Merge pull request #89 from cdanielmachado/development

Integrate development branch

.gitignore

@@ -8,3 +8,5 @@ docs/_build/*
 Dockerfile
 .idea/encodings.xml
 *.DS_Store
+carveme/data/input/bigg_proteins.dmnd
+carveme/data/input/bigg_proteins.dmnd

carveme/__init__.py

@@ -1,17 +1,17 @@
-from future import standard_library
-standard_library.install_aliases()
+
 import os
 from configparser import ConfigParser
-from framed import set_default_solver, set_default_parameter, Parameter
+from reframed import set_default_solver
+from reframed.solvers.solver import default_parameters, Parameter
 
-__version__ = '1.2.2'
+__version__ = '1.3.0'
 
 project_dir = os.path.abspath(os.path.dirname(__file__)) + '/'
 
 config = ConfigParser()
 config.read(project_dir + 'config.cfg')
 
 set_default_solver(config.get('solver', 'default_solver'))
-set_default_parameter(Parameter.FEASIBILITY_TOL, config.getfloat('solver', 'feas_tol'))
-set_default_parameter(Parameter.OPTIMALITY_TOL, config.getfloat('solver', 'opt_tol'))
-set_default_parameter(Parameter.INT_FEASIBILITY_TOL, config.getfloat('solver', 'int_feas_tol'))
+default_parameters[Parameter.FEASIBILITY_TOL] = config.getfloat('solver', 'feas_tol')
+default_parameters[Parameter.OPTIMALITY_TOL] = config.getfloat('solver', 'opt_tol')
+default_parameters[Parameter.INT_FEASIBILITY_TOL] = config.getfloat('solver', 'int_feas_tol')

scripts/build_universe → carveme/cli/build_universe.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 
-from __future__ import print_function
 from carveme import config, project_dir
 import argparse
 import os
@@ -10,10 +9,10 @@
 from carveme.universe.curation import curate_universe
 from carveme.universe.thermodynamics import compute_bigg_gibbs_energy
 from carveme.reconstruction.utils import load_biomass_db
-from framed.io.sbml import load_cbmodel
+from reframed import load_cbmodel
 
 
-def main(mode, noheuristics=False, nothermo=False, allow_unbalanced=False, allow_blocked=False,
+def maincall(mode, noheuristics=False, nothermo=False, allow_unbalanced=False, allow_blocked=False,
          biomass=None, biomass_db_path=None, normalize_biomass=False, taxa=None, outputfile=None):
 
     if mode == 'draft':
@@ -117,7 +116,7 @@ def main(mode, noheuristics=False, nothermo=False, allow_unbalanced=False, allow
         print('Unrecognized option:', mode)
 
 
-if __name__ == '__main__':
+def main():
     parser = argparse.ArgumentParser(description="Generate universal model to use with CarveMe")
 
     mode = parser.add_mutually_exclusive_group(required=True)
@@ -192,7 +191,7 @@ def main(mode, noheuristics=False, nothermo=False, allow_unbalanced=False, allow
     else:
         taxa = 'bacteria'
 
-    main(mode=mode,
+    maincall(mode=mode,
          nothermo=args.nothermo,
          noheuristics=args.noheuristics,
          allow_unbalanced=args.unbalanced,
@@ -203,3 +202,7 @@ def main(mode, noheuristics=False, nothermo=False, allow_unbalanced=False, allow
          taxa=taxa,
          outputfile=args.output)
 
+
+if __name__ == '__main__':
+    main()
+

scripts/carve → carveme/cli/carve.py

@@ -1,6 +1,3 @@
-#!/usr/bin/env python
-
-from __future__ import print_function
 from carveme import config, project_dir
 from carveme import __version__ as version
 from carveme.reconstruction.carving import carve_model, build_ensemble
@@ -10,11 +7,11 @@
 from carveme.reconstruction.ncbi_download import load_ncbi_table, download_ncbi_genome
 from carveme.reconstruction.scoring import reaction_scoring
 from carveme.reconstruction.diamond import run_blast, load_diamond_results
-from framed import load_cbmodel, Environment
+from reframed import load_cbmodel, save_cbmodel, Environment
+from reframed.io.sbml import sanitize_id
 import argparse
 import os
 import pandas as pd
-from framed.io.sbml import save_cbmodel, sanitize_id
 from multiprocessing import Pool
 from glob import glob
 
@@ -26,7 +23,7 @@ def build_model_id(name):
     return model_id
 
 
-def main(inputfile, input_type='protein', outputfile=None, diamond_args=None, universe=None, universe_file=None,
+def maincall(inputfile, input_type='protein', outputfile=None, diamond_args=None, universe=None, universe_file=None,
          ensemble_size=None, verbose=False, debug=False, flavor=None, gapfill=None, blind_gapfill=False, init=None,
          mediadb=None, default_score=None, uptake_score=None, soft_score=None, soft=None, hard=None, reference=None,
          ref_score=None, recursive_mode=False):
@@ -242,7 +239,7 @@ def main(inputfile, input_type='protein', outputfile=None, diamond_args=None, un
         print('Done.')
 
 
-if __name__ == '__main__':
+def main():
 
     parser = argparse.ArgumentParser(description="Reconstruct a metabolic model using CarveMe",
                                      formatter_class=argparse.RawTextHelpFormatter)
@@ -340,7 +337,7 @@ def main(inputfile, input_type='protein', outputfile=None, diamond_args=None, un
         if len(args.input) > 1:
             parser.error('Use -r when specifying more than one input file')
 
-        main(
+        maincall(
             inputfile=args.input[0],
             input_type=input_type,
             outputfile=args.output,
@@ -367,7 +364,7 @@ def main(inputfile, input_type='protein', outputfile=None, diamond_args=None, un
     else:
 
         def f(x):
-            main(
+            maincall(
                 inputfile=x,
                 input_type=input_type,
                 outputfile=args.output,
@@ -393,3 +390,7 @@ def f(x):
 
         p = Pool()
         p.map(f, args.input)
+
+
+if __name__ == '__main__':
+    main()

scripts/carveme_init → carveme/cli/carveme_init.py

@@ -1,18 +1,10 @@
-#!/usr/bin/env python
-
-from __future__ import print_function
-from future import standard_library
-standard_library.install_aliases()
 import urllib.request, urllib.parse, urllib.error
 import subprocess
 import os
-
-
 from carveme import project_dir
 
 
-if __name__ == '__main__':
-
+def main():
     source_url = 'https://github.com/cdanielmachado/carveme/raw/master/carveme/'
 
     downloads = [
@@ -58,3 +50,7 @@
         print('Failed to run diamond. Please make sure diamond is installed and add it to your PATH.')
     else:
         print('Done.')
+
+
+if __name__ == '__main__':
+    main()

scripts/gapfill → carveme/cli/gapfill.py

@@ -1,16 +1,13 @@
-#!/usr/bin/env python
-
-from __future__ import print_function
 from carveme import config, project_dir
 from carveme.reconstruction.gapfilling import multiGapFill
 from carveme.reconstruction.utils import load_media_db
-from framed import load_cbmodel, save_cbmodel
+from reframed import load_cbmodel, save_cbmodel
 import argparse
 import os
 
 
-def main(inputfile, media, mediadb=None, universe=None, universe_file=None, outputfile=None, flavor=None,
-         exchange_format=None, spent=None, verbose=False):
+def maincall(inputfile, media, mediadb=None, universe=None, universe_file=None, outputfile=None, flavor=None,
+         spent=None, verbose=False):
 
     if verbose:
         print('Loading model...')
@@ -65,7 +62,7 @@ def main(inputfile, media, mediadb=None, universe=None, universe_file=None, outp
 
     max_uptake = config.getint('gapfill', 'max_uptake')
     multiGapFill(model, universe_model, media, media_db, max_uptake=max_uptake, inplace=True,
-                 exchange_format=exchange_format, spent_model=spent_model)
+                 spent_model=spent_model)
 
     if verbose:
         m2, n2 = len(model.metabolites), len(model.reactions)
@@ -85,8 +82,7 @@ def main(inputfile, media, mediadb=None, universe=None, universe_file=None, outp
     if verbose:
         print('Done.')
 
-
-if __name__ == '__main__':
+def main():
     parser = argparse.ArgumentParser(description="GapFill a metabolic model for a given set of media")
 
     parser.add_argument('input', metavar='INPUTFILE',
@@ -110,8 +106,6 @@ def main(inputfile, media, mediadb=None, universe=None, universe_file=None, outp
     sbml.add_argument('--cobra', action='store_true', help="Input SBML in old cobra format")
     sbml.add_argument('--fbc2', action='store_true', help="Input SBML in sbml-fbc2 format")
 
-    parser.add_argument('--exchange-format', dest='exchange_format', help=argparse.SUPPRESS)
-
     args = parser.parse_args()
 
     if args.fbc2:
@@ -121,13 +115,15 @@ def main(inputfile, media, mediadb=None, universe=None, universe_file=None, outp
     else:
         flavor = None
 
-    main(inputfile=args.input,
+    maincall(inputfile=args.input,
          media=args.media.split(','),
          mediadb=args.mediadb,
          universe=args.universe,
          universe_file=args.universe_file,
          outputfile=args.output,
          flavor=flavor,
-         exchange_format=args.exchange_format,
          spent=args.spent,
-         verbose=args.verbose)
+         verbose=args.verbose)
+
+if __name__ == '__main__':
+    main()

scripts/merge_community → carveme/cli/merge_community.py

@@ -1,15 +1,11 @@
-#!/usr/bin/env python
-
-from __future__ import print_function
 import argparse
 import os
-from framed import load_cbmodel, save_cbmodel, Environment
-from framed.community.model import Community
+from reframed import load_cbmodel, save_cbmodel, Environment, Community
 from carveme import config, project_dir
 from carveme.reconstruction.utils import load_media_db
 
 
-def main(inputfiles, flavor=None, split_pool=False, no_biomass=False, init=None, mediadb=None, ext_comp_id=None, outputfile=None):
+def maincall(inputfiles, flavor=None, split_pool=False, no_biomass=False, init=None, mediadb=None, ext_comp_id=None, outputfile=None):
 
     if not flavor:
         flavor = config.get('sbml', 'default_flavor')
@@ -42,16 +38,16 @@ def main(inputfiles, flavor=None, split_pool=False, no_biomass=False, init=None,
             raise IOError('Failed to load media library:' + mediadb)
 
         if split_pool:
-            exchange_format = "'R_EX_M_{}_e_pool'"
+            fmt_func = lambda x: f"R_EX_M_{x}_e_pool"
         else:
-            exchange_format = "'R_EX_{}_e'"
-        init_env = Environment.from_compounds(media_db[init], exchange_format=exchange_format)
+            fmt_func = lambda x: f"R_EX_{x}_e"
+        init_env = Environment.from_compounds(media_db[init], fmt_func=fmt_func)
         init_env.apply(merged, inplace=True)
 
     save_cbmodel(merged, outputfile, flavor=flavor)
 
 
-if __name__ == '__main__':
+def main():
     parser = argparse.ArgumentParser(description="Merge single species models into a microbial community model")
 
     parser.add_argument('input', metavar='INPUTFILES', nargs='+', help="SBML input files (single species)")
@@ -87,7 +83,7 @@ def main(inputfiles, flavor=None, split_pool=False, no_biomass=False, init=None,
     else:
         flavor = None
 
-    main(inputfiles=args.input,
+    maincall(inputfiles=args.input,
          flavor=flavor,
          split_pool=args.split_pool,
          no_biomass=args.no_biomass,
@@ -97,4 +93,5 @@ def main(inputfiles, flavor=None, split_pool=False, no_biomass=False, init=None,
          outputfile=args.output)
 
 
-
+if __name__ == '__main__':
+    main()

carveme/reconstruction/carving.py

@@ -1,15 +1,13 @@
-from __future__ import print_function
-from builtins import zip
-from builtins import range
 import numpy as np
 import warnings
 import pandas as pd
 
-from framed.cobra.ensemble import EnsembleModel, save_ensemble
-from framed.io.sbml import parse_gpr_rule, save_cbmodel
-from framed.model.transformation import disconnected_metabolites
-from framed.solvers import solver_instance
-from framed.solvers.solver import VarType, Status
+from reframed.cobra.ensemble import EnsembleModel, save_ensemble
+from reframed.io.sbml import parse_gpr_rule, save_cbmodel
+from reframed.core.transformation import disconnected_metabolites
+from reframed.solvers import solver_instance
+from reframed.solvers.solver import VarType
+from reframed.solvers.solution import Status
 
 
 def inactive_reactions(model, solution):
@@ -99,46 +97,46 @@ def minmax_reduction(model, scores, min_growth=0.1, min_atpm=0.1, eps=1e-3, bigM
         solver._carveme_flag = True
 
         biomass = model.biomass_reaction
-        solver.add_constraint('min_growth', {biomass: 1}, '>', min_growth, update_problem=False)
-        solver.add_constraint('min_atpm', {'R_ATPM': 1}, '>', min_atpm, update_problem=False)
+        solver.add_constraint('min_growth', {biomass: 1}, '>', min_growth, update=False)
+        solver.add_constraint('min_atpm', {'R_ATPM': 1}, '>', min_atpm, update=False)
 
         solver.neg_vars = []
         solver.pos_vars = []
 
         for r_id in reactions:
             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.add_variable(y_r, 0, 1, vartype=VarType.BINARY, update=False)
                 solver.neg_vars.append(y_r)
             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.add_variable(y_f, 0, 1, vartype=VarType.BINARY, update=False)
                 solver.pos_vars.append(y_f)
 
         if uptake_score != 0:
             for r_id in model.reactions:
                 if r_id.startswith('R_EX'):
-                    solver.add_variable('y_' + r_id, 0, 1, vartype=VarType.BINARY, update_problem=False)
+                    solver.add_variable('y_' + r_id, 0, 1, vartype=VarType.BINARY, update=False)
 
         solver.update()
 
         for r_id in reactions:
             y_r, y_f = 'yr_' + r_id, 'yf_' + r_id
             if y_r in solver.neg_vars and y_f in solver.pos_vars:
-                solver.add_constraint('lb_' + r_id, {r_id: 1, y_f: -eps, y_r: bigM}, '>', 0, update_problem=False)
-                solver.add_constraint('ub_' + r_id, {r_id: 1, y_f: -bigM, y_r: eps}, '<', 0, update_problem=False)
-                solver.add_constraint('rev_' + r_id, {y_f: 1, y_r: 1}, '<', 1, update_problem=False)
+                solver.add_constraint('lb_' + r_id, {r_id: 1, y_f: -eps, y_r: bigM}, '>', 0, update=False)
+                solver.add_constraint('ub_' + r_id, {r_id: 1, y_f: -bigM, y_r: eps}, '<', 0, update=False)
+                solver.add_constraint('rev_' + r_id, {y_f: 1, y_r: 1}, '<', 1, update=False)
             elif y_f in solver.pos_vars:
-                solver.add_constraint('lb_' + r_id, {r_id: 1, y_f: -eps}, '>', 0, update_problem=False)
-                solver.add_constraint('ub_' + r_id, {r_id: 1, y_f: -bigM}, '<', 0, update_problem=False)
+                solver.add_constraint('lb_' + r_id, {r_id: 1, y_f: -eps}, '>', 0, update=False)
+                solver.add_constraint('ub_' + r_id, {r_id: 1, y_f: -bigM}, '<', 0, update=False)
             elif y_r in solver.neg_vars:
-                solver.add_constraint('lb_' + r_id, {r_id: 1, y_r: bigM}, '>', 0, update_problem=False)
-                solver.add_constraint('ub_' + r_id, {r_id: 1, y_r: eps}, '<', 0, update_problem=False)
+                solver.add_constraint('lb_' + r_id, {r_id: 1, y_r: bigM}, '>', 0, update=False)
+                solver.add_constraint('ub_' + r_id, {r_id: 1, y_r: eps}, '<', 0, update=False)
 
         if uptake_score != 0:
             for r_id in model.reactions:
                 if r_id.startswith('R_EX'):
-                    solver.add_constraint('lb_' + r_id, {r_id: 1, 'y_' + r_id: bigM}, '>', 0, update_problem=False)
+                    solver.add_constraint('lb_' + r_id, {r_id: 1, 'y_' + r_id: bigM}, '>', 0, update=False)
 
         solver.update()
 

carveme/reconstruction/diamond.py

@@ -1,4 +1,3 @@
-from __future__ import print_function
 import pandas as pd
 from subprocess import call
 import os