298 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7550, BS00741) 3590475-3590475 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7009, BS121) 42255-42255 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8654, BS0-6964) 121656-121656 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7976, BS149) 121963-121963 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6923, BS00591) 4609176-4609176 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6957, BS0-5445) 3276827-3276827 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7007, BS124) 42198-42198 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8719, BS00312) 4434696-4434696 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6779, BS0-7754) 2837379-2837379 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8653, BS0-6965) 121923-121923 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#7506, BS202) 121951-121951 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#8515, BS0-3021) 2663380-2663380 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6835, BS0-8373) 3376871-3376887 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6837, BS0-8371) 1014758-1014774 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6840, BS0-8374) 4422945-4422961 +),
(Complex (#6414): CRP-cAMP DNA-binding transcriptional dual regulator,
DNA (#6834, BS0-8372) 2735097-2735113 +)]
In [2]:
ome.query(Complex, Gene).join(ComplexComposition).join(Protein, ComplexComposition.component_id == Protein.id).\
join(Gene).all()
Out[2]:
[(Complex (#8888): None, Gene: (b0076, leuO) 84368-85312 (+)),
(Complex (#8889): None, Gene: (b0076, leuO) 84368-85312 (+)),
(Complex (#8890): None, Gene: (b0076, leuO) 84368-85312 (+)),
(Complex (#8894): None, Gene: (b0076, leuO) 84368-85312 (+)),
(Complex (#8895): None, Gene: (b0076, leuO) 84368-85312 (+)),
(Complex (#10102): None, Gene: (b0076, leuO) 84368-85312 (+)),
(Complex (#10103): None, Gene: (b0076, leuO) 84368-85312 (+)),
(Complex (#10104): None, Gene: (b0076, leuO) 84368-85312 (+)),
(Complex (#10105): None, Gene: (b0076, leuO) 84368-85312 (+)),
(Complex (#10106): None, Gene: (b0076, leuO) 84368-85312 (+)),
(Complex (#10107): None, Gene: (b0076, leuO) 84368-85312 (+)),
(Complex (#10411): None, Gene: (b0076, leuO) 84368-85312 (+)),
(Complex (#11292): None, Gene: (b0076, leuO) 84368-85312 (+)),
(Complex (#11293): None, Gene: (b0076, leuO) 84368-85312 (+)),
(Complex (#11497): None, Gene: (b0076, leuO) 84368-85312 (+)),
(Complex (#9572): None, Gene: (b0113, pdhR) 122092-122856 (+)),
(Complex (#10078): None, Gene: (b0113, pdhR) 122092-122856 (+)),
(Complex (#9976): None, Gene: (b0113, pdhR) 122092-122856 (+)),
(Complex (#10143): None, Gene: (b0113, pdhR) 122092-122856 (+)),
(Complex (#10149): None, Gene: (b0113, pdhR) 122092-122856 (+)),
(Complex (#10151): None, Gene: (b0113, pdhR) 122092-122856 (+)),
(Complex (#10209): None, Gene: (b0113, pdhR) 122092-122856 (+)),
(Complex (#10845): None, Gene: (b0113, pdhR) 122092-122856 (+)),
(Complex (#11444): None, Gene: (b0113, pdhR) 122092-122856 (+)),
(Complex (#11567): None, Gene: (b0113, pdhR) 122092-122856 (+)),
(Complex (#8919): None, Gene: (b0464, acrR) 484985-485632 (+)),
(Complex (#9682): None, Gene: (b0464, acrR) 484985-485632 (+)),
(Complex (#10945): None, Gene: (b0464, acrR) 484985-485632 (+)),
(Complex (#9293): None, Gene: (b0620, dpiA) 653085-653765 (+)),
(Complex (#9294): None, Gene: (b0620, dpiA) 653085-653765 (+)),
(Complex (#9295): None, Gene: (b0620, dpiA) 653085-653765 (+)),
(Complex (#9296): None, Gene: (b0620, dpiA) 653085-653765 (+)),
(Complex (#10065): None, Gene: (b0620, dpiA) 653085-653765 (+)),
(Complex (#9973): None, Gene: (b0620, dpiA) 653085-653765 (+)),
(Complex (#10140): None, Gene: (b0620, dpiA) 653085-653765 (+)),
(Complex (#10364): None, Gene: (b0620, dpiA) 653085-653765 (+)),
(Complex (#10365): None, Gene: (b0620, dpiA) 653085-653765 (+)),
(Complex (#9057): None, Gene: (b0846, ybjK) 886646-887182 (+)),
(Complex (#9058): None, Gene: (b0846, ybjK) 886646-887182 (+)),
(Complex (#9059): None, Gene: (b0846, ybjK) 886646-887182 (+)),
(Complex (#9063): None, Gene: (b0846, ybjK) 886646-887182 (+)),
(Complex (#9064): None, Gene: (b0846, ybjK) 886646-887182 (+)),
(Complex (#9065): None, Gene: (b0846, ybjK) 886646-887182 (+)),
(Complex (#9066): None, Gene: (b0846, ybjK) 886646-887182 (+)),
(Complex (#10473): None, Gene: (b0846, ybjK) 886646-887182 (+)),
(Complex (#10474): None, Gene: (b0846, ybjK) 886646-887182 (+)),
(Complex (#10476): None, Gene: (b0846, ybjK) 886646-887182 (+)),
(Complex (#10479): None, Gene: (b0846, ybjK) 886646-887182 (+)),
(Complex (#10482): None, Gene: (b0846, ybjK) 886646-887182 (+)),
(Complex (#8923): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#8925): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#8926): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#8927): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#8928): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#8938): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#8940): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#8941): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#8942): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9134): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9135): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9136): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9137): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9138): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9139): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9249): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9283): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9017): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9018): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9019): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9020): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9021): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9022): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9334): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9336): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9339): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9340): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9341): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9748): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9314): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9892): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9893): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#9634): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10161): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10216): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10217): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10233): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10235): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10236): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10240): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10242): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10243): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10528): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10529): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10530): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10531): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10532): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10533): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10541): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10542): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10543): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10604): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10605): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10606): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10607): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10608): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10609): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10647): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10648): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10649): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10650): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10651): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10694): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10695): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10713): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10811): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10812): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10813): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10814): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10815): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10816): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10817): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10818): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10820): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#10947): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11108): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11109): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11110): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11188): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11189): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11190): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11191): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11192): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11195): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11196): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11197): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11201): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11202): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11204): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11205): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11206): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11207): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11253): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11254): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11346): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11347): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11425): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11426): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#11428): None, Gene: (b0889, lrp) 931818-932312 (+)),
(Complex (#8805): None, Gene: (b1013, rutR) 1073465-1074103 (+)),
(Complex (#8806): None, Gene: (b1013, rutR) 1073465-1074103 (+)),
(Complex (#11245): None, Gene: (b1013, rutR) 1073465-1074103 (+)),
(Complex (#11246): None, Gene: (b1013, rutR) 1073465-1074103 (+)),
(Complex (#11247): None, Gene: (b1013, rutR) 1073465-1074103 (+)),
(Complex (#11248): None, Gene: (b1013, rutR) 1073465-1074103 (+)),
(Complex (#9101): None, Gene: (b1187, fadR) 1234161-1234880 (+)),
(Complex (#10057): None, Gene: (b1187, fadR) 1234161-1234880 (+)),
(Complex (#10152): None, Gene: (b1187, fadR) 1234161-1234880 (+)),
(Complex (#10153): None, Gene: (b1187, fadR) 1234161-1234880 (+)),
(Complex (#10162): None, Gene: (b1187, fadR) 1234161-1234880 (+)),
(Complex (#10165): None, Gene: (b1187, fadR) 1234161-1234880 (+)),
(Complex (#10325): None, Gene: (b1187, fadR) 1234161-1234880 (+)),
(Complex (#10510): None, Gene: (b1187, fadR) 1234161-1234880 (+)),
(Complex (#10511): None, Gene: (b1187, fadR) 1234161-1234880 (+)),
(Complex (#10884): None, Gene: (b1187, fadR) 1234161-1234880 (+)),
(Complex (#11073): None, Gene: (b1187, fadR) 1234161-1234880 (+)),
(Complex (#11085): None, Gene: (b1187, fadR) 1234161-1234880 (+)),
(Complex (#11296): None, Gene: (b1187, fadR) 1234161-1234880 (+)),
(Complex (#11330): None, Gene: (b1187, fadR) 1234161-1234880 (+)),
(Complex (#11514): None, Gene: (b1187, fadR) 1234161-1234880 (+)),
(Complex (#9553): None, Gene: (b1299, puuR) 1359935-1360492 (+)),
(Complex (#10497): None, Gene: (b1299, puuR) 1359935-1360492 (+)),
(Complex (#10981): None, Gene: (b1299, puuR) 1359935-1360492 (+)),
(Complex (#10982): None, Gene: (b1299, puuR) 1359935-1360492 (+)),
(Complex (#11316): None, Gene: (b1299, puuR) 1359935-1360492 (+)),
(Complex (#11317): None, Gene: (b1299, puuR) 1359935-1360492 (+)),
(Complex (#11318): None, Gene: (b1299, puuR) 1359935-1360492 (+)),
(Complex (#11319): None, Gene: (b1299, puuR) 1359935-1360492 (+)),
(Complex (#9029): None, Gene: (b1323, tyrR) 1384744-1386285 (+)),
(Complex (#9405): None, Gene: (b1323, tyrR) 1384744-1386285 (+)),
(Complex (#9406): None, Gene: (b1323, tyrR) 1384744-1386285 (+)),
(Complex (#9710): None, Gene: (b1328, ycjZ) 1390015-1390914 (+)),
(Complex (#9991): None, Gene: (b1450, mcbR) 1518286-1518951 (+)),
(Complex (#9992): None, Gene: (b1450, mcbR) 1518286-1518951 (+)),
(Complex (#8886): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#8915): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#9231): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#9526): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#9395): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#10024): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#10045): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#10047): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#9630): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#9663): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#10231): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#10351): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#10363): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#10480): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#10538): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#10567): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#10623): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#10629): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#10684): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#10867): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#10940): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#11171): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#11301): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#11560): None, Gene: (b1531, marA) 1617598-1617981 (+)),
(Complex (#9060): None, Gene: (b1540, ydfH) 1626376-1627062 (+)),
(Complex (#8858): None, Gene: (b1570, dicA) 1645958-1646365 (+)),
(Complex (#9711): None, Gene: (b1570, dicA) 1645958-1646365 (+)),
(Complex (#10350): None, Gene: (b1649, nemR) 1724047-1724646 (+)),
(Complex (#10076): None, Gene: (b2127, mlrA) 2212888-2213619 (+)),
(Complex (#10077): None, Gene: (b2127, mlrA) 2212888-2213619 (+)),
(Complex (#10080): None, Gene: (b2127, mlrA) 2212888-2213619 (+)),
(Complex (#10081): None, Gene: (b2127, mlrA) 2212888-2213619 (+)),
(Complex (#9354): None, Gene: (b2217, rcsB) 2314199-2314849 (+)),
(Complex (#9355): None, Gene: (b2217, rcsB) 2314199-2314849 (+)),
(Complex (#10984): None, Gene: (b2217, rcsB) 2314199-2314849 (+)),
(Complex (#11148): None, Gene: (b2217, rcsB) 2314199-2314849 (+)),
(Complex (#11256): None, Gene: (b2217, rcsB) 2314199-2314849 (+)),
(Complex (#11262): None, Gene: (b2217, rcsB) 2314199-2314849 (+)),
(Complex (#11278): None, Gene: (b2217, rcsB) 2314199-2314849 (+)),
(Complex (#11475): None, Gene: (b2217, rcsB) 2314199-2314849 (+)),
(Complex (#9717): None, Gene: (b2381, ypdB) 2498405-2499139 (+)),
(Complex (#10554): None, Gene: (b2381, ypdB) 2498405-2499139 (+)),
(Complex (#9744): None, Gene: (b2491, hyfR) 2609922-2611934 (+)),
(Complex (#9048): None, Gene: (b2837, galR) 2974621-2975652 (+)),
(Complex (#9053): None, Gene: (b2837, galR) 2974621-2975652 (+)),
(Complex (#9853): None, Gene: (b2837, galR) 2974621-2975652 (+)),
(Complex (#10398): None, Gene: (b2837, galR) 2974621-2975652 (+)),
(Complex (#10399): None, Gene: (b2837, galR) 2974621-2975652 (+)),
(Complex (#10457): None, Gene: (b2837, galR) 2974621-2975652 (+)),
(Complex (#10461): None, Gene: (b2837, galR) 2974621-2975652 (+)),
(Complex (#10556): None, Gene: (b2837, galR) 2974621-2975652 (+)),
(Complex (#10559): None, Gene: (b2837, galR) 2974621-2975652 (+)),
(Complex (#10145): None, Gene: (b3025, qseB) 3167850-3168509 (+)),
(Complex (#10929): None, Gene: (b3025, qseB) 3167850-3168509 (+)),
(Complex (#8770): None, Gene: (b3071, yqjI) 3214801-3215424 (+)),
(Complex (#8828): None, Gene: (b3071, yqjI) 3214801-3215424 (+)),
(Complex (#8929): None, Gene: (b3094, exuR) 3244674-3245450 (+)),
(Complex (#9286): None, Gene: (b3094, exuR) 3244674-3245450 (+)),
(Complex (#9288): None, Gene: (b3094, exuR) 3244674-3245450 (+)),
(Complex (#9039): None, Gene: (b3094, exuR) 3244674-3245450 (+)),
(Complex (#9776): None, Gene: (b3094, exuR) 3244674-3245450 (+)),
(Complex (#9777): None, Gene: (b3094, exuR) 3244674-3245450 (+)),
(Complex (#10357): None, Gene: (b3094, exuR) 3244674-3245450 (+)),
(Complex (#10359): None, Gene: (b3094, exuR) 3244674-3245450 (+)),
(Complex (#10829): None, Gene: (b3094, exuR) 3244674-3245450 (+)),
(Complex (#10966): None, Gene: (b3094, exuR) 3244674-3245450 (+)),
(Complex (#11251): None, Gene: (b3094, exuR) 3244674-3245450 (+)),
(Complex (#10521): None, Gene: (b3119, tdcR) 3265402-3265620 (+)),
(Complex (#8807): None, Gene: (b3261, fis) 3409293-3409589 (+)),
(Complex (#8808): None, Gene: (b3261, fis) 3409293-3409589 (+)),
(Complex (#9027): None, Gene: (b3261, fis) 3409293-3409589 (+)),
(Complex (#9028): None, Gene: (b3261, fis) 3409293-3409589 (+)),
(Complex (#9708): None, Gene: (b3261, fis) 3409293-3409589 (+)),
(Complex (#11031): None, Gene: (b3261, fis) 3409293-3409589 (+)),
(Complex (#11032): None, Gene: (b3261, fis) 3409293-3409589 (+)),
(Complex (#11037): None, Gene: (b3261, fis) 3409293-3409589 (+)),
(Complex (#11435): None, Gene: (b3261, fis) 3409293-3409589 (+)),
(Complex (#11436): None, Gene: (b3261, fis) 3409293-3409589 (+)),
(Complex (#11437): None, Gene: (b3261, fis) 3409293-3409589 (+)),
(Complex (#11438): None, Gene: (b3261, fis) 3409293-3409589 (+)),
(Complex (#11439): None, Gene: (b3261, fis) 3409293-3409589 (+)),
(Complex (#10263): None, Gene: (b3512, gadE) 3656389-3656916 (+)),
(Complex (#10264): None, Gene: (b3512, gadE) 3656389-3656916 (+)),
(Complex (#10265): None, Gene: (b3512, gadE) 3656389-3656916 (+)),
(Complex (#10353): None, Gene: (b3512, gadE) 3656389-3656916 (+)),
(Complex (#10882): None, Gene: (b3512, gadE) 3656389-3656916 (+)),
(Complex (#11088): None, Gene: (b3512, gadE) 3656389-3656916 (+)),
(Complex (#8996): None, Gene: (b3556, cspA) 3718072-3718284 (+)),
(Complex (#8997): None, Gene: (b3556, cspA) 3718072-3718284 (+)),
(Complex (#8998): None, Gene: (b3556, cspA) 3718072-3718284 (+)),
(Complex (#8822): None, Gene: (b3604, lldR) 3777077-3777853 (+)),
(Complex (#9709): None, Gene: (b3604, lldR) 3777077-3777853 (+)),
(Complex (#10058): None, Gene: (b3753, rbsR) 3936250-3937242 (+)),
(Complex (#10702): None, Gene: (b3753, rbsR) 3936250-3937242 (+)),
(Complex (#8891): None, Gene: (b3905, rhaS) 4095759-4096595 (+)),
(Complex (#9950): None, Gene: (b3905, rhaS) 4095759-4096595 (+)),
(Complex (#8839): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#8841): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#8842): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#9010): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#9013): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#9779): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#10027): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#9814): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#9835): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#9844): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#9847): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#10139): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#10274): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#10275): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#10276): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#10277): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#10278): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#10279): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#10280): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#10281): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#10282): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#10283): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#10387): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#10423): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#10788): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#10821): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#11095): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#11096): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#11097): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#11098): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#11099): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#11112): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#11433): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#11434): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#11440): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#11441): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#11593): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#11594): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#11595): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#11596): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#11597): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#11598): None, Gene: (b3961, oxyR) 4156513-4157430 (+)),
(Complex (#10326): None, Gene: (b3963, fabR) 4159090-4159794 (+)),
(Complex (#11143): None, Gene: (b3963, fabR) 4159090-4159794 (+)),
(Complex (#9496): None, Gene: (b4063, soxR) 4275492-4275956 (+)),
(Complex (#9986): None, Gene: (b4063, soxR) 4275492-4275956 (+)),
(Complex (#9284): None, Gene: (b4324, uxuR) 4552599-4553372 (+)),
(Complex (#9285): None, Gene: (b4324, uxuR) 4552599-4553372 (+)),
(Complex (#9612): None, Gene: (b4324, uxuR) 4552599-4553372 (+)),
(Complex (#9613): None, Gene: (b4324, uxuR) 4552599-4553372 (+)),
(Complex (#10356): None, Gene: (b4324, uxuR) 4552599-4553372 (+)),
(Complex (#10358): None, Gene: (b4324, uxuR) 4552599-4553372 (+)),
(Complex (#10963): None, Gene: (b4324, uxuR) 4552599-4553372 (+)),
(Complex (#10964): None, Gene: (b4324, uxuR) 4552599-4553372 (+)),
(Complex (#11167): None, Gene: (b4324, uxuR) 4552599-4553372 (+)),
(Complex (#11168): None, Gene: (b4324, uxuR) 4552599-4553372 (+)),
(Complex (#8905): None, Gene: (b0069, sgrR) 75644-77299 (-)),
(Complex (#9232): None, Gene: (b0069, sgrR) 75644-77299 (-)),
(Complex (#9233): None, Gene: (b0069, sgrR) 75644-77299 (-)),
(Complex (#10128): None, Gene: (b0313, betI) 327971-328558 (-)),
(Complex (#10130): None, Gene: (b0313, betI) 327971-328558 (-)),
(Complex (#10018): None, Gene: (b0338, cynR) 357015-357914 (-)),
(Complex (#10906): None, Gene: (b0338, cynR) 357015-357914 (-)),
(Complex (#9118): None, Gene: (b0345, lacI) 365652-366734 (-)),
(Complex (#9827): None, Gene: (b0345, lacI) 365652-366734 (-)),
(Complex (#9828): None, Gene: (b0345, lacI) 365652-366734 (-)),
(Complex (#11216): None, Gene: (b0571, cusR) 593983-594666 (-)),
(Complex (#11217): None, Gene: (b0571, cusR) 593983-594666 (-)),
(Complex (#8962): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#8963): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#8824): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#8827): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9163): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9191): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9192): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9040): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9042): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9043): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9044): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9045): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9046): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9577): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9578): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9107): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9110): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9432): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9435): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9673): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9674): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#10178): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#10179): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#10295): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#10435): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#10446): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#10777): None, Gene: (b0676, nagC) 699597-700817 (-)),
(Complex (#9919): None, Gene: (b0840, deoR) 881199-881957 (-)),
(Complex (#9920): None, Gene: (b0840, deoR) 881199-881957 (-)),
(Complex (#9922): None, Gene: (b0840, deoR) 881199-881957 (-)),
(Complex (#10109): None, Gene: (b0840, deoR) 881199-881957 (-)),
(Complex (#10741): None, Gene: (b0840, deoR) 881199-881957 (-)),
(Complex (#11328): None, Gene: (b0840, deoR) 881199-881957 (-)),
(Complex (#11331): None, Gene: (b0840, deoR) 881199-881957 (-)),
(Complex (#8947): None, Gene: (b1014, putA) 1074143-1078105 (-)),
(Complex (#10226): None, Gene: (b1014, putA) 1074143-1078105 (-)),
(Complex (#10228): None, Gene: (b1014, putA) 1074143-1078105 (-)),
(Complex (#11548): None, Gene: (b1014, putA) 1074143-1078105 (-)),
(Complex (#11559): None, Gene: (b1014, putA) 1074143-1078105 (-)),
(Complex (#9141): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#9486): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#9487): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#9488): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#9489): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#9490): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#9491): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#9492): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#9493): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#9494): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#9495): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#9658): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#9659): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#9660): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#9700): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#9703): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#10590): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#10936): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#10937): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#10938): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#10939): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#11025): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#11026): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#11027): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#11028): None, Gene: (b1040, csgD) 1101769-1102419 (-)),
(Complex (#8773): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#8893): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9159): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9190): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9207): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9209): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9211): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9026): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9049): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9050): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9055): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9056): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9344): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9345): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9713): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9714): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9723): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9724): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9731): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#10023): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9829): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9657): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9993): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#10194): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#10196): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#10198): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#10199): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#10248): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#10249): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#10250): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#10343): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#10344): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#10406): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#10853): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#10864): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#10865): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11111): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11115): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11116): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11118): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11233): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11234): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11235): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11236): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11237): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11238): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11239): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11240): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11241): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11242): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11297): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11490): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11491): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11495): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#11496): None, Gene: (b1237, hns) 1291732-1292145 (-)),
(Complex (#9425): None, Gene: (b1303, pspF) 1364959-1365936 (-)),
(Complex (#9427): None, Gene: (b1303, pspF) 1364959-1365936 (-)),
(Complex (#10268): None, Gene: (b1303, pspF) 1364959-1365936 (-)),
(Complex (#11212): None, Gene: (b1303, pspF) 1364959-1365936 (-)),
(Complex (#11215): None, Gene: (b1303, pspF) 1364959-1365936 (-)),
(Complex (#9015): None, Gene: (b1384, feaR) 1444402-1445307 (-)),
(Complex (#9016): None, Gene: (b1384, feaR) 1444402-1445307 (-)),
(Complex (#11059): None, Gene: (b1384, feaR) 1444402-1445307 (-)),
(Complex (#11528): None, Gene: (b1384, feaR) 1444402-1445307 (-)),
(Complex (#9358): None, Gene: (b1508, hipB) 1590200-1590466 (-)),
(Complex (#9359): None, Gene: (b1508, hipB) 1590200-1590466 (-)),
(Complex (#9360): None, Gene: (b1508, hipB) 1590200-1590466 (-)),
(Complex (#9361): None, Gene: (b1508, hipB) 1590200-1590466 (-)),
(Complex (#9208): None, Gene: (b1594, dgsA) 1665368-1666588 (-)),
(Complex (#9343): None, Gene: (b1594, dgsA) 1665368-1666588 (-)),
(Complex (#9108): None, Gene: (b1594, dgsA) 1665368-1666588 (-)),
(Complex (#9109): None, Gene: (b1594, dgsA) 1665368-1666588 (-)),
(Complex (#10324): None, Gene: (b1594, dgsA) 1665368-1666588 (-)),
(Complex (#11119): None, Gene: (b1594, dgsA) 1665368-1666588 (-)),
(Complex (#11121): None, Gene: (b1594, dgsA) 1665368-1666588 (-)),
(Complex (#11460): None, Gene: (b1594, dgsA) 1665368-1666588 (-)),
(Complex (#10498): None, Gene: (b1618, uidR) 1694486-1695076 (-)),
(Complex (#9862): None, Gene: (b1620, malI) 1696176-1697204 (-)),
(Complex (#10442): None, Gene: (b1620, malI) 1696176-1697204 (-)),
(Complex (#10032): None, Gene: (b1642, slyA) 1718414-1718848 (-)),
(Complex (#10033): None, Gene: (b1642, slyA) 1718414-1718848 (-)),
(Complex (#10034): None, Gene: (b1642, slyA) 1718414-1718848 (-)),
(Complex (#10035): None, Gene: (b1642, slyA) 1718414-1718848 (-)),
(Complex (#10859): None, Gene: (b1642, slyA) 1718414-1718848 (-)),
(Complex (#10860): None, Gene: (b1642, slyA) 1718414-1718848 (-)),
(Complex (#8912): None, Gene: (b1735, chbR) 1816629-1817471 (-)),
(Complex (#9734): None, Gene: (b1735, chbR) 1816629-1817471 (-)),
(Complex (#8855): None, Gene: (b1827, kdgR) 1907332-1908123 (-)),
(Complex (#10082): None, Gene: (b1827, kdgR) 1907332-1908123 (-)),
(Complex (#9984): None, Gene: (b1916, sdiA) 1994134-1994856 (-)),
(Complex (#9985): None, Gene: (b1916, sdiA) 1994134-1994856 (-)),
(Complex (#9987): None, Gene: (b1916, sdiA) 1994134-1994856 (-)),
(Complex (#10212): None, Gene: (b1916, sdiA) 1994134-1994856 (-)),
(Complex (#11100): None, Gene: (b1916, sdiA) 1994134-1994856 (-)),
(Complex (#8949): None, Gene: (b1987, cbl) 2057988-2058938 (-)),
(Complex (#9605): None, Gene: (b1987, cbl) 2057988-2058938 (-)),
(Complex (#9280): None, Gene: (b1988, nac) 2059040-2059957 (-)),
(Complex (#9282): None, Gene: (b1988, nac) 2059040-2059957 (-)),
(Complex (#9096): None, Gene: (b1988, nac) 2059040-2059957 (-)),
(Complex (#9097): None, Gene: (b1988, nac) 2059040-2059957 (-)),
(Complex (#9106): None, Gene: (b1988, nac) 2059040-2059957 (-)),
(Complex (#9810): None, Gene: (b1988, nac) 2059040-2059957 (-)),
(Complex (#9811): None, Gene: (b1988, nac) 2059040-2059957 (-)),
(Complex (#11048): None, Gene: (b1988, nac) 2059040-2059957 (-)),
(Complex (#11058): None, Gene: (b1988, nac) 2059040-2059957 (-)),
(Complex (#11306): None, Gene: (b1988, nac) 2059040-2059957 (-)),
(Complex (#11374): None, Gene: (b1988, nac) 2059040-2059957 (-)),
(Complex (#11379): None, Gene: (b1988, nac) 2059040-2059957 (-)),
(Complex (#11380): None, Gene: (b1988, nac) 2059040-2059957 (-)),
(Complex (#11587): None, Gene: (b1988, nac) 2059040-2059957 (-)),
(Complex (#9119): None, Gene: (b2105, rcnR) 2183546-2183818 (-)),
(Complex (#9996): None, Gene: (b2105, rcnR) 2183546-2183818 (-)),
(Complex (#10135): None, Gene: (b2105, rcnR) 2183546-2183818 (-)),
(Complex (#10138): None, Gene: (b2105, rcnR) 2183546-2183818 (-)),
(Complex (#11370): None, Gene: (b2125, yehT) 2210265-2210984 (-)),
(Complex (#9051): None, Gene: (b2151, galS) 2238650-2239690 (-)),
(Complex (#10390): None, Gene: (b2151, galS) 2238650-2239690 (-)),
(Complex (#10391): None, Gene: (b2151, galS) 2238650-2239690 (-)),
(Complex (#10462): None, Gene: (b2151, galS) 2238650-2239690 (-)),
(Complex (#10464): None, Gene: (b2151, galS) 2238650-2239690 (-)),
(Complex (#10555): None, Gene: (b2151, galS) 2238650-2239690 (-)),
(Complex (#10560): None, Gene: (b2151, galS) 2238650-2239690 (-)),
(Complex (#10986): None, Gene: (b2151, galS) 2238650-2239690 (-)),
(Complex (#11140): None, Gene: (b2151, galS) 2238650-2239690 (-)),
(Complex (#8884): None, Gene: (b2213, ada) 2307363-2308427 (-)),
(Complex (#9400): None, Gene: (b2213, ada) 2307363-2308427 (-)),
(Complex (#10789): None, Gene: (b2213, ada) 2307363-2308427 (-)),
(Complex (#11314): None, Gene: (b2213, ada) 2307363-2308427 (-)),
(Complex (#9651): None, Gene: (b2289, lrhA) 2403725-2404663 (-)),
(Complex (#9315): None, Gene: (b2531, iscR) 2659665-2660153 (-)),
(Complex (#9462): None, Gene: (b2531, iscR) 2659665-2660153 (-)),
(Complex (#9916): None, Gene: (b2531, iscR) 2659665-2660153 (-)),
(Complex (#9585): None, Gene: (b2531, iscR) 2659665-2660153 (-)),
(Complex (#10312): None, Gene: (b2531, iscR) 2659665-2660153 (-)),
(Complex (#10419): None, Gene: (b2531, iscR) 2659665-2660153 (-)),
(Complex (#10693): None, Gene: (b2531, iscR) 2659665-2660153 (-)),
(Complex (#10755): None, Gene: (b2531, iscR) 2659665-2660153 (-)),
(Complex (#10927): None, Gene: (b2531, iscR) 2659665-2660153 (-)),
(Complex (#10928): None, Gene: (b2531, iscR) 2659665-2660153 (-)),
(Complex (#11266): None, Gene: (b2537, hcaR) 2666028-2666918 (-)),
(Complex (#9081): None, Gene: (b2554, glrR) 2685491-2686825 (-)),
(Complex (#9082): None, Gene: (b2554, glrR) 2685491-2686825 (-)),
(Complex (#9086): None, Gene: (b2554, glrR) 2685491-2686825 (-)),
(Complex (#9194): None, Gene: (b2709, norR) 2828797-2830311 (-)),
(Complex (#10337): None, Gene: (b2709, norR) 2828797-2830311 (-)),
(Complex (#10339): None, Gene: (b2709, norR) 2828797-2830311 (-)),
(Complex (#10340): None, Gene: (b2709, norR) 2828797-2830311 (-)),
(Complex (#10779): None, Gene: (b2709, norR) 2828797-2830311 (-)),
(Complex (#10780): None, Gene: (b2709, norR) 2828797-2830311 (-)),
(Complex (#9683): None, Gene: (b2714, ascG) 2836276-2837289 (-)),
(Complex (#11537): None, Gene: (b2714, ascG) 2836276-2837289 (-)),
(Complex (#11539): None, Gene: (b2714, ascG) 2836276-2837289 (-)),
(Complex (#11540): None, Gene: (b2714, ascG) 2836276-2837289 (-)),
(Complex (#11541): None, Gene: (b2714, ascG) 2836276-2837289 (-)),
(Complex (#11542): None, Gene: (b2714, ascG) 2836276-2837289 (-)),
(Complex (#11543): None, Gene: (b2714, ascG) 2836276-2837289 (-)),
(Complex (#11544): None, Gene: (b2714, ascG) 2836276-2837289 (-)),
(Complex (#11545): None, Gene: (b2714, ascG) 2836276-2837289 (-)),
(Complex (#9614): None, Gene: (b2783, chpR) 2909113-2909361 (-)),
(Complex (#9618): None, Gene: (b2783, chpR) 2909113-2909361 (-)),
(Complex (#10177): None, Gene: (b2783, chpR) 2909113-2909361 (-)),
(Complex (#10180): None, Gene: (b2783, chpR) 2909113-2909361 (-)),
(Complex (#8908): None, Gene: (b2808, gcvA) 2939672-2940589 (-)),
(Complex (#9114): None, Gene: (b2808, gcvA) 2939672-2940589 (-)),
(Complex (#9115): None, Gene: (b2808, gcvA) 2939672-2940589 (-)),
(Complex (#9733): None, Gene: (b2808, gcvA) 2939672-2940589 (-)),
(Complex (#10269): None, Gene: (b2808, gcvA) 2939672-2940589 (-)),
(Complex (#10610): None, Gene: (b2808, gcvA) 2939672-2940589 (-)),
(Complex (#10708): None, Gene: (b2808, gcvA) 2939672-2940589 (-)),
(Complex (#10710): None, Gene: (b2808, gcvA) 2939672-2940589 (-)),
(Complex (#10712): None, Gene: (b2808, gcvA) 2939672-2940589 (-)),
(Complex (#10714): None, Gene: (b2808, gcvA) 2939672-2940589 (-)),
(Complex (#10625): None, Gene: (b3010, yqhC) 3152284-3153240 (-)),
(Complex (#10626): None, Gene: (b3010, yqhC) 3152284-3153240 (-)),
(Complex (#9485): None, Gene: (b3021, mqsA) 3165873-3166268 (-)),
(Complex (#9589): None, Gene: (b3021, mqsA) 3165873-3166268 (-)),
(Complex (#10850): None, Gene: (b3021, mqsA) 3165873-3166268 (-)),
(Complex (#10851): None, Gene: (b3021, mqsA) 3165873-3166268 (-)),
(Complex (#10852): None, Gene: (b3021, mqsA) 3165873-3166268 (-)),
(Complex (#9266): None, Gene: (b3118, tdcA) 3264149-3265087 (-)),
(Complex (#10156): None, Gene: (b3131, agaR) 3275878-3276687 (-)),
(Complex (#10157): None, Gene: (b3131, agaR) 3275878-3276687 (-)),
(Complex (#10158): None, Gene: (b3131, agaR) 3275878-3276687 (-)),
(Complex (#10159): None, Gene: (b3131, agaR) 3275878-3276687 (-)),
(Complex (#10160): None, Gene: (b3131, agaR) 3275878-3276687 (-)),
(Complex (#10184): None, Gene: (b3131, agaR) 3275878-3276687 (-)),
(Complex (#10186): None, Gene: (b3131, agaR) 3275878-3276687 (-)),
(Complex (#10187): None, Gene: (b3131, agaR) 3275878-3276687 (-)),
(Complex (#11478): None, Gene: (b3131, agaR) 3275878-3276687 (-)),
(Complex (#11479): None, Gene: (b3131, agaR) 3275878-3276687 (-)),
(Complex (#11486): None, Gene: (b3131, agaR) 3275878-3276687 (-)),
(Complex (#9187): None, Gene: (b3226, nanR) 3371720-3372511 (-)),
(Complex (#9188): None, Gene: (b3226, nanR) 3371720-3372511 (-)),
(Complex (#9333): None, Gene: (b3226, nanR) 3371720-3372511 (-)),
(Complex (#9422): None, Gene: (b3226, nanR) 3371720-3372511 (-)),
(Complex (#9424): None, Gene: (b3226, nanR) 3371720-3372511 (-)),
(Complex (#10470): None, Gene: (b3226, nanR) 3371720-3372511 (-)),
(Complex (#10471): None, Gene: (b3226, nanR) 3371720-3372511 (-)),
(Complex (#10472): None, Gene: (b3226, nanR) 3371720-3372511 (-)),
(Complex (#10691): None, Gene: (b3226, nanR) 3371720-3372511 (-)),
(Complex (#10807): None, Gene: (b3226, nanR) 3371720-3372511 (-)),
(Complex (#10808): None, Gene: (b3226, nanR) 3371720-3372511 (-)),
(Complex (#11211): None, Gene: (b3226, nanR) 3371720-3372511 (-)),
(Complex (#8914): None, Gene: (b3264, envR) 3410825-3411487 (-)),
(Complex (#9212): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#9213): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#9216): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#9270): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#9276): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#9277): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#9736): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#9737): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#9738): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#10761): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#10762): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#10763): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#10764): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#10765): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#10766): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#10768): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#10825): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#10826): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#10827): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#11320): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#11321): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#11322): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#11323): None, Gene: (b3423, glpR) 3557870-3558628 (-)),
(Complex (#8816): None, Gene: (b3438, gntR) 3575754-3576749 (-)),
(Complex (#8817): None, Gene: (b3438, gntR) 3575754-3576749 (-)),
(Complex (#9350): None, Gene: (b3438, gntR) 3575754-3576749 (-)),
(Complex (#9529): None, Gene: (b3438, gntR) 3575754-3576749 (-)),
(Complex (#9533): None, Gene: (b3438, gntR) 3575754-3576749 (-)),
(Complex (#9534): None, Gene: (b3438, gntR) 3575754-3576749 (-)),
(Complex (#9391): None, Gene: (b3438, gntR) 3575754-3576749 (-)),
(Complex (#9393): None, Gene: (b3438, gntR) 3575754-3576749 (-)),
(Complex (#9396): None, Gene: (b3438, gntR) 3575754-3576749 (-)),
(Complex (#9397): None, Gene: (b3438, gntR) 3575754-3576749 (-)),
(Complex (#10284): None, Gene: (b3438, gntR) 3575754-3576749 (-)),
(Complex (#10285): None, Gene: (b3438, gntR) 3575754-3576749 (-)),
(Complex (#10742): None, Gene: (b3438, gntR) 3575754-3576749 (-)),
(Complex (#10959): None, Gene: (b3438, gntR) 3575754-3576749 (-)),
(Complex (#11338): None, Gene: (b3438, gntR) 3575754-3576749 (-)),
(Complex (#11341): None, Gene: (b3438, gntR) 3575754-3576749 (-)),
(Complex (#11342): None, Gene: (b3438, gntR) 3575754-3576749 (-)),
(Complex (#9180): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#9181): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#9513): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#9515): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#9516): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#9517): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#9518): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#9520): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#9521): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#9522): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#9792): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#9840): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#9878): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#10544): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#10545): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#10546): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#10547): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#10548): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#10549): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#10551): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#10552): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#10553): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#10584): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#10717): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#10872): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#10873): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#10874): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#10875): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#10876): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#11089): None, Gene: (b3515, gadW) 3661913-3662641 (-)),
(Complex (#8921): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#9144): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#9145): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#9146): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#9147): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#9148): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#9149): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#9150): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#9151): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#9152): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#9077): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#9514): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#9519): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#10025): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#9877): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#9879): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#10352): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#10550): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#10587): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#10655): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#10656): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#10657): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#10658): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#10659): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#10660): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#10661): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#10881): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#11090): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#11091): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#11103): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#11104): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#11106): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#11107): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#11277): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#11336): None, Gene: (b3516, gadX) 3663009-3663833 (-)),
(Complex (#10628): None, Gene: (b3574, yiaJ) 3739707-3740555 (-)),
(Complex (#10743): None, Gene: (b3574, yiaJ) 3739707-3740555 (-)),
(Complex (#10271): None, Gene: (b3773, ilvY) 3954950-3955843 (-)),
(Complex (#10481): None, Gene: (b3773, ilvY) 3954950-3955843 (-)),
(Complex (#8795): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#10048): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#10049): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#9815): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#9898): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#9938): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#9939): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#9637): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#9664): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#9994): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#9964): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#9971): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#9972): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#10229): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#10230): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#10362): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#10477): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#10539): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#10565): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#10630): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#10682): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#10688): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#10869): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#10870): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#10941): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#11147): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#11300): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#11507): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#11510): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#11561): None, Gene: (b4062, soxS) 4275083-4275406 (-)),
(Complex (#9796): None, Gene: (b4118, melR) 4338743-4339651 (-)),
(Complex (#9797): None, Gene: (b4118, melR) 4338743-4339651 (-)),
(Complex (#10526): None, Gene: (b4118, melR) 4338743-4339651 (-)),
(Complex (#10527): None, Gene: (b4118, melR) 4338743-4339651 (-)),
(Complex (#10794): None, Gene: (b4191, ulaR) 4415721-4416476 (-)),
(Complex (#10795): None, Gene: (b4191, ulaR) 4415721-4416476 (-)),
(Complex (#10796): None, Gene: (b4191, ulaR) 4415721-4416476 (-)),
(Complex (#10797): None, Gene: (b4191, ulaR) 4415721-4416476 (-)),
(Complex (#11030): None, Gene: (b4260, pepA) 4482463-4483974 (-)),
(Complex (#11448): None, Gene: (b4260, pepA) 4482463-4483974 (-)),
(Complex (#11453): None, Gene: (b4260, pepA) 4482463-4483974 (-)),
(Complex (#9531): None, Gene: (b4264, idnR) 4488164-4489162 (-)),
(Complex (#8799): None, Gene: (b4396, rob) 4632464-4633333 (-)),
(Complex (#10050): None, Gene: (b4396, rob) 4632464-4633333 (-)),
(Complex (#9963): None, Gene: (b4396, rob) 4632464-4633333 (-)),
(Complex (#10273): None, Gene: (b4396, rob) 4632464-4633333 (-)),
(Complex (#10537): None, Gene: (b4396, rob) 4632464-4633333 (-)),
(Complex (#10540): None, Gene: (b4396, rob) 4632464-4633333 (-)),
(Complex (#10566): None, Gene: (b4396, rob) 4632464-4633333 (-)),
(Complex (#10624): None, Gene: (b4396, rob) 4632464-4633333 (-)),
(Complex (#10683): None, Gene: (b4396, rob) 4632464-4633333 (-)),
(Complex (#10866): None, Gene: (b4396, rob) 4632464-4633333 (-)),
(Complex (#10868): None, Gene: (b4396, rob) 4632464-4633333 (-)),
(Complex (#11267): None, Gene: (b4396, rob) 4632464-4633333 (-)),
(Complex (#11302): None, Gene: (b4396, rob) 4632464-4633333 (-)),
(Complex (#11549): None, Gene: (b4396, rob) 4632464-4633333 (-))]
In [8]:
ome.query(TU).join(Gene).filter(Gene.name=='sdhC').all()
Out[8]:
[]
In [11]:
ome.query(TU).first().genes
Out[11]:
[Gene: (b0721, sdhC) 754400-754789 (+),
Gene: (b0722, sdhD) 754783-755130 (+),
Gene: (b0723, sdhA) 755130-756896 (+),
Gene: (b0724, sdhB) 756912-757628 (+),
Gene: (b0726, sucA) 757929-760730 (+),
Gene: (b0727, sucB) 760745-761962 (+),
Gene: (b0728, sucC) 762237-763403 (+),
Gene: (b0729, sucD) 763403-764272 (+)]
In [10]:
ome.query(Complex).join(ComplexComposition).join(DnaBindingSite).first().children
Out[10]:
[Complex (#4645): GalR-galactose, DNA (#6269, BS0-7660) 3086033-3086033 +]
In [8]:
ome.query(Protein).limit(10).first().long_name
Out[8]:
u'predicted transcriptional accessory protein'
In [7]:
ome.query(data.GenomeData).count()
Out[7]:
182258L
In [ ]:
ome.query(Gene).filter_by(name='sucD').first().data
In [ ]:
In [3]:
ome.get_or_create(components.Component, name='test component')
Out[3]:
Component (#1): test component
In [5]:
ome.get_or_create(DNA, name='test rna', leftpos=1000, rightpos=2000, strand='+')
Out[5]:
DNA (#2, test rna) 1000-2000 +
In [6]:
ome.get_or_create(components.Gene, name='gapA', leftpos='3451', rightpos='5462', strand='+', locus_id='b1252')
Out[6]:
Gene (#2, b1252, gapA) 3451-5462 +
In [7]:
ome.get_or_create(DnaBindingSite, name='d', leftpos=1500, rightpos=1500, strand='+', centerpos=1500, width=0)
Out[7]:
DNA (#3, d) 1500-1500 +
In [11]:
a = ome.query(DnaBindingSite).join(GenomeRegion).filter(and_(GenomeRegion.leftpos > 1000, GenomeRegion.rightpos < 20000)).first()
In [9]:
ome.query(Complex).join(ComplexComposition, DNA).all()
Out[9]:
[Complex (#2318): None,
Complex (#2320): None,
Complex (#2322): None,
Complex (#2325): None,
Complex (#2329): None,
Complex (#2331): None,
Complex (#2332): None,
Complex (#2333): None,
Complex (#2334): None,
Complex (#2335): None,
Complex (#2337): None,
Complex (#2339): None,
Complex (#2341): None,
Complex (#2343): None,
Complex (#2345): None,
Complex (#2348): None,
Complex (#2349): None,
Complex (#2351): None,
Complex (#2352): None,
Complex (#2353): None,
Complex (#2357): None,
Complex (#2359): None,
Complex (#2360): None,
Complex (#2361): None,
Complex (#2363): None,
Complex (#2365): None,
Complex (#2366): None,
Complex (#2368): None,
Complex (#2369): None,
Complex (#2371): None,
Complex (#2372): None,
Complex (#2375): None,
Complex (#2376): None,
Complex (#2378): None,
Complex (#2379): None,
Complex (#2382): None,
Complex (#2383): None,
Complex (#2384): None,
Complex (#2385): None,
Complex (#2387): None,
Complex (#2388): None,
Complex (#2390): None,
Complex (#2392): None,
Complex (#2393): None,
Complex (#2395): None,
Complex (#2396): None,
Complex (#2397): None,
Complex (#2398): None,
Complex (#2399): None,
Complex (#2401): None,
Complex (#2403): None,
Complex (#2405): None,
Complex (#2407): None,
Complex (#2408): None,
Complex (#2409): None,
Complex (#2410): None,
Complex (#2411): None,
Complex (#2412): None,
Complex (#2413): None,
Complex (#2415): None,
Complex (#2416): None,
Complex (#2417): None,
Complex (#2418): None,
Complex (#2419): None,
Complex (#2421): None,
Complex (#2422): None,
Complex (#2424): None,
Complex (#2426): None,
Complex (#2427): None,
Complex (#2428): None,
Complex (#2429): None,
Complex (#2430): None,
Complex (#2431): None,
Complex (#2432): None,
Complex (#2433): None,
Complex (#2434): None,
Complex (#2435): None,
Complex (#2436): None,
Complex (#2437): None,
Complex (#2438): None,
Complex (#2440): None,
Complex (#2441): None,
Complex (#2442): None,
Complex (#2444): None,
Complex (#2445): None,
Complex (#2447): None,
Complex (#2449): None,
Complex (#2450): None,
Complex (#2452): None,
Complex (#2453): None,
Complex (#2455): None,
Complex (#2456): None,
Complex (#2457): None,
Complex (#2458): None,
Complex (#2459): None,
Complex (#2460): None,
Complex (#2461): None,
Complex (#2462): None,
Complex (#2463): None,
Complex (#2464): None,
Complex (#2465): None,
Complex (#2466): None,
Complex (#2467): None,
Complex (#2469): None,
Complex (#2470): None,
Complex (#2471): None,
Complex (#2472): None,
Complex (#2474): None,
Complex (#2475): None,
Complex (#2476): None,
Complex (#2478): None,
Complex (#2480): None,
Complex (#2481): None,
Complex (#2484): None,
Complex (#2486): None,
Complex (#2490): None,
Complex (#2491): None,
Complex (#2492): None,
Complex (#2494): None,
Complex (#2496): None,
Complex (#2497): None,
Complex (#2498): None,
Complex (#2499): None,
Complex (#2500): None,
Complex (#2501): None,
Complex (#2502): None,
Complex (#2503): None,
Complex (#2504): None,
Complex (#2505): None,
Complex (#2506): None,
Complex (#2507): None,
Complex (#2509): None,
Complex (#2511): None,
Complex (#2512): None,
Complex (#2513): None,
Complex (#2516): None,
Complex (#2517): None,
Complex (#2518): None,
Complex (#2519): None,
Complex (#2521): None,
Complex (#2522): None,
Complex (#2524): None,
Complex (#2525): None,
Complex (#2526): None,
Complex (#2528): None,
Complex (#2529): None,
Complex (#2531): None,
Complex (#2532): None,
Complex (#2534): None,
Complex (#2535): None,
Complex (#2536): None,
Complex (#2537): None,
Complex (#2538): None,
Complex (#2539): None,
Complex (#2540): None,
Complex (#2541): None,
Complex (#2543): None,
Complex (#2545): None,
Complex (#2547): None,
Complex (#2548): None,
Complex (#2550): None,
Complex (#2552): None,
Complex (#2553): None,
Complex (#2554): None,
Complex (#2555): None,
Complex (#2556): None,
Complex (#2557): None,
Complex (#2558): None,
Complex (#2559): None,
Complex (#2561): None,
Complex (#2563): None,
Complex (#2565): None,
Complex (#2566): None,
Complex (#2568): None,
Complex (#2569): None,
Complex (#2571): None,
Complex (#2573): None,
Complex (#2574): None,
Complex (#2575): None,
Complex (#2576): None,
Complex (#2577): None,
Complex (#2578): None,
Complex (#2579): None,
Complex (#2580): None,
Complex (#2581): None,
Complex (#2582): None,
Complex (#2583): None,
Complex (#2584): None,
Complex (#2585): None,
Complex (#2586): None,
Complex (#2587): None,
Complex (#2588): None,
Complex (#2589): None,
Complex (#2590): None,
Complex (#2591): None,
Complex (#2592): None,
Complex (#2593): None,
Complex (#2594): None,
Complex (#2595): None,
Complex (#2596): None,
Complex (#2598): None,
Complex (#2599): None,
Complex (#2600): None,
Complex (#2601): None,
Complex (#2602): None,
Complex (#2603): None,
Complex (#2604): None,
Complex (#2605): None,
Complex (#2606): None,
Complex (#2607): None,
Complex (#2608): None,
Complex (#2609): None,
Complex (#2610): None,
Complex (#2611): None,
Complex (#2612): None,
Complex (#2613): None,
Complex (#2614): None,
Complex (#2615): None,
Complex (#2617): None,
Complex (#2618): None,
Complex (#2619): None,
Complex (#2620): None,
Complex (#2622): None,
Complex (#2623): None,
Complex (#2624): None,
Complex (#2625): None,
Complex (#2626): None,
Complex (#2628): None,
Complex (#2630): None,
Complex (#2634): None,
Complex (#2636): None,
Complex (#2638): None,
Complex (#2644): None,
Complex (#2646): None,
Complex (#2648): None,
Complex (#2650): None,
Complex (#2652): None,
Complex (#2654): None,
Complex (#2656): None,
Complex (#2658): None,
Complex (#2660): None,
Complex (#2662): None,
Complex (#2664): None,
Complex (#2666): None,
Complex (#2668): None,
Complex (#2670): None,
Complex (#2672): None,
Complex (#2674): None,
Complex (#2676): None,
Complex (#2678): None,
Complex (#2680): None,
Complex (#2682): None,
Complex (#2684): None,
Complex (#2686): None,
Complex (#2690): None,
Complex (#2694): None,
Complex (#2696): None,
Complex (#2698): None,
Complex (#2700): None,
Complex (#2702): None,
Complex (#2704): None,
Complex (#2706): None,
Complex (#2708): None,
Complex (#2710): None,
Complex (#2712): None,
Complex (#2716): None,
Complex (#2718): None,
Complex (#2720): None,
Complex (#2722): None,
Complex (#2726): None,
Complex (#2728): None,
Complex (#2730): None,
Complex (#2734): None,
Complex (#2736): None,
Complex (#2740): None,
Complex (#2742): None,
Complex (#2744): None,
Complex (#2748): None,
Complex (#2750): None,
Complex (#2754): None,
Complex (#2756): None,
Complex (#2762): None,
Complex (#2764): None,
Complex (#2766): None,
Complex (#2770): None,
Complex (#2772): None,
Complex (#2774): None,
Complex (#2776): None,
Complex (#2778): None,
Complex (#2780): None,
Complex (#2782): None,
Complex (#2784): None,
Complex (#2786): None,
Complex (#2788): None,
Complex (#2790): None,
Complex (#2792): None,
Complex (#2794): None,
Complex (#2796): None,
Complex (#2798): None,
Complex (#2800): None,
Complex (#2802): None,
Complex (#2804): None,
Complex (#2806): None,
Complex (#2808): None,
Complex (#2810): None,
Complex (#2812): None,
Complex (#2814): None,
Complex (#2816): None,
Complex (#2818): None,
Complex (#2820): None,
Complex (#2822): None,
Complex (#2826): None,
Complex (#2828): None,
Complex (#2830): None,
Complex (#2834): None,
Complex (#2836): None,
Complex (#2838): None,
Complex (#2844): None,
Complex (#2846): None,
Complex (#2848): None,
Complex (#2850): None,
Complex (#2852): None,
Complex (#2854): None,
Complex (#2856): None,
Complex (#2858): None,
Complex (#2862): None,
Complex (#2864): None,
Complex (#2866): None,
Complex (#2868): None,
Complex (#2870): None,
Complex (#2872): None,
Complex (#2874): None,
Complex (#2876): None,
Complex (#2878): None,
Complex (#2880): None,
Complex (#2882): None,
Complex (#2884): None,
Complex (#2886): None,
Complex (#2888): None,
Complex (#2890): None,
Complex (#2892): None,
Complex (#2894): None,
Complex (#2896): None,
Complex (#2898): None,
Complex (#2900): None,
Complex (#2902): None,
Complex (#2904): None,
Complex (#2908): None,
Complex (#2910): None,
Complex (#2912): None,
Complex (#2914): None,
Complex (#2916): None,
Complex (#2918): None,
Complex (#2922): None,
Complex (#2924): None,
Complex (#2926): None,
Complex (#2928): None,
Complex (#2930): None,
Complex (#2932): None,
Complex (#2934): None,
Complex (#2936): None,
Complex (#2940): None,
Complex (#2942): None,
Complex (#2944): None,
Complex (#2946): None,
Complex (#2948): None,
Complex (#2950): None,
Complex (#2952): None,
Complex (#2954): None,
Complex (#2627): None,
Complex (#2629): None,
Complex (#2631): None,
Complex (#2633): None,
Complex (#2635): None,
Complex (#2637): None,
Complex (#2639): None,
Complex (#2641): None,
Complex (#2643): None,
Complex (#2645): None,
Complex (#2647): None,
Complex (#2649): None,
Complex (#2651): None,
Complex (#2653): None,
Complex (#2655): None,
Complex (#2659): None,
Complex (#2661): None,
Complex (#2663): None,
Complex (#2665): None,
Complex (#2667): None,
Complex (#2669): None,
Complex (#2671): None,
Complex (#2673): None,
Complex (#2675): None,
Complex (#2679): None,
Complex (#2683): None,
Complex (#2685): None,
Complex (#2687): None,
Complex (#2689): None,
Complex (#2691): None,
Complex (#2693): None,
Complex (#2695): None,
Complex (#2697): None,
Complex (#2699): None,
Complex (#2701): None,
Complex (#2703): None,
Complex (#2705): None,
Complex (#2707): None,
Complex (#2709): None,
Complex (#2711): None,
Complex (#2713): None,
Complex (#2715): None,
Complex (#2717): None,
Complex (#2721): None,
Complex (#2723): None,
Complex (#2725): None,
Complex (#2727): None,
Complex (#2731): None,
Complex (#2733): None,
Complex (#2735): None,
Complex (#2737): None,
Complex (#2739): None,
Complex (#2741): None,
Complex (#2743): None,
Complex (#2745): None,
Complex (#2747): None,
Complex (#2749): None,
Complex (#2751): None,
Complex (#2753): None,
Complex (#2755): None,
Complex (#2757): None,
Complex (#2759): None,
Complex (#2761): None,
Complex (#2763): None,
Complex (#2767): None,
Complex (#2769): None,
Complex (#2771): None,
Complex (#2773): None,
Complex (#2775): None,
Complex (#2777): None,
Complex (#2779): None,
Complex (#2781): None,
Complex (#2783): None,
Complex (#2785): None,
Complex (#2787): None,
Complex (#2789): None,
Complex (#2791): None,
Complex (#2793): None,
Complex (#2795): None,
Complex (#2797): None,
Complex (#2799): None,
Complex (#2801): None,
Complex (#2803): None,
Complex (#2807): None,
Complex (#2809): None,
Complex (#2811): None,
Complex (#2813): None,
Complex (#2815): None,
Complex (#2817): None,
Complex (#2819): None,
Complex (#2821): None,
Complex (#2823): None,
Complex (#2825): None,
Complex (#2827): None,
Complex (#2829): None,
Complex (#2831): None,
Complex (#2833): None,
Complex (#2835): None,
Complex (#2837): None,
Complex (#2839): None,
Complex (#2841): None,
Complex (#2843): None,
Complex (#2845): None,
Complex (#2847): None,
Complex (#2849): None,
Complex (#2851): None,
Complex (#2853): None,
Complex (#2855): None,
Complex (#2857): None,
Complex (#2859): None,
Complex (#2861): None,
Complex (#2863): None,
Complex (#2865): None,
Complex (#2867): None,
Complex (#2869): None,
Complex (#2871): None,
Complex (#2873): None,
Complex (#2875): None,
Complex (#2877): None,
Complex (#2879): None,
Complex (#2881): None,
Complex (#2883): None,
Complex (#2885): None,
Complex (#2887): None,
Complex (#2889): None,
Complex (#2891): None,
Complex (#2893): None,
Complex (#2895): None,
Complex (#2897): None,
Complex (#2901): None,
Complex (#2903): None,
Complex (#2905): None,
Complex (#2907): None,
Complex (#2909): None,
Complex (#2911): None,
Complex (#2913): None,
Complex (#2915): None,
Complex (#2921): None,
Complex (#2923): None,
Complex (#2925): None,
Complex (#2927): None,
Complex (#2929): None,
Complex (#2931): None,
Complex (#2933): None,
Complex (#2935): None,
Complex (#2937): None,
Complex (#2939): None,
Complex (#2941): None,
Complex (#2943): None,
Complex (#2945): None,
Complex (#2947): None,
Complex (#2949): None,
Complex (#2951): None,
Complex (#2953): None,
Complex (#2955): None,
Complex (#2956): None,
Complex (#2957): None,
Complex (#2958): None,
Complex (#2959): None,
Complex (#2961): None,
Complex (#2962): None,
Complex (#2963): None,
Complex (#2964): None,
Complex (#2965): None,
Complex (#2966): None,
Complex (#2967): None,
Complex (#2968): None,
Complex (#2969): None,
Complex (#2970): None,
Complex (#2972): None,
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Complex (#4846): None,
Complex (#4848): None,
Complex (#4850): None,
Complex (#4852): None,
Complex (#4854): None,
Complex (#4856): None,
Complex (#4860): None,
Complex (#4862): None,
Complex (#4864): None,
Complex (#4866): None,
Complex (#4868): None,
Complex (#4870): None,
Complex (#4872): None,
Complex (#4874): None,
Complex (#4876): None,
Complex (#4878): None,
Complex (#4880): None,
Complex (#4882): None,
Complex (#4884): None,
Complex (#4886): None,
Complex (#4888): None,
Complex (#4890): None,
Complex (#4892): None,
Complex (#4894): None,
Complex (#4896): None,
Complex (#4898): None,
Complex (#4900): None,
Complex (#4902): None,
Complex (#4904): None,
Complex (#4906): None,
Complex (#4908): None,
Complex (#4910): None,
Complex (#4912): None,
Complex (#4914): None,
Complex (#4916): None,
Complex (#4918): None,
Complex (#4920): None,
Complex (#4922): None,
Complex (#4924): None,
Complex (#4926): None,
Complex (#4928): None,
Complex (#4930): None,
Complex (#4932): None,
Complex (#4934): None,
Complex (#4936): None,
Complex (#4938): None,
Complex (#4940): None,
Complex (#4942): None,
Complex (#4944): None,
Complex (#4946): None,
Complex (#4927): None,
Complex (#4929): None,
Complex (#4931): None,
Complex (#4933): None,
Complex (#4935): None,
Complex (#4937): None,
Complex (#4939): None,
Complex (#4941): None,
Complex (#4943): None,
Complex (#4945): None,
Complex (#4947): None,
Complex (#4949): None,
Complex (#4951): None,
Complex (#4953): None,
Complex (#4955): None,
Complex (#4957): None,
Complex (#4959): None,
Complex (#4961): None,
Complex (#4965): None,
Complex (#4967): None,
Complex (#4969): None,
Complex (#4971): None,
Complex (#4973): None,
Complex (#4975): None,
Complex (#4977): None,
Complex (#4979): None,
Complex (#4981): None,
Complex (#4983): None,
Complex (#4985): None,
Complex (#4987): None,
Complex (#4989): None,
Complex (#4991): None,
Complex (#4993): None,
Complex (#4995): None,
Complex (#4997): None,
Complex (#4999): None,
Complex (#5001): None,
Complex (#5003): None,
Complex (#5005): None,
Complex (#5007): None,
Complex (#5009): None,
Complex (#5011): None,
Complex (#5017): None,
Complex (#5019): None,
Complex (#5021): None,
Complex (#5023): None,
Complex (#5025): None,
Complex (#5027): None,
Complex (#5029): None,
Complex (#5031): None,
Complex (#5033): None,
Complex (#5035): None,
Complex (#5037): None,
Complex (#5039): None,
Complex (#5041): None,
Complex (#5043): None,
Complex (#5045): None,
Complex (#5047): None,
Complex (#5049): None,
Complex (#5051): None,
Complex (#5055): None,
Complex (#5057): None,
Complex (#5059): None,
Complex (#5061): None,
Complex (#5063): None,
Complex (#5065): None,
Complex (#5067): None,
Complex (#5069): None,
Complex (#5071): None,
Complex (#5073): None,
Complex (#5075): None,
Complex (#5077): None,
Complex (#5079): None,
Complex (#5081): None,
Complex (#5083): None,
Complex (#5085): None,
Complex (#5087): None,
Complex (#5089): None,
Complex (#5091): None,
Complex (#5093): None,
Complex (#5095): None,
Complex (#5097): None,
Complex (#5099): None,
Complex (#5101): None,
Complex (#5103): None,
Complex (#5105): None,
Complex (#5107): None,
Complex (#5109): None,
Complex (#5111): None,
Complex (#5113): None,
Complex (#5115): None,
Complex (#5117): None,
Complex (#5119): None,
Complex (#5123): None,
Complex (#5127): None,
Complex (#5129): None,
Complex (#5131): None,
Complex (#5133): None,
Complex (#5135): None,
Complex (#5137): None,
Complex (#5139): None,
Complex (#5141): None,
Complex (#5143): None,
Complex (#5145): None,
Complex (#5147): None,
Complex (#5149): None,
Complex (#5151): None,
Complex (#5153): None,
Complex (#5155): None,
Complex (#5157): None,
Complex (#5159): None,
Complex (#5161): None,
Complex (#5163): None,
Complex (#5165): None,
Complex (#5167): None,
Complex (#5169): None,
Complex (#5171): None,
Complex (#5173): None,
Complex (#5175): None,
Complex (#5177): None,
Complex (#5179): None,
Complex (#5181): None,
Complex (#5183): None,
Complex (#5185): None,
Complex (#5187): None,
Complex (#5189): None,
Complex (#5191): None,
Complex (#5193): None,
Complex (#5195): None,
Complex (#5197): None,
Complex (#5199): None,
Complex (#5201): None,
Complex (#5203): None,
Complex (#5205): None,
Complex (#5207): None,
Complex (#5209): None,
Complex (#5211): None,
Complex (#5213): None,
Complex (#5215): None,
Complex (#5217): None,
Complex (#5219): None,
Complex (#5221): None,
Complex (#5223): None,
Complex (#5225): None,
Complex (#5227): None,
Complex (#5229): None,
Complex (#5231): None,
Complex (#5233): None,
Complex (#5235): None,
Complex (#5237): None,
Complex (#5239): None,
Complex (#5241): None,
Complex (#5243): None,
Complex (#5245): None,
Complex (#5247): None,
Complex (#5249): None,
Complex (#5251): None,
Complex (#5253): None,
Complex (#5255): None,
Complex (#5257): None,
Complex (#5259): None,
Complex (#5261): None,
Complex (#5263): None,
Complex (#5265): None,
Complex (#5267): None,
Complex (#5269): None,
Complex (#5271): None,
Complex (#5273): None,
Complex (#5275): None,
Complex (#5277): None,
Complex (#5279): None,
Complex (#5281): None,
Complex (#5283): None,
Complex (#5285): None,
Complex (#5287): None,
Complex (#5289): None,
Complex (#5291): None,
Complex (#5293): None,
Complex (#5295): None,
Complex (#5297): None,
Complex (#5299): None,
Complex (#5301): None,
Complex (#5303): None,
Complex (#5305): None,
Complex (#5307): None,
Complex (#5309): None,
Complex (#5311): None,
Complex (#5313): None,
Complex (#5315): None,
Complex (#5317): None,
Complex (#5319): None,
Complex (#5321): None,
Complex (#5323): None,
Complex (#5325): None,
Complex (#5327): None,
Complex (#5329): None,
Complex (#5331): None,
Complex (#5333): None,
Complex (#5335): None,
Complex (#5337): None,
Complex (#5339): None,
Complex (#5341): None,
Complex (#5345): None,
Complex (#5347): None,
Complex (#5349): None,
Complex (#5351): None,
Complex (#5353): None,
Complex (#5355): None,
Complex (#4948): None,
Complex (#4950): None,
Complex (#4952): None,
Complex (#4954): None,
Complex (#4956): None,
Complex (#4958): None,
Complex (#4960): None,
Complex (#4962): None,
Complex (#4964): None,
Complex (#4966): None,
Complex (#4968): None,
Complex (#4970): None,
Complex (#4972): None,
Complex (#4974): None,
Complex (#4976): None,
Complex (#4978): None,
Complex (#4980): None,
Complex (#4982): None,
Complex (#4984): None,
Complex (#4986): None,
Complex (#4988): None,
Complex (#4990): None,
Complex (#4992): None,
Complex (#4994): None,
Complex (#4996): None,
Complex (#4998): None,
Complex (#5000): None,
Complex (#5002): None,
Complex (#5004): None,
Complex (#5006): None,
Complex (#5008): None,
Complex (#5010): None,
Complex (#5012): None,
Complex (#5014): None,
Complex (#5016): None,
Complex (#5018): None,
Complex (#5020): None,
Complex (#5022): None,
Complex (#5024): None,
Complex (#5026): None,
Complex (#5028): None,
Complex (#5030): None,
Complex (#5032): None,
Complex (#5034): None,
Complex (#5036): None,
Complex (#5038): None,
Complex (#5040): None,
Complex (#5042): None,
Complex (#5044): None,
Complex (#5046): None,
Complex (#5048): None,
Complex (#5050): None,
Complex (#5052): None,
Complex (#5054): None,
Complex (#5056): None,
Complex (#5058): None,
Complex (#5060): None,
Complex (#5062): None,
Complex (#5064): None,
Complex (#5066): None,
Complex (#5068): None,
Complex (#5070): None,
Complex (#5072): None,
Complex (#5074): None,
Complex (#5076): None,
Complex (#5078): None,
Complex (#5080): None,
Complex (#5082): None,
Complex (#5084): None,
Complex (#5086): None,
Complex (#5088): None,
Complex (#5090): None,
Complex (#5092): None,
Complex (#5094): None,
Complex (#5096): None,
Complex (#5098): None,
Complex (#5100): None,
Complex (#5102): None,
Complex (#5104): None,
Complex (#5106): None,
Complex (#5108): None,
Complex (#5110): None,
Complex (#5112): None,
Complex (#5114): None,
Complex (#5116): None,
Complex (#5118): None,
Complex (#5120): None,
Complex (#5122): None,
Complex (#5124): None,
Complex (#5126): None,
Complex (#5128): None,
Complex (#5130): None,
Complex (#5132): None,
Complex (#5134): None,
Complex (#5136): None,
Complex (#5138): None,
Complex (#5140): None,
Complex (#5142): None,
Complex (#5144): None,
Complex (#5146): None,
Complex (#5148): None,
Complex (#5150): None,
Complex (#5152): None,
Complex (#5154): None,
Complex (#5156): None,
Complex (#5158): None,
Complex (#5160): None,
Complex (#5162): None,
Complex (#5164): None,
Complex (#5166): None,
Complex (#5168): None,
Complex (#5170): None,
Complex (#5174): None,
Complex (#5176): None,
Complex (#5178): None,
Complex (#5180): None,
Complex (#5182): None,
Complex (#5184): None,
Complex (#5186): None,
Complex (#5188): None,
Complex (#5190): None,
Complex (#5192): None,
Complex (#5194): None,
Complex (#5196): None,
Complex (#5198): None,
Complex (#5200): None,
Complex (#5202): None,
Complex (#5204): None,
Complex (#5206): None,
Complex (#5208): None,
Complex (#5210): None,
Complex (#5212): None,
Complex (#5214): None,
Complex (#5216): None,
Complex (#5218): None,
Complex (#5220): None,
Complex (#5222): None,
Complex (#5224): None,
Complex (#5226): None,
Complex (#5228): None,
Complex (#5230): None,
Complex (#5232): None,
Complex (#5234): None,
Complex (#5236): None,
Complex (#5238): None,
Complex (#5240): None,
Complex (#5242): None,
Complex (#5244): None,
Complex (#5246): None,
Complex (#5248): None,
Complex (#5250): None,
Complex (#5252): None,
Complex (#5254): None,
Complex (#5256): None,
Complex (#5258): None,
Complex (#5262): None,
Complex (#5264): None,
Complex (#5266): None,
Complex (#5268): None,
Complex (#5270): None,
Complex (#5272): None,
Complex (#5274): None,
Complex (#5276): None,
Complex (#5278): None,
Complex (#5280): None,
Complex (#5282): None,
Complex (#5284): None,
Complex (#5286): None,
Complex (#5288): None,
Complex (#5290): None,
Complex (#5292): None,
Complex (#5294): None,
Complex (#5296): None,
Complex (#5298): None,
Complex (#5300): None,
Complex (#5302): None,
Complex (#5304): None,
Complex (#5306): None,
Complex (#5308): None,
Complex (#5310): None,
Complex (#5312): None,
Complex (#5314): None,
Complex (#5316): None,
Complex (#5318): None,
Complex (#5320): None,
Complex (#5322): None,
Complex (#5324): None,
Complex (#5326): None,
Complex (#5328): None,
Complex (#5330): None,
Complex (#5332): None,
Complex (#5334): None,
Complex (#5336): None,
Complex (#5338): None,
Complex (#5340): None,
Complex (#5342): None,
Complex (#5344): None,
Complex (#5346): None,
Complex (#5348): None,
Complex (#5350): None,
Complex (#5352): None,
Complex (#5354): None]
In [6]:
ome.query(DnaBindingSite).filter(DnaBindingSite.genome_region.leftpos > 1000, DnaBindingSite.genome_region.rightpos < 2000).all()
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-6-ec3c8d678a8e> in <module>()
----> 1 ome.query(DnaBindingSite).filter(DnaBindingSite.genome_region.leftpos > 1000, DnaBindingSite.genome_region.rightpos < 2000).all()
/Library/Python/2.7/site-packages/sqlalchemy/orm/attributes.pyc in __getattr__(self, key)
187 type(self.comparator).__name__,
188 self,
--> 189 key)
190 )
191
AttributeError: Neither 'InstrumentedAttribute' object nor 'Comparator' object associated with DnaBindingSite.genome_region has an attribute 'leftpos'
In [9]:
{k: kwargs[k] for k in unique_cols}
Out[9]:
{'leftpos': 4630726.5, 'rightpos': 4630726.5, 'strand': '+'}
In [4]:
kwargs = {'leftpos': 4630726.5, 'rightpos': 4630726.5, 'strand': '+'}
unique_cols = ['leftpos', 'rightpos', 'strand']
In [4]:
ome.query(GenomeRegion).all()
Out[4]:
[GenomeRegion (#1): 786853-786853 (+ strand),
GenomeRegion (#2): 3681627-3681627 (+ strand),
GenomeRegion (#3): 4630727-4630727 (+ strand)]
In [5]:
ome.query(DnaBindingSite).all()
Out[5]:
[]
In [5]:
a = ome.query(components.Gene).filter(components.Gene.name.ilike('suc%')).first()
In [13]:
a = ome.query(base.GenomeRegion).limit(10).all()[2]
In [9]:
a.locus_id
Out[9]:
u'b0726'
In [24]:
ome.query(Complex).all()[110].children[2].name
Out[24]:
u'GUTA-MONOMER'
In [10]:
ome.query(Complex).join(ComplexComposition, SmallMolecule).count()
Out[10]:
97L
In [11]:
a = ome.query(components.Complex).first()
In [16]:
x = a.children[0]
In [17]:
x.parent
Out[17]:
[Complex (#1): MntR-Mn<sup>2+</sup>]
In [5]:
ome.get_or_create(components.Protein, name='protoheme IX ABC transporter', long_name='test')
---------------------------------------------------------------------------
IntegrityError Traceback (most recent call last)
<ipython-input-5-ba7b13e7fa1d> in <module>()
----> 1 ome.get_or_create(components.Protein, name='protoheme IX ABC transporter', long_name='test')
/Users/sfederow/ome/PrototypeDB/orm/base.pyc in get_or_create(session, class_type, **kwargs)
123 except:
124 session.add(class_type(**kwargs))
--> 125 session.commit()
126 result = session.query(class_type).filter_by(**kwargs).first()
127 return result
/Library/Python/2.7/site-packages/sqlalchemy/orm/session.pyc in commit(self)
763 raise sa_exc.InvalidRequestError("No transaction is begun.")
764
--> 765 self.transaction.commit()
766
767 def prepare(self):
/Library/Python/2.7/site-packages/sqlalchemy/orm/session.pyc in commit(self)
368 self._assert_active(prepared_ok=True)
369 if self._state is not PREPARED:
--> 370 self._prepare_impl()
371
372 if self._parent is None or self.nested:
/Library/Python/2.7/site-packages/sqlalchemy/orm/session.pyc in _prepare_impl(self)
348 if self.session._is_clean():
349 break
--> 350 self.session.flush()
351 else:
352 raise exc.FlushError(
/Library/Python/2.7/site-packages/sqlalchemy/orm/session.pyc in flush(self, objects)
1877 try:
1878 self._flushing = True
-> 1879 self._flush(objects)
1880 finally:
1881 self._flushing = False
/Library/Python/2.7/site-packages/sqlalchemy/orm/session.pyc in _flush(self, objects)
1995 except:
1996 with util.safe_reraise():
-> 1997 transaction.rollback(_capture_exception=True)
1998
1999 def is_modified(self, instance, include_collections=True,
/Library/Python/2.7/site-packages/sqlalchemy/util/langhelpers.pyc in __exit__(self, type_, value, traceback)
55 exc_type, exc_value, exc_tb = self._exc_info
56 self._exc_info = None # remove potential circular references
---> 57 compat.reraise(exc_type, exc_value, exc_tb)
58 else:
59 self._exc_info = None # remove potential circular references
/Library/Python/2.7/site-packages/sqlalchemy/orm/session.pyc in _flush(self, objects)
1959 self._warn_on_events = True
1960 try:
-> 1961 flush_context.execute()
1962 finally:
1963 self._warn_on_events = False
/Library/Python/2.7/site-packages/sqlalchemy/orm/unitofwork.pyc in execute(self)
368 self.dependencies,
369 postsort_actions):
--> 370 rec.execute(self)
371
372 def finalize_flush_changes(self):
/Library/Python/2.7/site-packages/sqlalchemy/orm/unitofwork.pyc in execute(self, uow)
521 persistence.save_obj(self.mapper,
522 uow.states_for_mapper_hierarchy(self.mapper, False, False),
--> 523 uow
524 )
525
/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 mapper, 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, mapper, table, insert)
592 else:
593 result = cached_connections[connection].\
--> 594 execute(statement, params)
595
596 primary_key = result.context.inserted_primary_key
/Library/Python/2.7/site-packages/sqlalchemy/engine/base.pyc in execute(self, object, *multiparams, **params)
715 type(object))
716 else:
--> 717 return meth(self, multiparams, params)
718
719 def _execute_function(self, func, multiparams, params):
/Library/Python/2.7/site-packages/sqlalchemy/sql/elements.pyc in _execute_on_connection(self, connection, multiparams, params)
315
316 def _execute_on_connection(self, connection, multiparams, params):
--> 317 return connection._execute_clauseelement(self, multiparams, params)
318
319 def unique_params(self, *optionaldict, **kwargs):
/Library/Python/2.7/site-packages/sqlalchemy/engine/base.pyc in _execute_clauseelement(self, elem, multiparams, params)
812 compiled_sql,
813 distilled_params,
--> 814 compiled_sql, distilled_params
815 )
816 if self._has_events:
/Library/Python/2.7/site-packages/sqlalchemy/engine/base.pyc in _execute_context(self, dialect, constructor, statement, parameters, *args)
925 parameters,
926 cursor,
--> 927 context)
928
929 if self._has_events:
/Library/Python/2.7/site-packages/sqlalchemy/engine/base.pyc in _handle_dbapi_exception(self, e, statement, parameters, cursor, context)
1074 self.dialect.dbapi.Error,
1075 connection_invalidated=self._is_disconnect),
-> 1076 exc_info
1077 )
1078
/Library/Python/2.7/site-packages/sqlalchemy/util/compat.pyc in raise_from_cause(exception, exc_info)
183 exc_info = sys.exc_info()
184 exc_type, exc_value, exc_tb = exc_info
--> 185 reraise(type(exception), exception, tb=exc_tb)
186
187 if py3k:
/Library/Python/2.7/site-packages/sqlalchemy/engine/base.pyc in _execute_context(self, dialect, constructor, statement, parameters, *args)
918 statement,
919 parameters,
--> 920 context)
921 except Exception as e:
922 self._handle_dbapi_exception(
/Library/Python/2.7/site-packages/sqlalchemy/engine/default.pyc in do_execute(self, cursor, statement, parameters, context)
423
424 def do_execute(self, cursor, statement, parameters, context=None):
--> 425 cursor.execute(statement, parameters)
426
427 def do_execute_no_params(self, cursor, statement, context=None):
IntegrityError: (IntegrityError) duplicate key value violates unique constraint "component_name_key"
DETAIL: Key (name)=(protoheme IX ABC transporter) already exists.
'INSERT INTO component (name, type) VALUES (%(name)s, %(type)s) RETURNING component.id' {'type': 'protein', 'name': 'protoheme IX ABC transporter'}
In [2]:
ome.query(components.Protein).filter_by(name='protoheme IX ABC transporter').one()
Out[2]:
Protein (#4, protoheme IX ABC transporter)
In [7]:
from sqlalchemy.orm import class_mapper
[key.name for key in class_mapper(components.Gene).primary_key]
Out[7]:
['id']
In [7]:
class_mapper.primary_key_from_instance()
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-7-a61ae87bf3ab> in <module>()
----> 1 class_mapper(components.Gene).primary_key_from_instance()
TypeError: primary_key_from_instance() takes exactly 2 arguments (1 given)
In [2]:
G = ome.get_or_create(components.Complex, name='G')
H = ome.get_or_create(components.Complex, name='H')
F = ome.get_or_create(components.Complex, name='F')
C = ome.get_or_create(components.Complex, name='C')
ome.get_or_create(components.ComplexComposition, complex_id=G.id, component_id=H.id, stoichiometry=1.)
ome.get_or_create(components.ComplexComposition, complex_id=G.id, component_id=F.id, stoichiometry=1.)
ome.get_or_create(components.ComplexComposition, complex_id=G.id, component_id=C.id, stoichiometry=1.)
D = ome.get_or_create(components.Protein, name='D')
E = ome.get_or_create(components.Protein, name='E')
ome.get_or_create(components.ComplexComposition, complex_id=F.id, component_id=D.id, stoichiometry=1.)
ome.get_or_create(components.ComplexComposition, complex_id=F.id, component_id=E.id, stoichiometry=1.)
A = ome.get_or_create(components.Protein, name='A')
B = ome.get_or_create(components.Complex, name='B')
ome.get_or_create(components.ComplexComposition, complex_id=C.id, component_id=A.id, stoichiometry=1.)
ome.get_or_create(components.ComplexComposition, complex_id=C.id, component_id=B.id, stoichiometry=1.)
I = ome.get_or_create(components.Protein, name='I')
J = ome.get_or_create(components.Protein, name='J')
ome.get_or_create(components.ComplexComposition, complex_id=B.id, component_id=I.id, stoichiometry=1.)
ome.get_or_create(components.ComplexComposition, complex_id=B.id, component_id=J.id, stoichiometry=1.)
Out[2]:
<PrototypeDB.orm.components.ComplexComposition at 0x1112d68d0>
In [5]:
C.children
Out[5]:
[Protein (#9876, None), Complex (#9877): None]
In [6]:
C.all_children
Out[6]:
[Protein (#9876, None),
Complex (#9877): None,
Protein (#9878, None),
Protein (#9879, None)]
In [5]:
ecocyc_ID = ome.get_or_create(base.DataSource, name="ecocyc").id
In [9]:
ome.get_or_create(base.id2otherid, id=D.id, other_id='test2', type='test',data_source_id=ecocyc_ID)
Out[9]:
test2 in (Data Source ecocyc (#1))
In [10]:
ome.query(base.id2otherid).all()
Out[10]:
[test2 in (Data Source ecocyc (#1))]
In [5]:
proteins = load_components.parseEco_dat('proteins.dat')
In [31]:
all_types = []
for key in proteins.keys()[0:40]:
try:
if 'Protein-Complexes' in proteins[key]['TYPES']:
print key
except:
continue
E1P-CPLX
CPLX0-3362
CPLX0-3361
ACETOLACTSYNIII-CPLX
ACYLCOASYN-CPLX
CARNDEHYDRA-CPLX
In [8]:
all_types = []
for key,values in proteins.iteritems():
try:
if 'Protein-Small-Molecule-Complexes' in values['TYPES']:
print key
except:
None
MONOMER0-2162
MONOMER0-1441
MONOMER0-158
MONOMER0-159
MONOMER0-155
MONOMER0-157
CPLX0-7681
CPLX0-7680
CPLX0-7689
MONOMER-47
MONOMER-48
MONOMER0-2221
MONOMER-60
MONOMER0-1781
MONOMER0-2201
CPLX0-7750
CPLX0-7746
CPLX0-7742
CPLX0-7743
CPLX-124
CPLX-127
MONOMER0-46
CPLX0-7729
CPLX0-8055
CPLX0-8054
CPLX0-8057
CPLX0-8056
CPLX0-8051
CPLX0-8059
CPLX0-8058
CPLX0-7749
CPLX0-7701
CPLX0-7702
CPLX0-8079
CPLX0-8077
CPLX0-8075
CPLX0-8074
CPLX0-8071
CPLX0-8070
MONOMER0-183
CPLX0-7541
CPLX-125
CPLX-123
CPLX-128
MONOMER0-49
CPLX0-7618
CPLX0-7619
MONOMER-58
CPLX0-7650
MONOMER0-2482
MONOMER0-161
MONOMER0-163
MONOMER0-941
CPLX0-7670
CPLX0-7671
CPLX0-7677
CPLX0-8062
MONOMER0-2261
MONOMER0-160
MONOMER0-162
MONOMER0-165
MONOMER0-164
CPLX0-7651
MONOMER0-2461
CPLX-172
CPLX0-8060
CPLX0-8061
MONOMER-53
MONOMER-55
MONOMER-54
MONOMER-57
MONOMER-56
MONOMER-59
MONOMER-2720
MONOMER0-2421
CPLX0-8026
CPLX0-8027
CPLX0-7752
CPLX0-7751
CPLX0-8047
CPLX0-8048
CPLX0-8076
CPLX0-7739
CPLX0-7735
CPLX0-7736
MONOMER0-1301
CPLX0-8069
CPLX0-7716
CPLX0-7715
CPLX0-7714
MONOMER0-562
MONOMER0-2101
CPLX0-8088
CPLX0-8083
CPLX0-8085
CPLX0-2781
MONOMER0-2081
CPLX0-6
CPLX0-7605
CPLX0-7606
MONOMER-51
MONOMER-52
CPLX0-7620
CPLX0-228
CPLX0-226
In [25]:
from trnlib.model_utility import *
In [26]:
model = load_model()
In [27]:
model.to_array_based_model()
Out[27]:
'iJO1366'
In [33]:
Out[33]:
<1x2583 sparse matrix of type '<type 'numpy.float64'>'
with 4 stored elements in Dictionary Of Keys format>
In [10]:
[x for x in data.query_genome_data([85],1000,2000,['+'])]
Out[10]:
[{u'_id': ObjectId('535dd7fb4eead34574c5e4d2'),
u'data_set_id': 85,
u'leftpos': 1000,
u'rightpos': 1000,
u'strand': u'+',
u'value': 12.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4d3'),
u'data_set_id': 85,
u'leftpos': 1001,
u'rightpos': 1001,
u'strand': u'+',
u'value': 14.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4d4'),
u'data_set_id': 85,
u'leftpos': 1002,
u'rightpos': 1002,
u'strand': u'+',
u'value': 14.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4d5'),
u'data_set_id': 85,
u'leftpos': 1003,
u'rightpos': 1003,
u'strand': u'+',
u'value': 14.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4d6'),
u'data_set_id': 85,
u'leftpos': 1004,
u'rightpos': 1004,
u'strand': u'+',
u'value': 14.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4d7'),
u'data_set_id': 85,
u'leftpos': 1005,
u'rightpos': 1005,
u'strand': u'+',
u'value': 13.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4d8'),
u'data_set_id': 85,
u'leftpos': 1006,
u'rightpos': 1006,
u'strand': u'+',
u'value': 13.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4d9'),
u'data_set_id': 85,
u'leftpos': 1007,
u'rightpos': 1007,
u'strand': u'+',
u'value': 13.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4da'),
u'data_set_id': 85,
u'leftpos': 1008,
u'rightpos': 1008,
u'strand': u'+',
u'value': 13.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4db'),
u'data_set_id': 85,
u'leftpos': 1009,
u'rightpos': 1009,
u'strand': u'+',
u'value': 13.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4dc'),
u'data_set_id': 85,
u'leftpos': 1010,
u'rightpos': 1010,
u'strand': u'+',
u'value': 13.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4dd'),
u'data_set_id': 85,
u'leftpos': 1011,
u'rightpos': 1011,
u'strand': u'+',
u'value': 13.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4de'),
u'data_set_id': 85,
u'leftpos': 1012,
u'rightpos': 1012,
u'strand': u'+',
u'value': 13.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4df'),
u'data_set_id': 85,
u'leftpos': 1013,
u'rightpos': 1013,
u'strand': u'+',
u'value': 13.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4e0'),
u'data_set_id': 85,
u'leftpos': 1014,
u'rightpos': 1014,
u'strand': u'+',
u'value': 13.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4e1'),
u'data_set_id': 85,
u'leftpos': 1015,
u'rightpos': 1015,
u'strand': u'+',
u'value': 13.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4e2'),
u'data_set_id': 85,
u'leftpos': 1016,
u'rightpos': 1016,
u'strand': u'+',
u'value': 13.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4e3'),
u'data_set_id': 85,
u'leftpos': 1017,
u'rightpos': 1017,
u'strand': u'+',
u'value': 14.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4e4'),
u'data_set_id': 85,
u'leftpos': 1018,
u'rightpos': 1018,
u'strand': u'+',
u'value': 15.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4e5'),
u'data_set_id': 85,
u'leftpos': 1019,
u'rightpos': 1019,
u'strand': u'+',
u'value': 15.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4e6'),
u'data_set_id': 85,
u'leftpos': 1020,
u'rightpos': 1020,
u'strand': u'+',
u'value': 15.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4e7'),
u'data_set_id': 85,
u'leftpos': 1021,
u'rightpos': 1021,
u'strand': u'+',
u'value': 13.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4e8'),
u'data_set_id': 85,
u'leftpos': 1022,
u'rightpos': 1022,
u'strand': u'+',
u'value': 12.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4e9'),
u'data_set_id': 85,
u'leftpos': 1023,
u'rightpos': 1023,
u'strand': u'+',
u'value': 12.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4ea'),
u'data_set_id': 85,
u'leftpos': 1024,
u'rightpos': 1024,
u'strand': u'+',
u'value': 10.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4eb'),
u'data_set_id': 85,
u'leftpos': 1025,
u'rightpos': 1025,
u'strand': u'+',
u'value': 10.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4ec'),
u'data_set_id': 85,
u'leftpos': 1026,
u'rightpos': 1026,
u'strand': u'+',
u'value': 12.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4ed'),
u'data_set_id': 85,
u'leftpos': 1027,
u'rightpos': 1027,
u'strand': u'+',
u'value': 12.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4ee'),
u'data_set_id': 85,
u'leftpos': 1028,
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u'strand': u'+',
u'value': 12.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4ef'),
u'data_set_id': 85,
u'leftpos': 1029,
u'rightpos': 1029,
u'strand': u'+',
u'value': 12.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4f0'),
u'data_set_id': 85,
u'leftpos': 1030,
u'rightpos': 1030,
u'strand': u'+',
u'value': 11.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4f1'),
u'data_set_id': 85,
u'leftpos': 1031,
u'rightpos': 1031,
u'strand': u'+',
u'value': 11.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4f2'),
u'data_set_id': 85,
u'leftpos': 1032,
u'rightpos': 1032,
u'strand': u'+',
u'value': 11.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4f3'),
u'data_set_id': 85,
u'leftpos': 1033,
u'rightpos': 1033,
u'strand': u'+',
u'value': 11.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4f4'),
u'data_set_id': 85,
u'leftpos': 1034,
u'rightpos': 1034,
u'strand': u'+',
u'value': 11.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4f5'),
u'data_set_id': 85,
u'leftpos': 1035,
u'rightpos': 1035,
u'strand': u'+',
u'value': 11.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4f6'),
u'data_set_id': 85,
u'leftpos': 1036,
u'rightpos': 1036,
u'strand': u'+',
u'value': 11.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4f7'),
u'data_set_id': 85,
u'leftpos': 1037,
u'rightpos': 1037,
u'strand': u'+',
u'value': 11.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4f8'),
u'data_set_id': 85,
u'leftpos': 1038,
u'rightpos': 1038,
u'strand': u'+',
u'value': 11.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4f9'),
u'data_set_id': 85,
u'leftpos': 1039,
u'rightpos': 1039,
u'strand': u'+',
u'value': 11.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4fa'),
u'data_set_id': 85,
u'leftpos': 1040,
u'rightpos': 1040,
u'strand': u'+',
u'value': 11.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4fb'),
u'data_set_id': 85,
u'leftpos': 1041,
u'rightpos': 1041,
u'strand': u'+',
u'value': 11.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4fc'),
u'data_set_id': 85,
u'leftpos': 1042,
u'rightpos': 1042,
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u'value': 11.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4fd'),
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u'value': 11.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e4fe'),
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{u'_id': ObjectId('535dd7fb4eead34574c5e4ff'),
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u'strand': u'+',
u'value': 11.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e500'),
u'data_set_id': 85,
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u'value': 11.0},
{u'_id': ObjectId('535dd7fb4eead34574c5e501'),
u'data_set_id': 85,
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{u'_id': ObjectId('535dd7fb4eead34574c5e502'),
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In [ ]:
Content source: steve-federowicz/om
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