mob-suite
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phac-nml
MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Hi! here is the rep_type annotated from mob_typer, the id like in below: 'Col(BS512)', 'Col(KPHS6)', 'Col(MG828)', 'Col(MG828),rep_cluster_2392', 'Col(MP18)', 'Col(VCM04)', 'Col(Ye4449)', 'Col156', 'Col156,Col156', 'Col156,IncFIB', ... 'rep_cluster_816', 'rep_cluster_850', 'rep_cluster_870', 'rep_cluster_889', 'rep_cluster_893', 'rep_cluster_910',...
How do I make/use a custom DB? There are some input files that are not specified % mob_cluster --mode build -f new_plasmids.fasta -p new_plasmids_mobtyper_report.txt -t new_plasmids_host_taxonomy.txt --outdir output_directory -f new_plasmids.fasta...
Thanks for the great tool and your help both on and offline. I'm curious about the decision to `fix_fasta_header` before processing the FASTA. This makes it basically impossible (as far...
# Issue ## Bug Specifying `--database_directory` to `mob_recon` causes it to error with the following: ```bash Traceback (most recent call last): File "/opt/conda/envs/test/bin/mob_recon", line 8, in sys.exit(main()) File "/opt/conda/envs/test/lib/python3.8/site-packages/mob_suite/mob_recon.py", line...
When `blastn` produces empty results, it deletes the file: https://github.com/phac-nml/mob-suite/blob/6fa359789a04877cc6d7863f380f31816480b43a/mob_suite/utils.py#L344 However, the calling function, `blast_mge`, checks for an empty results file. When that file doesn't exist, it throws a file-not-found...
**TL;DR; I think there's a problem with `mash`/`gsl` in the `conda` installation. This causes `mob_init` to fail (silently) in the "Sketching complete plasmid database" step.** When trying to run `mob_typer`,...
Hi, It's nice that mob-suite tells me the plasmid in the reference database which is closest to each plasmid it identifies in my sample, but it would be good if...
Hi because of error downloading the database when running the script, I had to download the database manually. How do I reference the mob_typer to the database that i downloaded...
Hi, I managed to install the MOBsite via pip. Now I have some other problem. We have one fasta file containing 50 random plasmid sequences. Nothing else is known about...
Hi, I tried to install MOB SUITE. I got the error. Here is the traceback. ``` conda install -c bioconda mob_suite Collecting package metadata (current_repodata.json): done Solving environment: failed with...