diff --git a/cobra/flux_analysis/summary.py b/cobra/flux_analysis/summary.py index f66bb643b..690f2a0fd 100644 --- a/cobra/flux_analysis/summary.py +++ b/cobra/flux_analysis/summary.py @@ -101,7 +101,7 @@ def rxn_summary(r): "} {0.id:>8} {0.reaction:>54}").format(row[1])) -def model_summary(model, threshold=1E-8, fva=None, digits=2): +def model_summary(model, threshold=1E-8, fva=None, decimals=2): """Print a summary of the input and output fluxes of the model. threshold: float @@ -109,7 +109,7 @@ def model_summary(model, threshold=1E-8, fva=None, digits=2): fva: int or None Whether or not to calculate and report flux variability in the output summary - digits: int + decimals: int number of digits after the decimal place to print """ @@ -129,11 +129,8 @@ def model_summary(model, threshold=1E-8, fva=None, digits=2): out_fluxes = pd.Series({r.reactants[0]: r.x for r in out_rxns}) in_fluxes = pd.Series({r.reactants[0]: r.x for r in in_rxns}) - # sort and round - out_fluxes.sort_values(ascending=False, inplace=True) - out_fluxes = out_fluxes.round(digits) - in_fluxes.sort_values(inplace=True) - in_fluxes = in_fluxes.round(digits) + out_fluxes = out_fluxes.sort_values(ascending=False).round(decimals) + in_fluxes = in_fluxes.sort_values().round(decimals) table = pd.np.array( [((a if a else ''), (b if b else ''), (c if c else '')) @@ -167,10 +164,9 @@ def model_summary(model, threshold=1E-8, fva=None, digits=2): 'err': half_span.loc[r.id]} for r in in_rxns}).T - out_fluxes.sort_values(by='x', ascending=False, inplace=True) - out_fluxes = out_fluxes.round(digits) - in_fluxes.sort_values(by='x', inplace=True) - in_fluxes = in_fluxes.round(digits) + out_fluxes = out_fluxes.sort_values( + by='x', ascending=False).round(decimals) + in_fluxes = in_fluxes.sort_values(by='x').round(decimals) in_fluxes_s = in_fluxes.apply( lambda x: u'{0:0.2f} \u00B1 {1:0.2f}'.format(x.x, x.err), diff --git a/documentation_builder/simulating.ipynb b/documentation_builder/simulating.ipynb index 88ecbe4a1..03a56591e 100644 --- a/documentation_builder/simulating.ipynb +++ b/documentation_builder/simulating.ipynb @@ -41,7 +41,7 @@ { "data": { "text/plain": [ - "" + "" ] }, "execution_count": 2, @@ -106,7 +106,7 @@ { "data": { "text/plain": [ - "0.8739215069684909" + "0.8739215069684305" ] }, "execution_count": 4, @@ -172,8 +172,8 @@ " % FLUX RXN ID REACTION \n", " 41.6% 16 GAPD g3p_c + nad_c + pi_c <=> 13dpg_c + h_c + nadh_c\n", " 24.1% 9.3 PDH coa_c + nad_c + pyr_c --> accoa_c + co2_c + nadh_c\n", - " 13.1% 5.1 MDH mal__L_c + nad_c <=> h_c + nadh_c + oaa_c\n", " 13.1% 5.1 AKGDH akg_c + coa_c + nad_c --> co2_c + nadh_c + succoa_c\n", + " 13.1% 5.1 MDH mal__L_c + nad_c <=> h_c + nadh_c + oaa_c\n", " 8.0% 3.1 Bioma... 1.496 3pg_c + 3.7478 accoa_c + 59.81 atp_c + 0.36...\n", "\n", "CONSUMING REACTIONS -- Nicotinamide adenine dinucleotide - reduced\n", @@ -263,7 +263,7 @@ { "data": { "text/plain": [ - "{: 1.0}" + "{: 1.0}" ] }, "execution_count": 9, @@ -292,7 +292,7 @@ { "data": { "text/plain": [ - "{: 1}" + "{: 1}" ] }, "execution_count": 10, @@ -320,7 +320,7 @@ { "data": { "text/plain": [ - "175.00000000002336" + "174.99999999999997" ] }, "execution_count": 11, @@ -349,7 +349,7 @@ { "data": { "text/plain": [ - "{: 1.0}" + "{: 1.0}" ] }, "execution_count": 12, @@ -396,17 +396,17 @@ " \n", " ACALD\n", " 0.00000\n", - " -0.00000\n", + " 0.00000\n", " \n", " \n", " ACALDt\n", - " 0.00000\n", " -0.00000\n", + " 0.00000\n", " \n", " \n", " ACKr\n", " -0.00000\n", - " -0.00000\n", + " 0.00000\n", " \n", " \n", " ACONTa\n", @@ -421,11 +421,11 @@ " \n", " ACt2r\n", " 0.00000\n", - " -0.00000\n", + " 0.00000\n", " \n", " \n", " ADK1\n", - " 0.00000\n", + " -0.00000\n", " 0.00000\n", " \n", " \n", @@ -436,12 +436,12 @@ " \n", " AKGt2r\n", " 0.00000\n", - " -0.00000\n", + " 0.00000\n", " \n", " \n", " ALCD2x\n", " 0.00000\n", - " -0.00000\n", + " 0.00000\n", " \n", " \n", " ATPM\n", @@ -475,8 +475,8 @@ " \n", " \n", " D_LACt2\n", - " -0.00000\n", - " -0.00000\n", + " 0.00000\n", + " 0.00000\n", " \n", " \n", " ENO\n", @@ -486,11 +486,11 @@ " \n", " ETOHt2r\n", " 0.00000\n", - " -0.00000\n", + " 0.00000\n", " \n", " \n", " EX_ac_e\n", - " 0.00000\n", + " -0.00000\n", " 0.00000\n", " \n", " \n", @@ -499,26 +499,26 @@ ], "text/plain": [ " maximum minimum\n", - "ACALD 0.00000 -0.00000\n", - "ACALDt 0.00000 -0.00000\n", - "ACKr -0.00000 -0.00000\n", + "ACALD 0.00000 0.00000\n", + "ACALDt -0.00000 0.00000\n", + "ACKr -0.00000 0.00000\n", "ACONTa 6.00725 6.00725\n", "ACONTb 6.00725 6.00725\n", - "ACt2r 0.00000 -0.00000\n", - "ADK1 0.00000 0.00000\n", + "ACt2r 0.00000 0.00000\n", + "ADK1 -0.00000 0.00000\n", "AKGDH 5.06438 5.06438\n", - "AKGt2r 0.00000 -0.00000\n", - "ALCD2x 0.00000 -0.00000\n", + "AKGt2r 0.00000 0.00000\n", + "ALCD2x 0.00000 0.00000\n", "ATPM 8.39000 8.39000\n", "ATPS4r 45.51401 45.51401\n", "Biomass_Ecoli_core 0.87392 0.87392\n", "CO2t -22.80983 -22.80983\n", "CS 6.00725 6.00725\n", "CYTBD 43.59899 43.59899\n", - "D_LACt2 -0.00000 -0.00000\n", + "D_LACt2 0.00000 0.00000\n", "ENO 14.71614 14.71614\n", - "ETOHt2r 0.00000 -0.00000\n", - "EX_ac_e 0.00000 0.00000" + "ETOHt2r 0.00000 0.00000\n", + "EX_ac_e -0.00000 0.00000" ] }, "execution_count": 13, @@ -561,12 +561,12 @@ " \n", " \n", " ACALD\n", - " -0.00000\n", + " 0.00000\n", " -2.54237\n", " \n", " \n", " ACALDt\n", - " 0.00000\n", + " -0.00000\n", " -2.54237\n", " \n", " \n", @@ -586,7 +586,7 @@ " \n", " \n", " ACt2r\n", - " -0.00000\n", + " 0.00000\n", " -3.81356\n", " \n", " \n", @@ -665,12 +665,12 @@ ], "text/plain": [ " maximum minimum\n", - "ACALD -0.00000 -2.54237\n", - "ACALDt 0.00000 -2.54237\n", + "ACALD 0.00000 -2.54237\n", + "ACALDt -0.00000 -2.54237\n", "ACKr -0.00000 -3.81356\n", "ACONTa 8.89452 0.84859\n", "ACONTb 8.89452 0.84859\n", - "ACt2r -0.00000 -3.81356\n", + "ACt2r 0.00000 -3.81356\n", "ADK1 17.16100 0.00000\n", "AKGDH 8.04593 0.00000\n", "AKGt2r 0.00000 -1.43008\n", @@ -718,7 +718,7 @@ "output_type": "stream", "text": [ "IN FLUXES OUT FLUXES OBJECTIVES \n", - "o2_e -21.80 ± 1.91 h2o_e 27.86 ± 2.86 Biomass_Ecoli_core 0.000\n", + "o2_e -21.80 ± 1.91 h2o_e 27.86 ± 2.86 Biomass_Ecoli_core 0.874\n", "glc__D_e -9.76 ± 0.24 co2_e 21.81 ± 2.86 \n", "nh4_e -4.84 ± 0.32 h_e 19.51 ± 2.86 \n", "pi_e -3.13 ± 0.08 for_e 2.86 ± 2.86 \n", @@ -734,6 +734,7 @@ } ], "source": [ + "model.optimize()\n", "model.summary(fva=0.95)" ] }, @@ -758,13 +759,14 @@ "PRODUCING REACTIONS -- Pyruvate\n", "-------------------------------\n", " % FLUX RXN ID REACTION \n", - " 50.0% 6.13 ± 6.13 PYK adp_c + h_c + pep_c --> atp_c + pyr_c\n", - " 50.0% 9.76 ± 0.24 GLCpts glc__D_e + pep_c --> g6p_c + pyr_c\n", + " 85.0% 9.76 ± 0.24 GLCpts glc__D_e + pep_c --> g6p_c + pyr_c\n", + " 15.0% 6.13 ± 6.13 PYK adp_c + h_c + pep_c --> atp_c + pyr_c\n", "\n", "CONSUMING REACTIONS -- Pyruvate\n", "-------------------------------\n", " % FLUX RXN ID REACTION \n", - "100.0% 11.34 ± 7.43 PDH coa_c + nad_c + pyr_c --> accoa_c + co2_c + nadh_c\n" + " 78.9% 11.34 ± 7.43 PDH coa_c + nad_c + pyr_c --> accoa_c + co2_c + nadh_c\n", + " 21.1% 0.85 ± 0.02 Bioma... 1.496 3pg_c + 3.7478 accoa_c + 59.81 atp_c + 0.36...\n" ] } ], @@ -817,7 +819,7 @@ { "data": { "text/plain": [ - "6.072919944699606e-14" + "1.1102230246251565e-16" ] }, "execution_count": 18, @@ -846,7 +848,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.4.3" + "version": "3.4.4" } }, "nbformat": 4,