Comments (3)
Hello Adrien,
I'll try to answer to both of your questions. So far m2m_analysis is not as flexible as it could be as it was implemented mainly in order to reproduce the figures from our manuscript.
1 - By default we look at the phylum and no other taxonomic level. We might modify that in the near future. I know that @ArnaudBelcour intends to work again on m2m_analysis
over the next few weeks. In the meantime should you want to look at the genus-level for instance, you could modify the code in this function, and in particular L315 which is where we retrieve the first four characters of phylum for counting. If you change rank[0]
for rank[4]
, you will calculate your stats at the genus level.
2 - Indeed we introduced a mapping step in the code in order to prevent long names to decrease readability in the figure. The matching between the new names and the original ones is given in output_dir/taxon_phylum.tsv
. If you do not want such mapping to be done, you can rerun the analysis without the --taxon taxon_id.tsv
argument. See the attached figures that were generated with and without the --taxon
argument.
I hope this helps, please let me know if this is unclear.
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Thank you very much for your replies!
Sorry about 2) that I missed that file in my output directory!
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No worries, we will clarify the documentation.
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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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