from trnlib.omeORM import *
from pandas import *
from numpy import array
from sqlalchemy import func
from IPython.core.display import HTML
ome = Session()
most_peaks = read_table('Fnr_ChIP_seq_all.txt', index_col=1)
HTML(most_peaks.sort().to_html())
170 | + | +.1 | +.2 | +.3 | - | -5.52 | |
---|---|---|---|---|---|---|---|
thrL | |||||||
G6272 | 528277 | + | + | + | + | + | -7.09 |
abrB | 747110 | + | + | + | + | + | -6.7 |
aceB | 4213382 | - | - | - | + | - | N/A |
acs/nrfA | 4285671 | + | + | + | + | + | -10.3 |
adhE/ychE | 1297573 | + | + | + | + | + | -5.74 |
aegA/narQ | 2583785 | - | - | - | + | + | N/A |
aer/ygjG | 3217288 | + | + | + | + | - | -10.23 |
anmK/slyB | 1717794 | + | + | + | + | + | -6.45 |
apt | 490536 | + | - | - | - | - | -5.67 |
aqpZ/ybjD | 915496 | + | + | + | + | - | -12.42 |
aroP/pdhR | 121981 | + | + | + | + | + | -7.1 |
asd/yhgN | 3573122 | + | + | + | + | - | -9.13 |
aspA/fxsA | 4366441 | + | + | - | + | + | -8.94 |
atpB | 3920225 | + | + | - | + | - | -7.2 |
caiF | 34065 | + | + | + | + | + | -5.1 |
can/yadG | 142603 | + | + | - | + | - | -6.18 |
carA | 29615 | + | + | + | + | - | -11.33 |
cfa | 1739387 | + | - | - | + | - | -4.63 |
clpA/serW | 925085 | - | + | - | - | - | -4.97 |
cspA | 3718007 | + | + | + | + | - | -11.07 |
cspF/ydfT | 1640402 | - | + | - | + | - | -5.56 |
cydA | 770405 | + | + | + | + | + | -13.45 |
cyoA | 451133 | - | - | - | + | - | N/A |
cysJ/queD | 2889857 | - | + | - | - | - | -5.93 |
dctR | 3652636 | - | + | - | - | - | -6.95 |
dcuA | 4364857 | - | + | - | - | - | -8.42 |
dcuB | 4347216 | + | + | + | + | + | -10.87 |
dcuC/pagP | 655340 | + | + | + | + | - | -10.96 |
ddlA/iraP | 400344 | + | + | + | + | - | -7.82 |
deaD | 3306070 | + | + | + | + | - | NaN |
dhaK/dhaR | 1250253 | - | + | + | + | - | -6.13 |
dmsA | 939992 | + | + | + | + | + | -10.34 |
dnaA/rpmH | 3882266 | + | + | + | + | - | NaN |
dusB | 3408206 | + | + | + | + | - | -6.9 |
exbB/metC | 3150130 | + | + | - | - | + | -5.72 |
fabF | 1151092 | + | + | - | + | - | -5.1 |
fadH | 3229415 | - | + | - | - | - | -4.39 |
fbaB/yegT | 2176754 | + | - | - | - | - | -6.74 |
fdhF | 4297433 | + | + | - | - | - | -5.53 |
feoA | 3537996 | + | - | - | + | - | -13.13 |
fepA/fes | 611865 | - | + | - | - | - | -5.22 |
fepB/entC | 624047 | - | + | - | + | - | -9.15 |
fepD/entS | 621417 | - | + | - | + | - | -6.5 |
fnr | 1397630 | + | + | + | + | - | -12.16 |
fnrS | 1407153 | + | + | + | + | - | -11.69 |
focA | 953746 | + | + | + | + | + | -7 |
frdA/poxA | 4380456 | + | + | + | + | + | -5.15 |
gadE | 3656507 | + | + | - | + | - | -11.04 |
gadE | 3656023 | + | + | - | + | - | -8.95 |
gadW/gadY | 3662892 | - | - | - | + | - | N/A |
gapC_1/cybB | 1488800 | - | - | - | + | - | N/A |
garP/garD | 3273193 | + | + | + | + | - | -11.26 |
glmZ/hemY | 3984609 | - | + | - | - | - | -5.16 |
glnB | 2685473 | - | + | - | - | - | -4.85 |
gntT | 3544552 | + | - | - | - | - | -6.02 |
guaB/xseA | 2632231 | + | + | + | + | + | -11.44 |
hcp | 913181 | + | + | + | + | + | -11.6 |
hdeA/hdeD | 3654886 | + | + | - | + | - | -7.03 |
hisG | 2088061 | + | + | + | + | - | -6.47 |
hsdR/mrr | 4584889 | + | + | + | - | + | -7.92 |
hybO | 3144396 | + | + | + | + | + | -6.53 |
hycA/hypA | 2848695 | + | + | + | - | - | -5.29 |
ibsD | 3192761 | + | + | - | - | - | -6.08 |
iclR/metH | 4221792 | - | - | - | + | - | N/A |
insA-1 | 20586 | + | - | - | + | - | -7.8 |
insA-5/uspC | 1977432 | - | - | - | + | - | N/A |
insAB-4/cspH | 1049863 | + | + | + | - | - | -5.76 |
insH-6/yoeA | 2066524 | + | + | + | + | + | -11.09 |
intA | 2754018 | + | + | - | + | - | NaN |
intB | 4494525 | - | + | - | - | - | -6.03 |
intF | 296412 | - | - | - | + | - | N/A |
isrB/yecR | 1986016 | - | + | - | - | - | -9.9 |
katG | 4131735 | + | + | + | - | - | -12 |
kch | 1308281 | - | - | - | + | - | N/A |
lasT | 4638594 | + | + | + | + | - | -13.41 |
leuP | 4604242 | + | + | + | + | - | -7.46 |
leuU | 3320105 | + | + | + | + | - | -7.16 |
lolB/hemA | 1262856 | + | - | + | + | - | -8.3 |
lrhA/yfbQ | 2405145 | - | - | - | + | - | N/A |
lysC/pgi | 4231475 | - | + | - | - | - | -4.49 |
matA/ykgL | 310756 | + | + | + | + | - | -6.55 |
mdtL | 3889560 | - | + | - | + | - | -6.94 |
mdtM/yjiP | 4566729 | + | + | + | + | - | -9.82 |
menD | 2377346 | + | + | + | + | - | -9.36 |
metR/metE | 4011275 | + | - | - | - | - | -8.15 |
mltA/metZ | 2945336 | + | + | + | + | - | -5.06 |
mngA | 766478 | - | - | - | + | - | N/A |
mraZ | 89279 | - | - | - | + | - | N/A |
msrB/gapA | 1860713 | + | + | + | + | - | -9.58 |
napF/yojO | 2301669 | + | - | - | + | - | -5.37 |
narG | 1278996 | + | + | + | + | - | -13.34 |
narX/narK | 1277080 | + | + | + | - | + | -16.52 |
ndh | 1165156 | + | + | + | + | + | -14.67 |
nikA | 3611593 | + | + | + | + | - | -9.55 |
nirB | 3491944 | + | + | + | + | + | -16.52 |
nohA/ynfO | 1634702 | + | + | + | + | + | -15.83 |
nohB | 579745 | + | + | + | + | + | -15.83 |
nrdD | 4460936 | + | + | + | + | + | -14.45 |
nsrR | 4404022 | - | + | - | - | - | -6.03 |
nuoA | 2403450 | + | + | + | + | + | -8.77 |
ompA | 1019297 | + | + | + | + | - | -9.13 |
ompC/micF | 2310722 | + | + | - | - | - | -5.86 |
ompF | 986314 | - | - | - | + | - | N/A |
oppA | 1298746 | + | - | + | + | - | -7.71 |
oppB | 1301035 | - | - | - | + | - | N/A |
pepE/rluF | 4228170 | - | + | - | - | - | -7.12 |
pfkA | 4105472 | + | + | + | - | - | -10.54 |
pheV/yghD | 3108350 | - | + | - | - | - | -4.56 |
pnp/psrO | 3309259 | + | - | - | - | - | -5.21 |
potA/pepT | 1185070 | + | + | + | + | - | -8.05 |
ppiA/tsgA | 3490525 | - | + | - | + | - | -10.91 |
proL | 2284296 | - | + | - | - | - | -4.83 |
ptsG | 1156965 | + | + | + | + | - | -9.18 |
ptsH | 2531616 | + | + | + | + | - | -8.57 |
purA | 4402756 | + | + | + | + | - | -6.68 |
pykA | 1935553 | + | + | + | + | + | -8.9 |
pyrD | 1003974 | + | + | + | + | + | -10.14 |
pyrG | 2907811 | + | + | + | + | - | -5.52 |
pyrL/G7878 | 4470582 | - | + | - | + | - | -7.14 |
raiA | 2735029 | + | + | - | + | - | -5.5 |
ravA/kup | 3929221 | + | + | + | + | + | -9.76 |
rfe | 3965827 | - | + | - | - | - | -4.02 |
rho | 3964346 | + | + | - | + | - | -5.61 |
ribB | 3182480 | + | - | - | - | - | -6.93 |
rimO/bssR | 877451 | + | + | + | + | - | -7.87 |
rimP | 3316312 | + | + | + | + | - | -4.87 |
rmf | 1014816 | + | - | - | + | - | -6.28 |
rplK | 4176422 | + | + | - | + | - | -5.26 |
rplM | 3376762 | + | + | - | + | - | -6.28 |
rpsJ | 3451329 | + | + | + | + | - | -4.78 |
rpsO | 3309706 | - | - | - | + | - | N/A |
rraA | 4117427 | + | + | - | - | - | -9.02 |
rydB | 1763161 | + | + | + | + | - | -8.88 |
secG | 3320479 | + | + | - | + | - | -7.16 |
serT/hyaA | 1031455 | + | + | - | + | - | -8.09 |
sfsB | 3332757 | - | + | - | - | - | -5.75 |
slyA/ydhI | 1718996 | + | + | + | + | + | -8.92 |
smf/def | 3431676 | + | + | - | - | - | -7.24 |
spf | 4048005 | + | + | + | + | - | -4.86 |
sspA | 3375694 | + | - | - | - | - | -6.13 |
ssrA | 2753666 | + | + | + | + | - | -6.43 |
sugE | 4374888 | + | + | - | - | - | -6.09 |
thrW/ykfI | 262283 | + | + | + | + | - | -6.89 |
tpiA | 4109595 | + | + | + | + | - | -8 |
tppB | 1710501 | - | - | - | + | - | N/A |
treR/mgtA | 4465528 | - | + | - | - | - | -7.47 |
tyrS | 1715354 | + | + | + | + | - | -7.56 |
upp/purM | 2618981 | + | + | + | + | + | -12.08 |
uspB/uspA | 3637954 | + | + | + | + | - | -9.23 |
uspF | 1433743 | + | + | + | + | - | -13.22 |
uvrA/ssb | 4272137 | + | + | - | - | - | -10.91 |
uxaB | 1608774 | + | + | + | + | - | -5.8 |
uxaC/exuT | 3242844 | + | + | + | + | + | -12.15 |
w/i yfcU | 2452937 | + | + | + | + | - | -7.04 |
yafT | 237005 | + | + | + | + | - | -5.3 |
yagA/yagE | 281405 | + | + | + | + | - | -9.04 |
yaiV | 393651 | - | + | - | - | - | -12.78 |
ybhK/moaA | 816051 | + | + | + | + | + | -11.98 |
ybiS/ybiT | 855098 | + | + | + | + | - | -5.67 |
ybiY/fsaA | 862807 | + | + | + | - | - | -13.06 |
ybjN | 892196 | - | + | - | + | - | -6.05 |
yccA | 1030727 | + | + | + | + | - | -9.55 |
ycfP | 1164183 | + | + | + | + | + | -6.98 |
ycgF | 1214022 | + | - | - | + | - | -11.34 |
yciC/ompW | 1311943 | + | + | + | + | + | -13.56 |
yciI/tonB | 1309141 | + | + | - | + | - | -6.26 |
ydbK/ydbJ | 1438991 | + | - | - | - | - | -5.76 |
yddG/fdnG | 1545309 | + | + | + | + | + | -12.93 |
ydfZ | 1627210 | + | + | + | + | + | -12.09 |
ydgJ/blr | 1702469 | + | - | + | + | - | -10.18 |
ydhR | 1744589 | + | + | + | + | - | -5.55 |
ydhY | 1752706 | + | + | + | + | - | -13.34 |
ydiP/ydiQ | 1777227 | + | + | + | - | + | -14.58 |
ydjX | 1831407 | + | + | + | + | - | -6.85 |
yeaI | 1868480 | + | + | + | + | - | -13.68 |
yecH/tyrP | 1987521 | + | + | + | + | - | -7.05 |
yedD | 2006195 | + | - | - | + | - | -5.01 |
yeeJ | 2042711 | - | + | - | - | - | -6.08 |
yeeO/asnU | 2057899 | + | + | + | + | - | -6.08 |
yeiQ | 2264162 | + | + | + | + | - | -9.51 |
yfaL | 2341665 | + | + | - | + | - | -6.45 |
yfaL/nrdA | 2342590 | + | + | + | + | - | -7.49 |
yfbV/ackA | 2411404 | + | + | + | + | + | -8.96 |
yfcC | 2415092 | + | + | + | + | + | -8.64 |
yfcZ/fadL | 2459154 | + | + | + | + | - | -10.4 |
yfeX | 2548637 | + | + | + | - | - | -7.48 |
yffL | 2558359 | + | + | + | + | + | -8.84 |
yffQ | 2561450 | + | - | - | + | - | -7.72 |
yffS | 2562444 | + | + | + | + | + | -11.69 |
yfgF/yfgG | 2627146 | + | + | + | + | - | -14.9 |
yfiD/ung | 2714607 | + | + | + | + | + | -5.75 |
yfiF/trxC | 2716583 | + | + | + | + | - | -7.15 |
yfiR | 2739858 | + | - | - | - | - | -7.39 |
yfjH | 2756262 | + | + | - | + | - | -11.05 |
yfjL/rnlA | 2763603 | + | + | + | - | - | -5.3 |
yfjL/rnlA | 2753568 | + | + | + | + | - | -5.3 |
ygcN | 2890619 | + | + | + | + | - | -7.11 |
yghB | 3151595 | + | + | + | + | + | -6.15 |
yhaB | 3265573 | + | + | + | + | + | -13.17 |
yhbT/yhbU | 3299423 | + | + | + | + | + | -8.72 |
yhcC/gltB | 3352500 | + | + | + | + | - | -10.08 |
yhcC/gltB | 3352160 | + | + | - | + | + | -10.08 |
yhiD | 3654213 | + | + | + | + | - | -7.03 |
yhiN/pitA | 3635599 | + | + | + | + | + | -8.05 |
yhjJ | 3679159 | - | + | - | - | - | -5.74 |
yhjY/tag | 3710913 | + | - | - | - | - | -6.86 |
yibN/gpmM | 3783221 | + | + | + | + | - | -5.94 |
yibV | 3767021 | - | + | - | - | - | -4.43 |
yjeH/groS | 4368546 | + | + | + | - | - | -7.68 |
yjiM | 4563930 | + | + | + | + | - | -7.36 |
yjiT | 4570327 | + | + | - | + | - | -7.46 |
yjiV | 4571618 | + | + | + | + | - | -15.83 |
yjjI/deoC | 4615188 | + | + | - | - | - | -8.33 |
yjjP/yjjQ | 4600895 | + | + | - | - | - | -7.95 |
yliE | 872201 | + | - | - | - | - | -5.49 |
yncL/ydcX | 1515350 | + | + | + | + | + | -13.06 |
yneM/mgrR | 1620843 | - | + | - | - | - | -6.69 |
ynfE | 1656063 | + | + | + | + | - | -11.5 |
ynfK | 1665276 | + | + | + | + | + | -9.37 |
ynhF/purR | 1735542 | + | + | + | + | - | -6.77 |
ynjE | 1837436 | + | + | + | + | - | -8.84 |
yqeC/mocA | 3013117 | + | + | - | - | - | -5.76 |
yqgD/metK | 3084695 | + | - | - | + | - | -5.55 |
yqhC/yqhD | 3153204 | + | + | + | + | - | -9.43 |
ysaA | 3739624 | + | + | - | + | - | -5.39 |
zupT/ribB | 3181647 | + | + | + | + | - | -7.97 |
kiley_discrepancies = {
'w/i insA-1':'two significant peaks, ribosomal contamination',\
'carA': 'weak insignificant peaks',\
'mraZ': 'no signal',\
'can/yadG': 'no signal',\
'5\' of thrW/ykfI': 'two weak peaks',\
'yagA/yagE': 'multiple weak insignificant peaks, phage contamination',\
'intF': 'no signal, phage contamination',\
'matA': 'no signal, near insertion element',\
'yaiV': 'no signal',\
'cyoA': 'very weak insignificant peak',\
'apt': 'no signal',\
'w/i G6272': '?',\
'nohB': 'strong peak but definitely a phage',\
'fepA/fes': 'weak insignificant peaks',\
'fepD/entS': 'weak insignificant peaks',\
'fepB/entC': 'weak variable peaks',\
'dcuC/pagP': 'no signal',\
'w/i mngA': 'no signal',\
'yliE': 'no signal',\
'ybjN': 'two weak peaks',\
'5\' of clpA/serW': 'no signal',\
'ompF': 'weak contaminated signal',\
'yccA': 'weak insignificant signal',\
'serT/hyaA': 'serT is a tRNA',\
'5\' of insAB-4/cspH': 'two weak peaks, insertion element contamination',\
'matA/ykgL': 'no signal',\
'fabF': 'weak variable peaks',\
'w/i ycgF': 'no signal',\
'lolB/hemA': 'weak variable signal',\
'kch': 'very weak signal',\
'yciI/tonB': 'no signal',\
'gapC_1/cybB': 'weak variable peak',\
'5\' of yneM/mgrR': 'no signal small RNA region',\
'5\' of cspF/ydfT': 'weak variable signal',\
'ydgJ/blr': 'weak variable signal',\
'tyrS': 'weak variable signal',\
'cfa': 'weak variable signal',\
'ydhR': 'weak variable peaks',\
'ydiP/ydiQ': 'no signal',\
'insA-5/uspC': 'no signal',\
'isrB/yecR': 'no signal',\
'yedD': 'weak variable signal',\
'yeeJ': 'no signal',\
'yeeO/asnU': 'weak variable signal',\
'insH-6/yoeA': 'definite peak but phage related',\
'hisG': 'no signal',\
'fbaB/yegT': 'very weak signal',\
'w/i proL': 'no signal',\
'napF/yojO': 'no signal',\
'yfeX': 'weak variable signal',\
'aegA/narQ': 'no signal',\
'yfgF/yfgG': 'weak variable signal',\
'glnB': 'no signal',\
'yfiF/trxC': 'weak variable signal',\
'raiA (w/i G7353)': 'no signal',\
'yfiR': 'no signal',\
'yjfL/rnlA (w/i yfjM)': 'four significant out of 12 but likely phage related',\
'hycA/hypA': 'no signal',\
'yqeC/mocA': 'weak variable signal',\
'5\' of pheV/yghD': 'no signal',\
'exbB/metC (w/i G7562)': 'no signal',\
'yqhC/yqhD': 'weak variable signal',\
'ribB': 'no signal',\
'ibsD': 'weak variable signal',\
'aer/ygjG': 'very weak signal',\
'ssrA': 'weak variable signal',\
'intA': 'weak variable signal, phage related',\
'w/i yfjH': 'weak variable signal',\
'fadH': 'very weak signal',\
'pnp/psrO': 'no signal',\
'sfsB': 'no signal',\
'sspA': 'weak variable signal',\
'rplM': 'weak variable signal, ribosomal',\
'dusB': 'very weak signal',\
'smf/def': 'no signal',\
'rpsJ': 'weak, variable, ribosomal',\
'ppiA/tsgA': 'weak variable signal',\
'feoA': 'very weak signal',\
'gntT': 'no signal',\
'dctR': 'variable signal',\
'gadW/gadY': 'weak variable signal',\
'w/i yhjJ': 'no signal',\
'w/i yhjY/tag': 'no signal',\
'cspA': 'strong but variable peak',\
'ysaA': 'weak variable signal',\
'mdtL': 'weak variable peaks',\
'atpB (w/i atpI)': 'strong highly variable peaks',\
'rho': 'weak variable peaks',\
'rfe': 'no signal',\
'5\' of glmZ/hemY': 'no signal',\
'metR/metE': 'weak variable signal',\
'spf': 'weak signal',\
'pfkA': 'weak signal',\
'tpiA': 'no signal',\
'rraA': 'no signal',\
'rplK': 'ribosomal',\
'aceB': 'no signal',\
'pepE/rluF': 'no signal',\
'iclR/metH': 'no signal',\
'lysC/pgi': 'no signal',\
'uvrA/ssb': 'no signal',\
'fdhF': 'very weak signal',\
'dcuB': 'weak variable signal',\
'dcuA': 'very weak signal',\
'aspA/fxsA': 'weak signal, only two significant overlapping out of 12',\
'sugE': 'very weak signal',\
'nsrR': 'no signal',\
'treR/mgtA': 'weak variable signal',\
'pyrL/G7878': 'very weak variable signal',\
'intB': 'no signal',\
'yjiM': 'weak variable signal',\
'mdtM/yjiP': 'very weak variable signal',\
'yjiT': 'very weak signal',\
'yjiV (w/i yjiT)' : 'very weak signal',\
'yjjP/yjjQ': 'very weak signal',\
'yjjI/deoC': 'very weak signal'
}
len(kiley_discrepancies.keys())
116