In [1]:

    

from om import base, settings
from om.components import *
from om.data import *
from om.util import *
from scipy.spatial.distance import pdist, squareform
from scipy.cluster.hierarchy import linkage, dendrogram

import pandas as pd
import numpy as np
import math,cobra


ome = base.Session()

ged = GeneExpressionData
dged = DifferentialGeneExpressionData
cpge = ChIPPeakGeneExpression


    

    




cobra/io/__init__.py:17 UserWarning: cobra.io.sbml requires libsbml

In [7]:

    

ome.query(DifferentialExpression).all()


    

In [6]:

    

24990/4165.


    

    
Out[6]:





6.0

In [2]:

    

from om import data
from om.loading import data_loading

exp_objects = ome.query(data.NormalizedExpression).\
                                   join(data.AnalysisComposition, data.NormalizedExpression.id == data.AnalysisComposition.analysis_id).\
                                   join(data.ArrayExperiment, data.ArrayExperiment.id == data.AnalysisComposition.data_set_id).all()
contrasts = data_loading.find_single_factor_pairwise_contrasts(exp_objects)


    

In [8]:

    

for e1,e2 in contrasts: print e1.name,e2.name


    

    




affyexp_wt_acetate_NH4Cl_O2 affyexp_wt_fructose_NH4Cl_O2
affyexp_delta-cra_acetate_NH4Cl_O2 affyexp_wt_acetate_NH4Cl_O2
affyexp_delta-fnr_glucose_NH4Cl_anaerobic affyexp_wt_glucose_NH4Cl_anaerobic
affyexp_delta-fnr_glucose_NH4Cl_O2 affyexp_delta-fnr_glucose_NH4Cl_anaerobic
affyexp_delta-narLnarP_glucose_NH4Cl_NO3 affyexp_delta-narLnarP_glucose_NH4Cl_anaerobic
affyexp_delta-narLnarP_glucose_NH4Cl_NO3 affyexp_wt_glucose_NH4Cl_NO3
affyexp_delta-narLnarP_glucose_NH4Cl_anaerobic affyexp_wt_glucose_NH4Cl_anaerobic
affyexp_delta-arcAfnr_glucose_NH4Cl_O2 affyexp_delta-arcAfnr_glucose_NH4Cl_anaerobic
affyexp_delta-arcAfnr_glucose_NH4Cl_anaerobic affyexp_wt_glucose_NH4Cl_anaerobic
affyexp_delta-purR_glucose_adenine_O2 affyexp_wt_glucose_adenine_O2
affyexp_wt_glucose_adenine_O2 affyexp_wt_glucose_leucine_O2
affyexp_delta-crp_fructose_NH4Cl_O2 affyexp_wt_fructose_NH4Cl_O2
affyexp_delta-cra_acetate_NH4Cl_O2 affyexp_delta-cra_glucose_NH4Cl_O2
affyexp_delta-purR_glucose_NH4Cl_O2 affyexp_delta-purR_glucose_adenine_O2
affyexp_delta-arcAfnr_glucose_NH4Cl_O2 affyexp_wt_glucose_NH4Cl_O2
affyexp_delta-crp_fructose_NH4Cl_O2 affyexp_delta-crp_glucose_NH4Cl_O2
affyexp_delta-lrp_glucose_NH4Cl_O2 affyexp_delta-lrp_glucose_leucine_O2
affyexp_delta-narP_glucose_NH4Cl_NO3 affyexp_wt_glucose_NH4Cl_NO3
affyexp_delta-narP_glucose_NH4Cl_NO3 affyexp_delta-narP_glucose_NH4Cl_anaerobic
affyexp_wt_glucose_NH4Cl_NO3 affyexp_wt_glucose_NH4Cl_O2
affyexp_wt_glucose_NH4Cl_O2 affyexp_wt_glucose_NH4Cl_anaerobic
affyexp_delta-arcA_glucose_NH4Cl_O2 affyexp_wt_glucose_NH4Cl_O2
affyexp_delta-fnr_glucose_NH4Cl_O2 affyexp_wt_glucose_NH4Cl_O2
affyexp_delta-narL_glucose_NH4Cl_NO3 affyexp_delta-narL_glucose_NH4Cl_anaerobic
affyexp_delta-narL_glucose_NH4Cl_anaerobic affyexp_wt_glucose_NH4Cl_anaerobic
affyexp_delta-narL_glucose_NH4Cl_NO3 affyexp_wt_glucose_NH4Cl_NO3
affyexp_wt_glucose_NH4Cl_NO3 affyexp_wt_glucose_NH4Cl_anaerobic
affyexp_delta-arcA_glucose_NH4Cl_anaerobic affyexp_wt_glucose_NH4Cl_anaerobic
affyexp_delta-arcA_glucose_NH4Cl_O2 affyexp_delta-arcA_glucose_NH4Cl_anaerobic
affyexp_delta-cra_glucose_NH4Cl_O2 affyexp_delta-cra_glucose_NH4Cl_anaerobic
affyexp_delta-narP_glucose_NH4Cl_anaerobic affyexp_wt_glucose_NH4Cl_anaerobic
affyexp_delta-lrp_glucose_leucine_O2 affyexp_wt_glucose_leucine_O2

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