# -*- coding: utf-8 -*-
"""
Description:
Read a PGDB folder (from BIOCYC/PATHWAYTOOLS) and create a padmet.
1./ To create a padmet without any genes information extracted use the first usage with:
pgdb: path to pgdb folder
output: path to the padmet to create
version: to specify the version of the pgdb (20.0, 22.0)
db: to sepcify the name of the database (METACYC, ECOCYC, ...)
enhance: to also read the file metabolic-reaction.xml and add the to the padmet
2./ To create a padmet and add only reactions from pgdb if they are in padmetRef specifie.
Copy information of the reaction not from the pgdb but from the padmetRef.
This allow to uniform reaction to the same version of metacyc represented in the padmetRef
For example, in some case 2 pgdb from different version can contain different information for a same reaction,pathway...
In this case use:
padmetRef: path to the padmet of reference
3./ To create a padmet wth genes information extracted use:
extract-gene
3.1/ To remove from the final padmet all reactions without genes associated use:
no-orphan
4./ To read the metabolic-reaction.xml file, a sbml with some missing reactions in PGDB use:
enhance
For more information of the parsing process read information below.
classes.dat:
For each class:
create new node / class = class
UNIQUE-ID (1) => node.id = UNIQUE-ID
COMMON-NAME (0-n) => node.Misc['COMMON-NAME'] = COMMON-NAME
TYPES (0-n) => for each, check or create new node class, create rlt (node is_a_class types)
SYNONYMS (0-n) => for each, create new node name, create rlt (node has_name synonyms)
compounds.dat:
for each compound:
create new node / class = compound
UNIQUE-ID (1) => node.id = UNIQUE-ID
COMMON-NAME (0-n) => node.Misc['COMMON-NAME'] = COMMON-NAME
INCHI-KEY (0-1) {InChIKey=XXX} => node.misc['INCHI_KEY': XXX]
MOLECULAR-WEIGHT (0-1) => node.misc()['MOLECULAR_WEIGHT'] = MOLECULAR-WEIGHT
SMILES (0-1) => node.misc()['SMILES'] = SMILES
TYPES (0-n) => for each, check or create new node class, create rlt (node is_a_class types)
SYNONYMS (0-n) => for each, create new node name, create rlt (node has_name name)
DBLINKS (0-n) {(db "id" ...)} => for each, create new node xref, create rlt (node has_xref xref)
proteins.dat:
for each protein:
create new node / class = protein
UNIQUE-ID (1) => node.id = UNIQUE-ID
COMMON-NAME (0-n) => node.Misc['COMMON-NAME'] = COMMON-NAME
INCHI-KEY (0-1) {InChIKey=XXX} => node.misc['INCHI_KEY': XXX]
MOLECULAR-WEIGHT (0-1) => node.misc()['MOLECULAR_WEIGHT'] = MOLECULAR-WEIGHT
SMILES (0-1) => node.misc()['SMILES'] = SMILES
TYPES (0-n) => for each, check or create new node class, create rlt (node is_a_class types)
SYNONYMS (0-n) => for each, create new node name, create rlt (node has_name name)
DBLINKS (0-n) {(db "id" ...)} => for each, create new node xref, create rlt (node has_xref xref)
SPECIES (0-1) => for each, check or create new node class, create rlt (node is_in_species class)
reactions.dat:
for each reaction:
create new node / class = reaction + node.misc()["DIRECTION"] = "UNKNOWN" by default
UNIQUE-ID (1) => node.id = UNIQUE-ID
COMMON-NAME (0-n) => node.Misc['COMMON-NAME'] = COMMON-NAME
EC-NUMBER (0-n) => node.Misc['EC-NUMBER'] = EC-NUMBER
REACTION-DIRECTION (0-1) => node.Misc['DIRECTION'] = reaction-direction, if REVERSIBLE, else: LEFT-TO-RIGHT
RXN-LOCATIONS (0,n) => node.misc['COMPARTMENT'] = rxn-location
TYPES (0-n) => check or create new node class, create rlt (node.id is_a_class types's_node.id)
DBLINKS (0-n) {(db "id" ...)} => create new node xref, create rlt (node has_xref xref's_node.id)
SYNONYMS (0-n) => create new node name, create rlt (node has_name name's_node.id)
--
for LEFT and RIGHT, also check 2 next lines if info about 'coefficient' or 'compartment'
defaut value: coefficient/stoichiometry = 1, compartment = unknown
also check if the direction is 'RIGHT-TO-LEFT', if yes, inverse consumes and produces relations
then change direction to 'LEFT-TO-RIGHT'
LEFT (1-n) => create rlt (node.id consumes left's_node.id)
RIGHT (1-n) => create rlt (node.id produces right's_node.id)
enzrxns.dat:
for each association enzyme/reaction:
create new rlt / type = catalyses
ENZYME (1) => stock enzyme as 'enzyme catalyses'
REACTION (1-n) => for each reaction after, create relation 'enzyme catalyses reaction'
pathways.dat:
for each pathway:
create new node / class = pathway
UNIQUE-ID (1) => node._id = UNIQUE-ID
TYPES (0-n) => check or create new node class, create rlt (node is_a_class types)
COMMON-NAME (0-n) => node.Misc['COMMON-NAME'] = COMMON-NAME
DBLINKS (0-n) {(db "id" ...)} => create new node xref, create rlt (node has_xref xref)
SYNONYMS (0-n) => create new node name, create rlt (node has_name name)
IN-PATHWAY (0-n) => check or create new node pathway, create rlt (node is_in_pathway name)
REACTION-LIST (0-n) => check or create new node pathway, create rlt (node is_in_pathway name)
::
usage:
pgdb_to_padmet.py --pgdb=DIR --output=FILE [--version=V] [--db=ID] [--padmetRef=FILE] [--source=STR] [-v] [--enhance]
pgdb_to_padmet.py --pgdb=DIR --output=FILE --extract-gene [--no-orphan] [--version=V] [--db=ID] [--padmetRef=FILE] [--source=STR] [-v] [--enhance]
options:
-h --help Show help.
--version=V Xcyc version [default: N.A].
--db=ID Biocyc database corresponding to the pgdb (metacyc, ecocyc, ...) [default: N.A].
--output=FILE padmet file corresponding to the DB.
--pgdb=DIR directory containg all the .dat files of metacyc (data).
--padmetRef=FILE padmet of reference.
--source=STR Tag associated to the source of the reactions, used to ensure traceability [default: GENOME].
--enhance use the metabolic-reactions.xml file to enhance the database.
--extract-gene use the genes_file (use if its a specie's pgdb, if metacyc, do not use).
--no-orhpan use the genes_file (use if its a specie's pgdb, if metacyc, do not use).
-v print info.
"""
from padmet.utils.connection import pgdb_to_padmet
import docopt
#1 Parsing .dat
#2 creating nodes and relations
[docs]def main():
#parsing args
args = docopt.docopt(__doc__)
version = args["--version"]
db = args["--db"]
source = args["--source"]
output = args["--output"]
pgdb_folder = args["--pgdb"]
enhanced_db = args["--enhance"]
extract_gene = args["--extract-gene"]
no_orphan = args["--no-orphan"]
padmetRef_file = args["--padmetRef"]
verbose = args["-v"]
padmet = pgdb_to_padmet.from_pgdb_to_padmet(pgdb_folder, db , version, source, extract_gene, no_orphan, enhanced_db, padmetRef_file, verbose)
padmet.generateFile(output)
if __name__ == "__main__":
main()