Commit feff14ab authored by AITE Meziane's avatar AITE Meziane

README updated, added convert sbml db

parent 34ca7d24
#In coming
---
title: padmet-utils - Documentation
author: Meziane AITE
date: 2017-04-20
version: 2.4
geometry: margin=2cm
date: 2017-06-19
version: 2.5
---
################################################################################
......@@ -15,7 +14,6 @@ heterogeneous knowledge and data sources, including the information reported by
## Installation
From git repository:
cd ~/programs
git clone https://gitlab.inria.fr/maite/padmet-utils.git
......@@ -23,33 +21,37 @@ From git repository:
.
├── README.md
├── LICENSE
├── connection
│ ├── biggAPI_to_padmet.py
│ ├── biggTSV_to_padmet.py
│ ├── compounds_to_sbml.py
│ ├── enhanced_meneco_output.py
│ ├── enhanced_sgs_output.py
│ ├── extract_rxn_sbml.py
│ ├── extract_rxn_with_gene_assoc.py
│ ├── gbk_to_faa.py
│ ├── gene_to_targets.py
│ ├── gramma-boolean-rapsody.py
│ ├── padmet_to_askomic.py
│ ├── padmet_to_asp.py
│ ├── padmet_to_sbml.py
│ ├── pgdb_to_padmet.py
│ ├── post_pantograph_gbr.py
│ ├── pre_pantograph.py
│ ├── reactions_to_sbml.py
│ ├── sbml_to_gene.py
│ ├── sbml_to_gene_assoc.py
│ ├── sbml_to_padmet.py
│ └── wikipage_creation.py
├── exploration
│ ├── change_biomass_cobra.py
│ ├── change_biomass_cobra_allspecies.py
│ ├── change_biomass_cobra_givencpd.py
│ ├── check_db.py
│ ├── compare_sbml_padmet.py
│ ├── convert_sbml_db.py
│ ├── extract_pwy_sources.py
│ ├── extract_pwy_sources_with_filter.py
│ ├── fba_test.py
│ ├── fba_all_species.py
│ ├── fba_given_species.py
│ ├── fba_on_reaction.py
│ ├── get_pwy_from_rxn.py
│ ├── report_network.py
│ └── visu_path.py
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
Require internet access !
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
Create a padmet file from 2 tsv files (reactions.tsv and metabolites.tsv)
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
Convert a list of compounds to an sbml file. Often in sbml, the compartment of the
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
The standard output of meneco return ids of reactions corresponding to the solution for gapfilling.
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
1./ extract all data from sgs output
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
From a given sbml file, create a sbml with only the reactions associated to a gene.
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
convert GBK to FAA with Bio package
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
From a list of genes, recovere from the linked reactions the list of products.
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
convert a padmet representing a database (padmetRef) and/or a padmet representing a model (padmetSpec)
......@@ -44,7 +59,6 @@ from itertools import izip_longest
import os
import csv
import docopt
import time
def main():
args = docopt.docopt(__doc__)
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
Convert PADMet to ASP following this predicats:
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
Use the script padmet_to_sbml to convert padmet to a sbml file
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
Before running pantograph it is necessary to check if the metabolic network
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
Convert a list of reactions to SBML file.
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
usage:
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
There are 3 cases of convertion sbml to padmet:
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
Create the files containing the wikicode for each page of the wiki relative to a
......
# -*- coding: utf-8 -*-
"""
@author: Meziane AITE, meziane.aite@inria.fr
Description:
usage:
get_pwy_from_rxn.py --padmet=FILE --cdt_file=FILE --output=FILE
options:
-h --help Show help.
--reaction_file=FILE pathname of the file containing the reactions id, 1/line
--padmetRef=FILE pathname of the padmet representing the database.
--output=FILE pathname of the file with line = pathway id, all reactions id, reactions ids from reaction file, ratio. sep = "\t"
"""
from padmet.padmetSpec import PadmetSpec
import docopt
import csv
def main():
"""
args = docopt.docopt(__doc__)
cdt_file = args["--condition_file"]
padmet_file = args["--padmet"]
output = args["--output"]
"""
padmet_file = "/home/maite/padmet_tools/test/arnaud/draft.padmet"
cdt_file = "/home/maite/padmet_tools/test/arnaud/diff_TenorD3_vs_TenorD0_T2_SANS_T2MD6TB.csv"
output = "/home/maite/padmet_tools/test/arnaud/output.csv"
padmet = PadmetSpec(padmet_file)
#read cdt_file:
with open(cdt_file, 'r') as csvfile:
reader = csv.DictReader(csvfile, delimiter=";")
#k: gene_id, v = float, FC value
dict_gene_exp = dict([(dict_line[""],float((dict_line["log2FoldChange"].replace(",",".")))) for dict_line in reader])
#k: pwy_id, v = set of gene_id
all_pwys = [node.id for node in padmet.dicOfNode.values() if node.type == "pathway"]
with open(output, 'w') as f:
header = ["pathway_id", "common_name","dict_reactions_genes","dict_reactions_FC","UP/DOWN/BOTH"]
line = ";".join(header)+"\n"
f.write(line)
for pwy_id in all_pwys:
try:
pwy_cname = padmet.dicOfNode[pwy_id].misc["COMMON_NAME"][0]
except KeyError:
pwy_cname = ""
#pwy_id = all_pwys[0]
all_gene_associated = set()
rxn_associated = [rlt.id_in for rlt in padmet.dicOfRelationOut[pwy_id] if rlt.type == "is_in_pathway"]
dict_rxn_gene = {}
for rxn_id in rxn_associated:
#rxn_id = rxn_associated[0]
gene_associated = set([rlt.id_out for rlt in padmet.dicOfRelationIn[rxn_id] if rlt.type == "is_linked_to"])
all_gene_associated.update(gene_associated)
dict_rxn_gene[rxn_id] = list(gene_associated)
if len(all_gene_associated) > 0:
dict_specific_gene_exp = dict([(k,v) for k,v in dict_gene_exp.items() if k in all_gene_associated])
if dict_specific_gene_exp:
nbUp = len([fc_value for fc_value in dict_specific_gene_exp.values() if fc_value > 0])
if nbUp == len(dict_specific_gene_exp.keys()):
direction = "UP"
elif nbUp == 0:
direction = "DOWN"
else:
direction = "BOTH"
line = [pwy_id, pwy_cname, str(dict_rxn_gene),str(dict_specific_gene_exp),direction]
line = ";".join(line)+"\n"
f.write(line)
if __name__ == "__main__":
main()
\ No newline at end of file
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
For a given sbml file, return the DBs of each reaction, based on metanetx file.
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
compare reactions in sbml and padmet files
......
This diff is collapsed.
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
......
#!/usr/bin/python
#-*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Clemence FRIOUX, clemence.frioux@inria.fr
Description:
For each compound in ListOfSpecies,the biomass reaction is (re)created with
......
#!/usr/bin/python
#-*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Clemence FRIOUX, clemence.frioux@inria.fr
Description:
For a given compound, the biomass reaction is recreated with
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
Run flux balance analyse with cobra package. If the flux is >0. Run also FVA
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with padmet-utils. If not, see <http://www.gnu.org/licenses/>.
@author: Meziane AITE, meziane.aite@inria.fr
Description:
From a file containing a list of reaction, return the pathways where this reactions
......
# -*- coding: utf-8 -*-
"""
This file is part of padmet-utils.
padmet-utils is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
padmet-utils is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License