Merge pull request #19 from cdanielmachado/py3

merge py3 with master

.gitignore

@@ -19,5 +19,7 @@ carveme.egg-info/*
 
 *.pyc
 
+.eggs/*
+
 docs/_build/*
 Dockerfile

carveme/__init__.py

@@ -1,5 +1,7 @@
+from future import standard_library
+standard_library.install_aliases()
 import os
-from ConfigParser import ConfigParser
+from configparser import ConfigParser
 from framed import set_default_solver, set_default_parameter, Parameter
 
 __version__ = '1.1.0'

carveme/reconstruction/carving.py

@@ -1,3 +1,6 @@
+from __future__ import print_function
+from builtins import zip
+from builtins import range
 import numpy as np
 import warnings
 import pandas as pd
@@ -66,7 +69,7 @@ def minmax_reduction(model, scores, min_growth=0.1, min_atpm=0.1, eps=1e-3, bigM
     objective = {}
 
     scores = scores.copy()
-    reactions = scores.keys()
+    reactions = list(scores.keys())
 
     if not soft_constraints:
         soft_constraints = {}
@@ -94,11 +97,11 @@ def minmax_reduction(model, scores, min_growth=0.1, min_atpm=0.1, eps=1e-3, bigM
         solver.pos_vars = []
 
         for r_id in reactions:
-            if model.reactions[r_id].lb < 0 or model.reactions[r_id].lb is None:
+            if model.reactions[r_id].lb is None or model.reactions[r_id].lb < 0:
                 y_r = 'yr_' + r_id
                 solver.add_variable(y_r, 0, 1, vartype=VarType.BINARY, update_problem=False)
                 solver.neg_vars.append(y_r)
-            if model.reactions[r_id].ub > 0 or model.reactions[r_id].ub is None:
+            if model.reactions[r_id].ub is None or model.reactions[r_id].ub > 0:
                 y_f = 'yf_' + r_id
                 solver.add_variable(y_f, 0, 1, vartype=VarType.BINARY, update_problem=False)
                 solver.pos_vars.append(y_f)
@@ -226,7 +229,7 @@ def carve_model(model, reaction_scores, outputfile=None, flavor=None, inplace=Tr
     if sol.status == Status.OPTIMAL:
         inactive = inactive_reactions(model, sol)
     else:
-        print "MILP solver failed: {}".format(sol.message)
+        print("MILP solver failed: {}".format(sol.message))
         return
 
     if debug_output:
@@ -245,7 +248,7 @@ def carve_model(model, reaction_scores, outputfile=None, flavor=None, inplace=Tr
                 gpr = parse_gpr_rule(row['GPR'], prefix='G_')
                 model.set_gpr_association(r_id, gpr, add_genes=True)
             except:
-                print 'Failed to parse:', row['GPR']
+                print('Failed to parse:', row['GPR'])
 
     cleanup_metadata(model)
 

carveme/reconstruction/diamond.py

@@ -1,3 +1,4 @@
+from __future__ import print_function
 import pandas as pd
 from subprocess import call
 import os
@@ -63,7 +64,7 @@ def run_blast(inputfile, input_type, outputfile, database, args=None, verbose=Tr
     cmd += args.split()
 
     if verbose:
-        print ' '.join(cmd)
+        print(' '.join(cmd))
 
     with open(os.devnull, 'w') as devnull:
         try:

carveme/reconstruction/gapfilling.py

@@ -1,3 +1,6 @@
+from __future__ import division
+from __future__ import print_function
+from past.utils import old_div
 from carveme.reconstruction.utils import medium_to_constraints
 from framed.model.transformation import disconnected_metabolites
 from framed.solvers import solver_instance
@@ -60,7 +63,7 @@ def gapFill(model, universe, constraints=None, min_growth=0.1, scores=None, inpl
 
         solver.update()
 
-    objective = {'y_'+r_id: 1.0 / (1.0 + scores.get(r_id, 0.0)) for r_id in new_reactions}
+    objective = {'y_'+r_id: old_div(1.0, (1.0 + scores.get(r_id, 0.0))) for r_id in new_reactions}
 
     solution = solver.solve(linear=objective, minimize=True, constraints=constraints)
 
@@ -123,7 +126,7 @@ def multiGapFill(model, universe, media, media_db, min_growth=0.1, max_uptake=10
             gapFill(model, universe, constraints=constraints, min_growth=min_growth,
                     scores=scores, inplace=True, bigM=bigM, solver=solver, tag=medium_name)
         else:
-            print 'Medium {} not in database, ignored.'.format(medium_name)
+            print('Medium {} not in database, ignored.'.format(medium_name))
 
     return model
 

carveme/reconstruction/ncbi_download.py

@@ -1,5 +1,8 @@
+from __future__ import print_function
+from future import standard_library
+standard_library.install_aliases()
 import pandas as pd
-import urllib
+import urllib.request, urllib.parse, urllib.error
 import os
 
 
@@ -11,7 +14,7 @@ def load_ncbi_table(inputfile):
 def download_ncbi_genome(accession, refseq_table, prefer_protein=True):
 
     if accession not in refseq_table.index:
-        print 'Invalid accession code'
+        print('Invalid accession code')
         return
 
     entry = refseq_table.loc[accession, :]
@@ -24,9 +27,9 @@ def download_ncbi_genome(accession, refseq_table, prefer_protein=True):
 
         outputfile = '{}.faa.gz'.format(accession)
 
-        _, result = urllib.urlretrieve(url, outputfile)
+        _, result = urllib.request.urlretrieve(url, outputfile)
 
-        if result.gettype() != 'application/x-gzip':
+        if result.get_content_type() != 'application/x-gzip':
             os.remove(outputfile)
         else:
             downloaded = True
@@ -37,9 +40,9 @@ def download_ncbi_genome(accession, refseq_table, prefer_protein=True):
 
         outputfile = '{}.fna.gz'.format(accession)
 
-        _, result = urllib.urlretrieve(url, outputfile)
+        _, result = urllib.request.urlretrieve(url, outputfile)
 
-        if result.gettype() != 'application/x-gzip':
+        if result.get_content_type() != 'application/x-gzip':
             os.remove(outputfile)
         else:
             downloaded = True

carveme/reconstruction/scoring.py

@@ -1,3 +1,5 @@
+from __future__ import division
+from past.utils import old_div
 import pandas as pd
 
 
@@ -118,7 +120,7 @@ def reaction_scoring(annotation, gprs, spontaneous_score=0.0, debug_output=None)
         reaction_scores.to_csv(debug_output + '_reaction_scores.tsv', sep='\t', index=False)
 
     if avg_score != 0:
-        reaction_scores['normalized_score'] = reaction_scores['score'] / avg_score
+        reaction_scores['normalized_score'] = old_div(reaction_scores['score'], avg_score)
         return reaction_scores
     else:
         return None

carveme/reconstruction/utils.py

@@ -1,3 +1,5 @@
+from builtins import str
+from builtins import zip
 from collections import OrderedDict
 from warnings import warn
 

carveme/universe/bigg_download.py

@@ -1,3 +1,9 @@
+from __future__ import division
+from __future__ import print_function
+from builtins import str
+from builtins import map
+from builtins import range
+from past.utils import old_div
 import requests
 import pandas as pd
 import sys
@@ -15,7 +21,7 @@
 
 
 def progress(i, n):
-    p = int(((i+1)*100.0)/n)
+    p = int(old_div(((i+1)*100.0),n))
     sys.stdout.write("\r{}%".format(p))
     sys.stdout.flush()
 
@@ -43,9 +49,9 @@ def get_request(url, max_tries=10):
             break
 
     if data is None:
-        print 'max number of attempts exceeded:', max_tries
+        print('max number of attempts exceeded:', max_tries)
     elif i > 0:
-        print 'failed attempts', i
+        print('failed attempts', i)
 
     return data
 
@@ -188,7 +194,7 @@ def build_bigg_universe_model(outputfile=None):
         CBModel: universe model
     """
 
-    print 'Downloading universal data from BiGG...'
+    print('Downloading universal data from BiGG...')
     model = CBModel('bigg_universe')
     bigg_rxns = get_request(reactions_url)
 
@@ -197,7 +203,7 @@ def build_bigg_universe_model(outputfile=None):
         build_reaction(model, entry['bigg_id'])
         progress(i, n)
 
-    print '\n'
+    print('\n')
 
     if outputfile:
         save_cbmodel(model, outputfile)
@@ -221,7 +227,7 @@ def download_model_specific_data(outputfile=None):
 
     """
 
-    print 'Downloading model-specific data from BiGG...'
+    print('Downloading model-specific data from BiGG...')
 
     data = get_request(models_url)
     rows = []
@@ -247,7 +253,7 @@ def download_model_specific_data(outputfile=None):
             rows.append((r_id, model_id, lb, ub, subsystem, gpr))
 
         progress(i, n)
-    print '\n'
+    print('\n')
 
     columns = ['reaction', 'model',  'lower_bound', 'upper_bound', 'subsystem', 'GPR']
     df = pd.DataFrame(rows, columns=columns)

carveme/universe/curation.py

@@ -1,3 +1,4 @@
+from __future__ import print_function
 import numpy as np
 from framed.model.transformation import disconnected_metabolites
 from carveme.reconstruction.utils import create_exchange_reactions, add_biomass_equation, create_sink_reactions, \
@@ -312,15 +313,15 @@ def curate_universe(model, model_specific_data, bigg_models, biomass_eq, taxa=No
         essencial reactions/metabolites that would otherwise be structurally blocked).
     """
 
-    print 'Starting universe curation...'
-    print '(initial size: {} x {})\n'.format(len(model.metabolites), len(model.reactions))
+    print('Starting universe curation...')
+    print('(initial size: {} x {})\n'.format(len(model.metabolites), len(model.reactions)))
 
     trusted_models = bigg_models.query('trusted == True').index.tolist()
 
     add_bounds_from_extracted_data(model, model_specific_data, trusted_models)
 
     if taxa:
-        print 'Filtering by taxa:', taxa
+        print('Filtering by taxa:', taxa)
         kingdom_map = bigg_models['domain'].to_dict()
 
         if taxa in {'cyanobacteria', 'bacteria'}:
@@ -340,10 +341,10 @@ def curate_universe(model, model_specific_data, bigg_models, biomass_eq, taxa=No
         other_compartments = set(model.compartments.keys()) - valid_compartments
         model.remove_compartments(other_compartments, delete_metabolites=True, delete_reactions=True)
 
-        print '(size: {} x {})\n'.format(len(model.metabolites), len(model.reactions))
+        print('(size: {} x {})\n'.format(len(model.metabolites), len(model.reactions)))
 
     if thermodynamics_data is not None:
-        print 'Computing thermodynamics...',
+        print('Computing thermodynamics...', end=' ')
 
         dG0 = thermodynamics_data['dG0'].to_dict()
         sdG0 = thermodynamics_data['sdG0'].to_dict()
@@ -354,10 +355,10 @@ def curate_universe(model, model_specific_data, bigg_models, biomass_eq, taxa=No
             x0 = None
 
         compute_flux_bounds(model, dG0, sdG0, x0, method=thermodynamics_method, inplace=True, override_trusted=False)
-        print 'done\n'
+        print('done\n')
 
 
-    print 'Applying manual curation rules...',
+    print('Applying manual curation rules...', end=' ')
 
     if use_heuristics:
         reversibility_heuristics(model, no_reverse_atp=True, no_proton_pumps=False, override_trusted=False)
@@ -368,7 +369,7 @@ def curate_universe(model, model_specific_data, bigg_models, biomass_eq, taxa=No
             if r_id in model.reactions:
                 model.set_flux_bounds(r_id, lb, ub)
 
-    print 'done\n'
+    print('done\n')
 
     if remove_unbalanced:
 
@@ -377,11 +378,11 @@ def curate_universe(model, model_specific_data, bigg_models, biomass_eq, taxa=No
             for m_id in ['M_photon_e', 'M_photon_p', 'M_photon_c']:
                 model.metabolites[m_id].metadata['FORMULA'] = ''
 
-        print 'Removing unbalanced reactions...'
+        print('Removing unbalanced reactions...')
         remove_unbalanced_reactions(model)
-        print '(size: {} x {})\n'.format(len(model.metabolites), len(model.reactions))
+        print('(size: {} x {})\n'.format(len(model.metabolites), len(model.reactions)))
 
-    print 'Creating pseudo-reactions...'
+    print('Creating pseudo-reactions...')
 
     create_exchange_reactions(model, default_lb=-1000, default_ub=1000)
 
@@ -392,14 +393,14 @@ def curate_universe(model, model_specific_data, bigg_models, biomass_eq, taxa=No
 
     add_maintenance_atp(model)
 
-    print '(size: {} x {})\n'.format(len(model.metabolites), len(model.reactions))
+    print('(size: {} x {})\n'.format(len(model.metabolites), len(model.reactions)))
 
     if remove_blocked:
-        print 'Removing blocked reactions and dead-end metabolites...'
+        print('Removing blocked reactions and dead-end metabolites...')
         simplify(model)
-        print '(size: {} x {})\n'.format(len(model.metabolites), len(model.reactions))
+        print('(size: {} x {})\n'.format(len(model.metabolites), len(model.reactions)))
 
     if outputfile:
         save_cbmodel(model, outputfile)
 
-    print 'Done.'
+    print('Done.')

carveme/universe/thermodynamics.py

@@ -1,3 +1,6 @@
+from __future__ import division
+from builtins import zip
+from past.utils import old_div
 import pandas as pd
 import numpy as np
 from framed import load_cbmodel
@@ -100,7 +103,7 @@ def calculate_deltaG0s(model, kegg_compounds, pH=default_pH, I=default_I, T=defa
 
     """
     kegg_rxns = build_kegg_reactions(model, kegg_compounds)
-    kmodel = KeggModel.from_formulas(kegg_rxns.values(), raise_exception=True)
+    kmodel = KeggModel.from_formulas(list(kegg_rxns.values()), raise_exception=True)
     kmodel.add_thermo(CC.init())
     dG0, sdG0, _ = kmodel.get_transformed_dG0(pH, I, T)
 
@@ -170,7 +173,7 @@ def dG_bounds(model, r_id, dG0, sdG0=None, x0=None, excluded=None, T=default_T):
         if m_id in excluded:
             continue
         elif m_id in x0:
-            x_min = x0[m_id] / sqrt(measured_fold_change)
+            x_min = old_div(x0[m_id], sqrt(measured_fold_change))
             x_max = x0[m_id] * sqrt(measured_fold_change)
         else:
             x_min = concentration_min
@@ -183,8 +186,8 @@ def dG_bounds(model, r_id, dG0, sdG0=None, x0=None, excluded=None, T=default_T):
             prod_min.append(x_min ** coeff)
             prod_max.append(x_max ** coeff)
 
-    dG_min = dG0[r_id] - sdG0[r_id] + R * T * np.log(np.prod(prod_min) / np.prod(reac_max))
-    dG_max = dG0[r_id] + sdG0[r_id] + R * T * np.log(np.prod(prod_max) / np.prod(reac_min))
+    dG_min = dG0[r_id] - sdG0[r_id] + R * T * np.log(old_div(np.prod(prod_min), np.prod(reac_max)))
+    dG_max = dG0[r_id] + sdG0[r_id] + R * T * np.log(old_div(np.prod(prod_max), np.prod(reac_min)))
 
     return dG_min, dG_max
 

requirements_dev.txt

@@ -1,5 +1,6 @@
 framed==0.3.5
 pandas>=0.20.0
+requests>=2.18
 
 
 

scripts/build_universe

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 
+from __future__ import print_function
 from carveme import config, project_dir
 import argparse
 import os
@@ -113,7 +114,7 @@ def main(mode, noheuristics=False, nothermo=False, allow_unbalanced=False, allow
                         remove_blocked=(not allow_blocked))
 
     else:
-        print 'Unrecognized option:', mode
+        print('Unrecognized option:', mode)
 
 
 if __name__ == '__main__':