Comments (3)
Hi @cfrioux, Hi @ArnaudBelcour,
This would be great! When will this option become available?
Best regards,
Noor Alsmadi
from metage2metabo.
Creating a list of targets for all the reachable compounds of the community (community scope) is not implemented yet.
I do not have time to properly include it in m2m these days, but, I've got a snippet to do it, if you're interested.
import sys
import json
from metage2metabo.sbml_management import create_species_sbml
# inputs
jsonfile = sys.argv[1]
output_file_sbml = sys.argv[2]
# read scope file and retrieve targets
with open(jsonfile, "r") as f:
raw = json.load(f)
targets = raw["com_scope"]
# create a SBML with the targets
create_species_sbml(targets, output_file_sbml)
You write the above script in a file (let's say scope_to_targets.py
) and call it this way:
python scope_to_targets.py community_analysis/comm_scopes.json community_analysis/comm_scopes.sbml
from metage2metabo.
Added in #61.
from metage2metabo.
Related Issues (20)
- I have the following problems when running the t2d_m2m_target_producers.R file: HOT 8
- Multiple errors when running test data HOT 7
- A better focus on the host metabolism when a host is provided HOT 1
- Issue with pathway tools API limitation and PGDB entries verification HOT 4
- Compute deadend and orphan metabolites
- Non optimal powergraph visualisation HOT 2
- m2m_analysis powergraph not working as expected HOT 27
- m2m recon not working with gbff file inputs HOT 4
- Error with analysis graph when using taxon_id HOT 5
- CRITICAL:metage2metabo.m2m.reconstruction:Something went wrong running Pathway Tools. See the log file in /home/chencong/output3/pgdb_log/log_error.txt HOT 6
- No /home/chencong/.ncbirc file, please fix it before using the program HOT 5
- [Question] Where can I find seed files? HOT 4
- Install metage2metabo problem HOT 5
- How to prepare inputs for metage2metabo HOT 3
- mpwt could not find the version of Pathway Tools HOT 1
- Individual scopes include seeds even if non producible or absent from the GSMNs HOT 3
- Do not allow abbreviation in command arguments. HOT 1
- Sanitize use of tarfile extractall. HOT 1
- gff file format problem while running m2m recon HOT 1
- When using `--pwt-xml`, the xml files extracted from Pathway Tools can be incompatible with python-libsbml. HOT 1
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from metage2metabo.