Matthew Schechter

## February 3, 2022 - Time to start using github projects more efficiently! We will now translate meeting action items into TODOs on the [project page](https://github.com/merenlab/anvio/projects/1) - @matthewlawrenceklein and @isaacfink21...

## March 31, 2022 - We had a great genome-view demo on Tuesday and got excellent suggestions. At the moment, these seem like the most actionable items to address: -...

# WD `/Users/mschechter/scratch` # Original command anvi-export-locus -c Staphylococcus_aureus_subsp__aureus_NCTC_8325_GCF_000013425_1-contigs.db \ --num-genes 5,5 \ --search-term Bacterial_16S_rRNA \ --use-hmm \ --hmm-sources Ribosomal_RNAs \ -O s_epidermidis_rrn_locus ``` Genes to report ..............................: 5 genes...

@meren I recently made a [PR](https://github.com/merenlab/anvio/pull/1678 ) to add filter functionality for `anvi-run-hmms` by utilizing target and query coverages but I have worked on any part of the code base...

Thanks for running it on your end! I unfortunately am still getting the same error as above. Maybe it's my R version? 

Thanks for the suggestion @meren! `anvi-script-filter-hmm-hits-table` now will record the self attributes `HMM_dom_filter_sources`, `HMM_dom_filter_target_coverage `, and `HMM_dom_filter_query_coverage ` as CSVs in a contigsDB! What are the next steps for making...

@meren and I spoke about his comment above offline and here are the actions items to address it: - `anvi-run-hmms`: - [x] If a user is using `domtblout`, there needs...

@meren I attempted to make the sanity check that compares the genes in the incoming domain-hits-table and the HMM_hits table in the contigsDB being filtered. Please let me know what...

If I remove `--snv-data USA0006_SNVs.txt` the script works: ```bash anvi-script-visualize-split-coverages -i split_cov_USA0006.txt -o USA0006_INSPECT.pdf --sample-data sample_data_colors.txt --free-y-scale TRUE --max-coverage 80000 --snv-marker-transparency 0.9 --snv-marker-width 0.1 ```  @efogarty11 does this plot...

Hey @mooreryan, the anvio env now install R version 4 something by default since we use `conda install -y -c bioconda r-base`. > Regarding a double having dimnames, are you...