In [1]:
from om import base, settings
from om.util import *
import pandas as pd
import cobra
ome = base.Session()
model = cobra.io.read_sbml_model('/Users/dbuser/Dropbox/om_data/annotation/iJO1366.xml')
cobra/io/__init__.py:17 UserWarning: cobra.io.sbml requires libsbml
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-1-0accedd4b1f3> in <module>()
6
7 ome = base.Session()
----> 8 model = cobra.io.read_sbml_model('/Users/dbuser/Dropbox/om_data/annotation/iJO1366.xml')
AttributeError: 'module' object has no attribute 'read_sbml_model'
In [2]:
from om.data import *
In [5]:
ome.query(ChIPExperiment).all()
Out[5]:
[ChIPExperiment (#1, chipExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_2_anti-myc): chipExo ArcA 2,
ChIPExperiment (#2, chipExo-ArcA_ArcA8myc_glucose_NH4Cl_anaerobic_3_anti-myc): chipExo ArcA 3,
ChIPExperiment (#3, chipExo-Crp_Ar3_glycerol_NH4Cl_O2_1_anti-crp): chipExo Crp 1,
ChIPExperiment (#4, chipExo-Crp_Ar3_glycerol_NH4Cl_O2_2_anti-crp): chipExo Crp 2,
ChIPExperiment (#5, chipExo-Crp_Ar3_glycerol_NH4Cl_O2_3_anti-crp): chipExo Crp 3,
ChIPExperiment (#6, chipExo-Crp_Crp8myc_fructose_NH4Cl_O2_1_anti-crp): chipExo Crp 1,
ChIPExperiment (#7, chipExo-Crp_Crp8myc_fructose_NH4Cl_O2_1_anti-myc): chipExo Crp 1,
ChIPExperiment (#8, chipExo-Crp_Crp8myc_fructose_NH4Cl_O2_2_anti-crp): chipExo Crp 2,
ChIPExperiment (#9, chipExo-Crp_Crp8myc_fructose_NH4Cl_O2_2_anti-myc): chipExo Crp 2,
ChIPExperiment (#10, chipExo-Crp_Crp8myc_fructose_NH4Cl_O2_3_anti-crp): chipExo Crp 3,
ChIPExperiment (#11, chipExo-Crp_Crp8myc_fructose_NH4Cl_O2_3_anti-myc): chipExo Crp 3,
ChIPExperiment (#12, chipExo-Crp_Crp8myc_glucose_NH4Cl_O2_1_anti-myc): chipExo Crp 1,
ChIPExperiment (#13, chipExo-Crp_Crp8myc_glucose_NH4Cl_O2_2_anti-myc): chipExo Crp 2,
ChIPExperiment (#14, chipExo-Crp_Crp8myc_glycerol_NH4Cl_O2_1_anti-crp): chipExo Crp 1,
ChIPExperiment (#15, chipExo-Crp_Crp8myc_glycerol_NH4Cl_O2_1_anti-mock-crp): chipExo Crp 1,
ChIPExperiment (#16, chipExo-Crp_Crp8myc_glycerol_NH4Cl_O2_1_anti-mock-myc): chipExo Crp 1,
ChIPExperiment (#17, chipExo-Crp_Crp8myc_glycerol_NH4Cl_O2_1_anti-myc): chipExo Crp 1,
ChIPExperiment (#18, chipExo-Crp_Crp8myc_glycerol_NH4Cl_O2_2_anti-crp): chipExo Crp 2,
ChIPExperiment (#19, chipExo-Crp_Crp8myc_glycerol_NH4Cl_O2_3_anti-myc): chipExo Crp 3,
ChIPExperiment (#20, chipExo-Crp_delAr1_glycerol_NH4Cl_O2_1_anti-crp): chipExo Crp 1,
ChIPExperiment (#21, chipExo-Crp_delAr1_glycerol_NH4Cl_O2_2_anti-crp): chipExo Crp 2,
ChIPExperiment (#22, chipExo-Crp_delAr1_glycerol_NH4Cl_O2_3_anti-crp): chipExo Crp 3,
ChIPExperiment (#23, chipExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_1_anti-crp): chipExo Crp 1,
ChIPExperiment (#24, chipExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_2_anti-crp): chipExo Crp 2,
ChIPExperiment (#25, chipExo-Crp_delAr1delAr2_glycerol_NH4Cl_O2_3_anti-crp): chipExo Crp 3,
ChIPExperiment (#26, chipExo-Crp_delAr2_glycerol_NH4Cl_O2_1_anti-crp): chipExo Crp 1,
ChIPExperiment (#27, chipExo-Crp_delAr2_glycerol_NH4Cl_O2_2_anti-crp): chipExo Crp 2,
ChIPExperiment (#28, chipExo-Crp_delAr2_glycerol_NH4Cl_O2_3_anti-crp): chipExo Crp 3,
ChIPExperiment (#29, chipExo-Crp_delta-crp_glycerol_NH4Cl_O2_1_anti-crp): chipExo Crp 1,
ChIPExperiment (#30, chipExo-Crp_delta-crp_glycerol_NH4Cl_O2_2_anti-crp): chipExo Crp 2,
ChIPExperiment (#31, chipExo-Crp_delta-crp_glycerol_NH4Cl_O2_3_anti-crp): chipExo Crp 3,
ChIPExperiment (#32, chipExo-Crp_wt_fructose_NH4Cl_O2_1_anti-crp): chipExo Crp 1,
ChIPExperiment (#33, chipExo-Crp_wt_fructose_NH4Cl_O2_1_anti-mock-crp): chipExo Crp 1,
ChIPExperiment (#34, chipExo-Crp_wt_fructose_NH4Cl_O2_2_anti-crp): chipExo Crp 2,
ChIPExperiment (#35, chipExo-Crp_wt_fructose_NH4Cl_O2_3_anti-crp): chipExo Crp 3,
ChIPExperiment (#36, chipExo-Crp_wt_fructose_NH4Cl_O2_4_anti-crp): chipExo Crp 4,
ChIPExperiment (#37, chipExo-Crp_wt_fructose_NH4Cl_O2_5_anti-crp): chipExo Crp 5,
ChIPExperiment (#38, chipExo-Crp_wt_glucose_NH4Cl_O2_1_anti-crp): chipExo Crp 1,
ChIPExperiment (#39, chipExo-Crp_wt_glucose_NH4Cl_O2_2_anti-crp): chipExo Crp 2,
ChIPExperiment (#40, chipExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp): chipExo Crp 1,
ChIPExperiment (#41, chipExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-crp_rif): chipExo Crp 1,
ChIPExperiment (#42, chipExo-Crp_wt_glycerol_NH4Cl_O2_1_anti-mock-crp): chipExo Crp 1,
ChIPExperiment (#43, chipExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp): chipExo Crp 2,
ChIPExperiment (#44, chipExo-Crp_wt_glycerol_NH4Cl_O2_2_anti-crp_rif): chipExo Crp 2,
ChIPExperiment (#45, chipExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp): chipExo Crp 3,
ChIPExperiment (#46, chipExo-Crp_wt_glycerol_NH4Cl_O2_3_anti-crp_rif): chipExo Crp 3,
ChIPExperiment (#47, chipExo-Crp_wt_glycerol_NH4Cl_O2_4_anti-crp): chipExo Crp 4,
ChIPExperiment (#48, chipExo-Crp_wt_glycerol_NH4Cl_O2_5_anti-crp): chipExo Crp 5,
ChIPExperiment (#49, chipExo-Crp_wt_glycerol_NH4Cl_O2_6_anti-crp): chipExo Crp 6,
ChIPExperiment (#50, chipExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_2_anti-myc): chipExo Fnr 2,
ChIPExperiment (#51, chipExo-Fnr_Fnr8myc_glucose_NH4Cl_anaerobic_3_anti-myc): chipExo Fnr 3,
ChIPExperiment (#52, chipExo-RpoA_wt_glucose_NH4Cl_O2_1_anti-rpoA): chipExo RpoA 1,
ChIPExperiment (#53, chipExo-RpoA_wt_glucose_NH4Cl_O2_2_anti-rpoA): chipExo RpoA 2,
ChIPExperiment (#54, chipExo-RpoD_wt_fructose_NH4Cl_O2_1_anti-rpod): chipExo RpoD 1,
ChIPExperiment (#55, chipExo-RpoD_wt_fructose_NH4Cl_O2_2_anti-rpod): chipExo RpoD 2,
ChIPExperiment (#56, chipExo-RpoD_wt_fructose_NH4Cl_O2_3_anti-rpod): chipExo RpoD 3,
ChIPExperiment (#57, chipExo-RpoD_wt_glucose_NH4Cl_O2_1_anti-rpod): chipExo RpoD 1,
ChIPExperiment (#58, chipExo-RpoD_wt_glucose_NH4Cl_O2_2_anti-rpod): chipExo RpoD 2,
ChIPExperiment (#59, chipExo-RpoD_wt_glucose_NH4Cl_O2_3_anti-rpod): chipExo RpoD 3,
ChIPExperiment (#60, chipExo-RpoD_wt_glycerol_NH4Cl_O2_1_anti-rpod): chipExo RpoD 1,
ChIPExperiment (#61, chipExo-RpoD_wt_glycerol_NH4Cl_O2_2_anti-rpod): chipExo RpoD 2,
ChIPExperiment (#62, chipExo-RpoD_wt_glycerol_NH4Cl_O2_3_anti-rpod): chipExo RpoD 3,
ChIPExperiment (#63, chipExo-Fur_Fur8myc_glucose_NH4Cl_O2_1_anti-myc_dpd): chipExo Fur 1,
ChIPExperiment (#64, chipExo-Fur_Fur8myc_glucose_NH4Cl_O2_1_anti-myc_FeCl2): chipExo Fur 1,
ChIPExperiment (#65, chipExo-Fur_Fur8myc_glucose_NH4Cl_O2_2_anti-myc_dpd): chipExo Fur 2,
ChIPExperiment (#66, chipExo-Fur_Fur8myc_glucose_NH4Cl_O2_2_anti-myc_FeCl2): chipExo Fur 2,
ChIPExperiment (#67, chipExo-Nac_Nac8myc_glucose_cytidine_O2_1_anti-myc): chipExo Nac 1,
ChIPExperiment (#68, chipExo-Nac_Nac8myc_glucose_cytidine_O2_2_anti-myc): chipExo Nac 2,
ChIPExperiment (#69, chipExo-Nac_Nac8myc_glucose_cytosine_O2_1_anti-myc): chipExo Nac 1,
ChIPExperiment (#70, chipExo-Nac_Nac8myc_glucose_cytosine_O2_2_anti-myc): chipExo Nac 2,
ChIPExperiment (#71, chipExo-Nac_Nac8myc_glucose_glutamine_O2_1_anti-myc): chipExo Nac 1,
ChIPExperiment (#72, chipExo-Nac_Nac8myc_glucose_glutamine_O2_2_anti-myc): chipExo Nac 2,
ChIPExperiment (#73, chipExo-Nac_Nac8myc_glucose_NH4Cl_O2_1_anti-myc): chipExo Nac 1,
ChIPExperiment (#74, chipExo-Nac_Nac8myc_glucose_NH4Cl_O2_2_anti-myc): chipExo Nac 2,
ChIPExperiment (#75, chipExo-NtrC_NtrC8myc_glucose_cytidine_O2_1_anti-myc): chipExo NtrC 1,
ChIPExperiment (#76, chipExo-NtrC_NtrC8myc_glucose_cytidine_O2_2_anti-myc): chipExo NtrC 2,
ChIPExperiment (#77, chipExo-NtrC_NtrC8myc_glucose_cytosine_O2_1_anti-myc): chipExo NtrC 1,
ChIPExperiment (#78, chipExo-NtrC_NtrC8myc_glucose_cytosine_O2_2_anti-myc): chipExo NtrC 2,
ChIPExperiment (#79, chipExo-NtrC_NtrC8myc_glucose_glutamine_O2_1_anti-myc): chipExo NtrC 1,
ChIPExperiment (#80, chipExo-NtrC_NtrC8myc_glucose_glutamine_O2_2_anti-myc): chipExo NtrC 2,
ChIPExperiment (#81, chipExo-NtrC_NtrC8myc_glucose_NH4Cl_O2_1_anti-myc): chipExo NtrC 1,
ChIPExperiment (#82, chipExo-NtrC_NtrC8myc_glucose_NH4Cl_O2_2_anti-myc): chipExo NtrC 2,
ChIPExperiment (#83, chipExo-RpoD_wt_glucose_cytidine_O2_1_anti-rpod): chipExo RpoD 1,
ChIPExperiment (#84, chipExo-RpoD_wt_glucose_cytidine_O2_2_anti-rpod): chipExo RpoD 2,
ChIPExperiment (#85, chipExo-RpoD_wt_glucose_cytosine_O2_1_anti-rpod): chipExo RpoD 1,
ChIPExperiment (#86, chipExo-RpoD_wt_glucose_cytosine_O2_2_anti-rpod): chipExo RpoD 2,
ChIPExperiment (#87, chipExo-RpoD_wt_glucose_glutamine_O2_1_anti-rpod): chipExo RpoD 1,
ChIPExperiment (#88, chipExo-RpoD_wt_glucose_glutamine_O2_2_anti-rpod): chipExo RpoD 2,
ChIPExperiment (#89, chipExo-RpoD_wt_glucose_NH4Cl_O2_4_anti-rpod_nitrogenstudy): chipExo RpoD 4,
ChIPExperiment (#90, chipExo-RpoD_wt_glucose_NH4Cl_O2_5_anti-rpod): chipExo RpoD 5,
ChIPExperiment (#91, chipExo-RpoD_wt_glucose_NH4Cl_O2_6_anti-rpod): chipExo RpoD 6,
ChIPExperiment (#92, chipExo-RpoD_wt_glucose_NH4Cl_O2_7_anti-rpod_nitrogenstudy): chipExo RpoD 7,
ChIPExperiment (#93, chipExo-RpoN_wt_glucose_NH4Cl_O2_1_anti-rpon): chipExo RpoN 1,
ChIPExperiment (#94, chipExo-RpoN_wt_glucose_NH4Cl_O2_2_anti-rpon): chipExo RpoN 2,
ChIPExperiment (#95, chipExo-RpoS_wt_glucose_NH4Cl_O2_1_anti-rpos): chipExo RpoS 1,
ChIPExperiment (#96, chipExo-RpoS_wt_glucose_NH4Cl_O2_2_anti-rpos): chipExo RpoS 2]
In [2]:
get_regulation_data(model.reactions.GAPD, expanded_dataset=True)
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-2-5e86bc877cdc> in <module>()
----> 1 get_regulation_data(model.reactions.GAPD, expanded_dataset=True)
TypeError: get_regulation_data() got an unexpected keyword argument 'expanded_dataset'
In [3]:
pd.DataFrame(get_regulation_data(model.reactions.SUCDi.id, expanded_dataset=True))
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-3-e234d17127f1> in <module>()
----> 1 pd.DataFrame(get_regulation_data(model.reactions.SUCDi.id, expanded_dataset=True))
TypeError: get_regulation_data() got an unexpected keyword argument 'expanded_dataset'
In [ ]:
Content source: steve-federowicz/om
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