WARNING:
This tool was a test during my PhD. Currently it is not working and I will not update it, so don't use it. It is kept for test purpose.
Rhea_mapper is a Python3 (Python >= 3.6) tool to create draft metabolic network from genomes, sparql query on Rhea or Uniprot and from tsv files containing list of Rhea reactions or Uniprot protein IDs.
This project is licensed under the GNU General Public License - see the LICENSE file for details.
Python 3 (Python 3.6 is tested). rhea_mapper uses a certain number of Python dependencies:
- biopython to handle fasta files.
- cobra to create sbml files.
- rdflib to load rhea.rdf and query it.
- sparqlwrapper to query Uniprot and Rhea sparql endpoint.
And another tool:
- OrthoFinder to find orthologs to uniprot with experimental evidence linked to rhea.
pip install rhea_mapper
rhea_mapper has 4 main commands: genome, sparql, database and from_file.
usage: rhea_mapper [-h] [-v] {database,genome,sparql,taxonomy,from_file} ...
Create Rhea sbml files from genomes. For specific help on each subcommand use:
rhea_mapper {cmd} --help
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
subcommands:
valid subcommands:
{database,genome,sparql,taxonomy,from_file}
database Create rhea_mapper database [internet connection
required]
genome metabolic network reconstruction from genome
sparql Using a SPARQL query for reaction ID on Rhea or
protein ID on Uniprot, create the corresponding
metabolic network
taxonomy With a taxonomy, query Uniprot to create the
corresponding metabolic network
from_file Using a tsv file with list of Rhea reaction or Uniprot
protein, create the corresponding metabolic network
Requires: Orthofinder for genome if you provide a fasta
This command downloads and creates the files needed by rhea_mapper to work. As it downlaods files, this funciton requires an internet connection.
By using the RDF file of Rhea, rhea_mapper will create a SBMl file, with some specificity:
- the direction of reactions can be: arbitrary, follow MetaCyc reaction direction or follow KEGG reaction direction.
- for the variable stoichiometric coefficient (n, n-1, n+1, 2n) in reaction, n has been set to 2.
- genes linked to Rhea reactions with experimental evidence are associated to these reactions.
usage: rhea_mapper database [-h] -d DATABASE
Create rhea_mapper database [internet connection required]
optional arguments:
-h, --help show this help message and exit
-d DATABASE, --database DATABASE
Database folder, if not existing it will be created
It will create an output_folder containing:
- ncbi_taxonomy.dmp: taxonomy file from the NCBI containing for each taxon ID the corresponding taxon name.
- rhea.rdf: the RDF file of Rhea database.
- rhea2ec.tsv: mapping between Rhea reaction and EC number.
- rhea2uniprot_sprot.tsv: mapping between Rhea reaction and Uniprot protein ID.
- uniprot_sprot.fasta: fasta containg all amino-acids sequences from Swissprot.
- uniprot_ec_evidence.tsv: tsv file containing Uniprot protein ID linked to EC number with experimental evidence.
- uniprot_go_evidence.tsv: tsv file containing Uniprot protein ID linked to GO terms with experimental evidence.
- uniprot_rhea_evidence.tsv: tsv file containing Uniprot protein ID linked to Rhea reaction with experimental evidence.
- uniprot_rhea_evidence.fasta: fasta file containing protein linked to Rhea reaction with experimental evidence.
- rhea.sbml: SBML file created by rhea_mapper using the rhea.rdf file and the uniprot_rhea_evidence.tsv (to have gene association).
- version.json: contains the version number of Rhea database and Uniprot database in this folder.
Rhea files come from the Rhea download page.
uniprot_sprot.fasta is downloaded from the Uniprot download page. It is the Reviewed (Swiss-Prot).
uniprot_rhea_evidence.* files are created with a SPARQL query on the Uniprot SPARQL endpoint.
This genome takes as input folders with subfolders containing a tsv file with annotation (gene linked to EC number) and a fasta file (proteome of the species of interest).
Then it will map the EC to Rhea reactions.
in a second step it will take the proteome to search for orthologs against a database of Uniprot protein linked to Rhea reactions with experimental evidence.
Then a sbml file will be created.
usage: rhea_mapper genome [-h] [-f FOLDER] -o OUTPUT -d DATABASE [-c CPU]
metabolic network reconstruction from genome
optional arguments:
-h, --help show this help message and exit
-f FOLDER, --folder FOLDER
Input folder containing either annotation, genomes or
both
-o OUTPUT, --output OUTPUT
Output folder
-d DATABASE, --database DATABASE
Database folder, if not existing it will be created
-c CPU, --cpu CPU cpu number for multi-process
The structure of the input_folder is:
input_folder
├── organism_1
│ └── organism_1.gbk
├── organism_2
│ └── organism_2.tsv
│ └── organism_2.fasta
├── organism_3
│ └── organism_3.tsv
├── organism_4
│ └── organism_4.fasta
..
└── organism_n
└── organism_n.gbk
GenBank files will be converted into the format use by rhea_mapper genome meaning a tsv file + a fasta file. It is also possible to give only a fasta file or a tsv file.
The fasta file must contain amino-acids sequences.
The tsv file must be structured like:
| gene | EC_Number |
|---|---|
| gene_1 | X.X.X.X |
| ... | |
| gene_n | X.X.X.X |
Using a sparql query, rhea_mapper will query either a rhea rdf file from its database, the uniprot sparql endpoint or the rhea sparql endpoint.
A Uniprot query must contain the predicate of protein Id from uniprot (?predicate a up:Protein). The set of proteins find by the sparql query will then be used to create a draft metabolic network. Rhea_mapper will use the reconstruction method of genome to have a sbml file.
For the Rhea query, it must a set of Rhea reactions (?predicate rdfs:subClassOf rh:Reaction). Then using these IDs, rhea_mapper will create the corresponding sbml files.
usage: rhea_mapper sparql [-h] [-s SPARQL] -e ENDPOINT -d DATABASE -o OUTPUT
[-c CPU]
Using a SPARQL query for reaction ID on Rhea or protein ID on Uniprot, create
the corresponding metabolic network
optional arguments:
-h, --help show this help message and exit
-s SPARQL, --sparql SPARQL
SPARQL query file
-e ENDPOINT, --endpoint ENDPOINT
Endpoint either 'uniprot' or 'rhea' or 'rhea_endpoint
-d DATABASE, --database DATABASE
Database folder, if not existing it will be created
-o OUTPUT, --output OUTPUT
Output folder
-c CPU, --cpu CPU cpu number for multi-process
From an organism name or a taxonomy group, rhea_mapper will query Uniprot to retrieve the proteins associated to this organism/taxonomy and will create a draft metabolic network form it.
usage: rhea_mapper taxonomy [-h] -d DATABASE -o OUTPUT [-c CPU]
[--organism ORGANISM] [--taxonomy TAXONOMY]
With a taxonomy, query Uniprot to create the corresponding metabolic network
optional arguments:
-h, --help show this help message and exit
-d DATABASE, --database DATABASE
Database folder, if not existing it will be created
-o OUTPUT, --output OUTPUT
Output folder
-c CPU, --cpu CPU cpu number for multi-process
--organism ORGANISM Name of organism or group of organism to query uniprot
for Protein
--taxonomy TAXONOMY TSV file with taxonomy name of organism
Using a tsv file with either Rhea reactions ID or Uniprot protein IDs, rhea_mapper will create draft metabolic network.
For the Rhea reactions, it will create a sbml file.
For the Uniprot protein, it will use the reconstruction method of genome to have a sbml file.
usage: rhea_mapper from_file [-h] -l LIST -d DATABASE -o OUTPUT [-c CPU] -r
REFERENCE
Using a tsv file with list of Rhea reaction or Uniprot protein, create the
corresponding metabolic network
optional arguments:
-h, --help show this help message and exit
-l LIST, --l LIST File containing list of Rhea reacitons IDs or protein
IDs
-d DATABASE, --database DATABASE
Database folder, if not existing it will be created
-o OUTPUT, --output OUTPUT
Output folder
-c CPU, --cpu CPU cpu number for multi-process
-r REFERENCE, --reference REFERENCE
Database for reference either 'uniprot' or 'rhea'