fluxpyt package

Submodules

fluxpyt.bootstrap module

Created on Wed Aug 23 12:06:00 2017

@author: Trunil

fluxpyt.bootstrap.bootstrap(**kws)[source]

inputs:

kws:
rxnList: Optional. List of reactions for which bootstrapping is to be done.
It should be in form of python list

ylim = Optional. It should be a tuple. e.g. (0,10).

Example

bootstrap(‘tca’,rxnList=[‘V01’,’V02’],ylim=(0,10))

fluxpyt.build_model module

Created on Sat Feb 6 21:09:50 2016

@author: Trunil

Reads and build model from csv. Note 2Jul2016: this program reads csv model into stoichiometric matrix with list of rxns and metabolites

fluxpyt.build_model.build_model(fileName)[source]
fluxpyt.build_model.get_linenumber()[source]

Get line number in the code. Usefull to find which line of the code this function occurrs.

fluxpyt.build_model.make_stoich_matrix(reactions, reaction_formulae, excludedMetabolites=[])[source]
Stoichiometric matrix (S) from reaction formulae
Reactions must be written in form:

A -> 2 B

A + B <-> C

fluxpyt.build_model.metabolite_list(reaction_formulae, excludedMetabolites=[])[source]
Make list of metabolites from reaction formula.
Reactions must be written in form:
A -> 2 B C <- A + B A + B <-> C
fluxpyt.build_model.modify_rxn_for_S(rxn, excludedMetabolites=[])[source]
fluxpyt.build_model.read_mfa_model(filename)[source]

Import and read csv file. Returns the model in lists that separate columns

fluxpyt.build_model.test_model_build()[source]

fluxpyt.create_atm_transition_equations module

Created on Mon Jul 4 12:46:38 2016

Generates elementary reaction list.

@author: Trunil

fluxpyt.create_atm_transition_equations.create_atm_transition_equations(rxnIDs, rxnList, atm_transition_rxns, moleculeList)[source]
Input:
rxnList = reaction formulae in form of list atm_transition_rxns = respective atom transition reaction list moleculeList = list of molecules observed (emu types e.g. A:0111)
Output:
reaction list with atom transitions, new metabolite (emu types) list
fluxpyt.create_atm_transition_equations.findMolRxns(rxnIDs, molecule, rxnList, atm_transition_rxns)[source]
fluxpyt.create_atm_transition_equations.get_coeff(rxn)[source]
fluxpyt.create_atm_transition_equations.get_formula(molecule, rxn, atm_rxn)[source]
fluxpyt.create_atm_transition_equations.get_new_molecule(rxn, moleculeList, current_molecule)[source]
fluxpyt.create_atm_transition_equations.insert_hash(list)[source]
fluxpyt.create_atm_transition_equations.num_sort(num)[source]
fluxpyt.create_atm_transition_equations.rewrite_molecule(molecule, rxn, atm_rxn, mol_index)[source]
fluxpyt.create_atm_transition_equations.test()[source]
fluxpyt.create_atm_transition_equations.write_rxn_full(rxn)[source]

fluxpyt.draw_flux_map module

Created on Thu Sep 21 11:07:25 2017

@author: Trunil

fluxpyt.draw_flux_map.draw_flux_map(filename)[source]

Input: filename of flux diagram in svg format.

fluxpyt.free_flux_null module

Created on Mon Jun 19 10:39:54 2017

@author: Trunil

fluxpyt.free_flux_null.get_null_mat(stoich_matrix, model_metabolite)[source]

fluxpyt.glpk_solve module

Created on Sun Aug 7 12:37:26 2016

@author: Trunil

fluxpyt.glpk_solve.glpk_solve(mat, c, b, bounds, rxnNames, maximize=False)[source]
fluxpyt.glpk_solve.parse_output(fileName, rxnNames)[source]
fluxpyt.glpk_solve.write_constraint(constr_name, vec, rxnNames, model)[source]

fluxpyt.input_substrate_emu module

Created on Tue Aug 2 15:44:59 2016

@author: Trunil

fluxpyt.input_substrate_emu.cal_substrate_mid(fileName, elementary_rxn_list)[source]

Calculates substrate mids.

Note: Only 13C carbon mids can be calculated for now.

Input:
  1. fileName: substrate input file name. (csv format file)
  2. elementary_rxn_list: list of elementary reactions.
assumption:
  1. nat = [0.9893, 0.0107] ... naturnal carbon isotope abundance
  2. lab = [0.01,0.99]... labeled carbon abundance
fluxpyt.input_substrate_emu.detect_substrate_emus(substrates, labeling)[source]
fluxpyt.input_substrate_emu.genInSubEMU(substrate_info, network_substrate_emus)[source]
fluxpyt.input_substrate_emu.list_network_subs_emus(elementary_rxn_list, substrates)[source]
fluxpyt.input_substrate_emu.read_substrate_input(fileName)[source]
fluxpyt.input_substrate_emu.sort_sub_input(substrates, labeling, ratios)[source]

fluxpyt.main module

Created on Mon Jul 4 12:23:46 2016

Main module of FluxPyt.

Collects user inputs.

All the modules are run through this.

@author: Trunil

fluxpyt.main.main()[source]

fluxpyt.make_emu_model module

fluxpyt.make_emu_networks module

Created on Wed Jul 12 11:35:14 2017

@author: Trunil

fluxpyt.make_emu_networks.make_networks(mol_rxnIDs, elementary_rxn_list, measured_emus, known_mids)[source]

fluxpyt.mid_corr module

Created on Wed Mar 8 12:03:26 2017

Adapted from function corrMatGen in Openflux

@author: Trunil

fluxpyt.mid_corr.corrMatGen(output_size, input_size=0, molecularFormula='')[source]

function CM = corrMatGen(output_size, input_size, molform)

Returns correction matrix.

example: outputMDV = CM * inputMDV

Inputs:
output_size: int. length of output MDV (truncated length) (number of values in measured MID
e.g. pyruvate has 3 carbons (ideally 4 mids) but only three are measured or detected.)

input_size: int. lenght of input MDV (carbon backbone + 1)

molform: molecular formula without carbon backbone.

fluxpyt.mid_corr.corrMatGen1(output_row, input_size=0, molecularFormula='')[source]

function CM = corrMatGen(output_size, input_size, molform)

Generates correction matrix.

example: outputMDV = CM * inputMDV

Inputs:

output_row: list of output rows i.e. masses to be calculated
e.g. [0,1,2] will give corrected mids of M+0 , M+1 and M+2 .

input_size: int. lenght of input MDV (carbon backbone + 1)

molform: molecular formula without carbon backbone.

fluxpyt.mid_corr.getAtoms(pos, molecularFormula)[source]
fluxpyt.mid_corr.getCoefficients(pos, molecularFormula)[source]
fluxpyt.mid_corr.isletter(molecularFormula)[source]
fluxpyt.mid_corr.mid_correct(emu, mol_formula, num_obs, max_obs, mid)[source]
fluxpyt.mid_corr.stepCV(CV, columns)[source]
fluxpyt.mid_corr.test()[source]

fluxpyt.mid_vec_gen module

Generate correction vector for a given natural isotope distribution vector and number of atomic elements
iDist = isotope_dist = isotopomer distribution vector of the atom ele = num_atom = number of elements of the same atom

Similar to corr_vect = cVectGen(iDist, ele) in openFLux by Lake-Ee Quek, AIBN Created on Mon Jul 18 16:44:48 2016

@author: Trunil

fluxpyt.mid_vec_gen.mid_round(vector)[source]
fluxpyt.mid_vec_gen.mid_vec_gen(iDist, ele=0)[source]
fluxpyt.mid_vec_gen.sum_row(matrix)[source]
fluxpyt.mid_vec_gen.test()[source]

fluxpyt.monte_carlo module

Created on Sun Jun 25 12:36:28 2017

Monte Carlo for confidence interval estimation

@author: Trunil

fluxpyt.monte_carlo.monte_carlo(num_data=500)[source]

num_data = number of data sets to be genrated for monte_carlo analysis numIter = number of iteration of least square minimazation for single data set

fluxpyt.priliminary_fba module

Created on Thu Jul 14 11:50:41 2016

@author: Trunil

fluxpyt.priliminary_fba.create_objective(stoich_matrix, model_metabolite, rxnInd='minTotal', maximize=False, boundTag=True)[source]
fluxpyt.priliminary_fba.flux_range(rxnId, model_metabolite, stoich_matrix, bounds)[source]
fluxpyt.priliminary_fba.flux_variability(stoich_matrix, model_metabolite, bounds)[source]
fluxpyt.priliminary_fba.make_bounds(model_metabolite, minTotal=False)[source]
fluxpyt.priliminary_fba.priliminary_fba(model_metabolite, stoich_matrix)[source]

Checks model feasibility. Returns flux variability and initial solution.

fluxpyt.priliminary_fba.sort_glpk_solution(glpk_solution, rxnNames)[source]

fluxpyt.solve_mfa_lm module

Created on Thu Jun 8 10:55:41 2017

Function to solve MFA problem using lmfit package

@author: Trunil

fluxpyt.solve_mfa_lm.correct_mids(cal_mids, **kws)[source]
fluxpyt.solve_mfa_lm.iter_cb(params, iter, resid, **kws)[source]
fluxpyt.solve_mfa_lm.make_objective(rxnId, rxnList)[source]
fluxpyt.solve_mfa_lm.prob_func(x)[source]
fluxpyt.solve_mfa_lm.residual(params, **kws)[source]
fluxpyt.solve_mfa_lm.solve_mfa_problem(stoich_matrix, model_metabolite, rxnId_networks, rxn_networks, measured_mids, substrate_mids, rates, bounds, initial_sol, userInput, optimal_flux_dist=[], extra_params=[], **kws)[source]

fluxpyt.solve_mid_networks module

Solves the elementory metabolite unit networks.

Solves mids for only one set of flux_distribution

Created on Fri Jul 15 10:57:23 2016

@author: Trunil

fluxpyt.solve_mid_networks.append_mids(mids1, mids2)[source]

used when we have two lists of mids. Joins these two

fluxpyt.solve_mid_networks.get_mids(mids)[source]

arranges mid values and emus in list

fluxpyt.solve_mid_networks.solve_mid_networks(rxnId_networks, rxn_networks, substrate_mids, rates, flux_dist)[source]
fluxpyt.solve_mid_networks.solve_network(rxn_ids, emu_net, known_mids, rates, flux_dist)[source]
fluxpyt.solve_mid_networks.update_mids(rxnIds, rxns, mids)[source]

fluxpyt.utility module

Created on Tue Jul 19 10:44:54 2016

@author: Trunil

fluxpyt.utility.find(a, b, exclude=False)[source]

a = list b = item to be found

fluxpyt.utility.nCr(n, r)[source]

http://stackoverflow.com/questions/4941753/is-there-a-math-ncr-function-in-python

fluxpyt.utility.pause()[source]
fluxpyt.utility.prod(array)[source]

array = list of lists

fluxpyt.utility.size(array)[source]

array should be numpy array or list of lists

fluxpyt.utility.space()[source]
fluxpyt.utility.split_rxn(rxn)[source]
fluxpyt.utility.sum_matrix(matrix)[source]

gives sum of elements in a matrix. matrix = list of list of numbers

Module contents