In [1]:

    

from om import base, settings
from om.data import *
from om.components import *

from IPython.display import HTML
from matplotlib import pylab as plt

from math import log
from itertools import combinations
import pandas as pd

ome = base.Session()
genome_data = omics_database.genome_data
%matplotlib inline


    

In [10]:

    

with open('/Volumes/extra/Dropbox/crp/data/annotation/ecocyc_tu.gff','wb') as tu_file:
    for tu in ome.query(TU).all():
        tu_file.write('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % 
                      ('NC_000913','ecocyc_TUs', 'transcript', tu.genome_region.leftpos,
                       tu.genome_region.rightpos, '.', tu.genome_region.strand, '.', tu.name))


    

In [2]:

    

ome.query(RNASeqExperiment).all()


    

    
Out[2]:





[RNASeqExperiment (#97, RNAseq_Ar3_glycerol_NH4Cl_O2_1_1.0):  1,
 RNASeqExperiment (#98, RNAseq_Ar3_glycerol_NH4Cl_O2_2_1.0):  2,
 RNASeqExperiment (#99, RNAseq_Ar3_glycerol_NH4Cl_O2_3_1.0):  3,
 RNASeqExperiment (#100, RNAseq_bw25113_acetate_NH4Cl_O2_1_thiamine_1.0):  1,
 RNASeqExperiment (#101, RNAseq_bw25113_acetate_NH4Cl_O2_2_thiamine_1.0):  2,
 RNASeqExperiment (#102, RNAseq_bw25113_fumarate_NH4Cl_O2_1_thiamine_1.0):  1,
 RNASeqExperiment (#103, RNAseq_bw25113_fumarate_NH4Cl_O2_2_thiamine_1.0):  2,
 RNASeqExperiment (#104, RNAseq_bw25113_glutamine_NH4Cl_O2_1_thiamine_1.0):  1,
 RNASeqExperiment (#105, RNAseq_bw25113_glutamine_NH4Cl_O2_2_thiamine_1.0):  2,
 RNASeqExperiment (#106, RNAseq_bw25113_pyruvate_NH4Cl_O2_1_thiamine_1.0):  1,
 RNASeqExperiment (#107, RNAseq_bw25113_pyruvate_NH4Cl_O2_2_thiamine_1.0):  2,
 RNASeqExperiment (#108, RNAseq_delAr1_glycerol_NH4Cl_O2_1_1.0):  1,
 RNASeqExperiment (#109, RNAseq_delAr1_glycerol_NH4Cl_O2_2_1.0):  2,
 RNASeqExperiment (#110, RNAseq_delAr1_glycerol_NH4Cl_O2_3_1.0):  3,
 RNASeqExperiment (#111, RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_1_1.0):  1,
 RNASeqExperiment (#112, RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_2_1.0):  2,
 RNASeqExperiment (#113, RNAseq_delAr1delAr2_glycerol_NH4Cl_O2_3_1.0):  3,
 RNASeqExperiment (#114, RNAseq_delAr2_glycerol_NH4Cl_O2_1_1.0):  1,
 RNASeqExperiment (#115, RNAseq_delAr2_glycerol_NH4Cl_O2_2_1.0):  2,
 RNASeqExperiment (#116, RNAseq_delAr2_glycerol_NH4Cl_O2_3_1.0):  3,
 RNASeqExperiment (#117, RNAseq_delfur_glucose_NH4Cl_O2_1_dpd_1.0):  1,
 RNASeqExperiment (#118, RNAseq_delfur_glucose_NH4Cl_O2_1_FeCl2_1.0):  1,
 RNASeqExperiment (#119, RNAseq_delfur_glucose_NH4Cl_O2_2_dpd_1.0):  2,
 RNASeqExperiment (#120, RNAseq_delfur_glucose_NH4Cl_O2_2_FeCl2_1.0):  2,
 RNASeqExperiment (#121, RNAseq_delta-crp_fructose_NH4Cl_O2_1_1.0):  1,
 RNASeqExperiment (#122, RNAseq_delta-crp_fructose_NH4Cl_O2_2_1.0):  2,
 RNASeqExperiment (#123, RNAseq_delta-crp_fructose_NH4Cl_O2_3_1.0):  3,
 RNASeqExperiment (#124, RNAseq_delta-crp_glucose_NH4Cl_O2_1_1.0):  1,
 RNASeqExperiment (#125, RNAseq_delta-crp_glucose_NH4Cl_O2_2_1.0):  2,
 RNASeqExperiment (#126, RNAseq_delta-crp_glucose_NH4Cl_O2_3_1.0):  3,
 RNASeqExperiment (#127, RNAseq_delta-crp_glycerol_NH4Cl_O2_1_1.0):  1,
 RNASeqExperiment (#128, RNAseq_delta-crp_glycerol_NH4Cl_O2_2_1.0):  2,
 RNASeqExperiment (#129, RNAseq_delta-crp_glycerol_NH4Cl_O2_3_1.0):  3,
 RNASeqExperiment (#130, RNAseq_wt_fructose_NH4Cl_O2_1_1.0):  1,
 RNASeqExperiment (#131, RNAseq_wt_fructose_NH4Cl_O2_2_1.0):  2,
 RNASeqExperiment (#132, RNAseq_wt_glucose_cytidine_O2_1_1.0):  1,
 RNASeqExperiment (#133, RNAseq_wt_glucose_cytidine_O2_2_1.0):  2,
 RNASeqExperiment (#134, RNAseq_wt_glucose_cytosine_O2_1_1.0):  1,
 RNASeqExperiment (#135, RNAseq_wt_glucose_cytosine_O2_2_1.0):  2,
 RNASeqExperiment (#136, RNAseq_wt_glucose_glutamine_O2_1_1.0):  1,
 RNASeqExperiment (#137, RNAseq_wt_glucose_glutamine_O2_2_1.0):  2,
 RNASeqExperiment (#138, RNAseq_wt_glucose_NH4Cl_O2_1_1.0):  1,
 RNASeqExperiment (#139, RNAseq_wt_glucose_NH4Cl_O2_1_dpd_1.0):  1,
 RNASeqExperiment (#140, RNAseq_wt_glucose_NH4Cl_O2_1_FeCl2_1.0):  1,
 RNASeqExperiment (#141, RNAseq_wt_glucose_NH4Cl_O2_2_1.0):  2,
 RNASeqExperiment (#142, RNAseq_wt_glucose_NH4Cl_O2_2_dpd_1.0):  2,
 RNASeqExperiment (#143, RNAseq_wt_glucose_NH4Cl_O2_2_FeCl2_1.0):  2,
 RNASeqExperiment (#144, RNAseq_wt_glucose_NH4Cl_O2_3_1.0):  3,
 RNASeqExperiment (#145, RNAseq_wt_glucose_NH4Cl_O2_4_1.0):  4,
 RNASeqExperiment (#146, RNAseq_wt_glucose_NH4Cl_O2_5_1.0):  5,
 RNASeqExperiment (#147, RNAseq_wt_glycerol_NH4Cl_O2_1_1.0):  1,
 RNASeqExperiment (#148, RNAseq_wt_glycerol_NH4Cl_O2_2_1.0):  2]

In [ ]: