PubUpdate_08-08-24

AaronFeller · Aug 8, 2024 · 5142ba7 · 5142ba7
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diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,5 @@
 # Ignore tmp folder
 analysis/IBDMDB/tmp/
 blast_evalue.ipynb
+analysis/IBDMDB/data/Old
+analysis/Comparison/data/
diff --git a/README.md b/README.md
@@ -13,7 +13,8 @@ conda activate <environment_name>
 
 ### Installing dependencies:
 ```bash
-conda install biopython=1.79 blast=2.14 hmmer=3.3 mafft=7.508 numpy=1.24 pandas=1.5 snakemake=7.18 -c conda-forge -c bioconda
+conda install mamba -c conda-forge
+mamba install biopython=1.79 blast=2.14 hmmer=3.3 mafft=7.508 numpy=1.24 pandas=1.5 snakemake=7.18 -c conda-forge -c bioconda
 ```
 
 ### Downloading repository:

diff --git a/...mparison/Comparing_Cinful&MicSearch.ipynb → ...mparison/Comparing_Cinful&MicSearch.ipynb b/...mparison/Comparing_Cinful&MicSearch.ipynb → ...mparison/Comparing_Cinful&MicSearch.ipynb
diff --git a/.../Enterobacteriaceae_CinPro_Analysis.ipynb → .../Enterobacteriaceae_CinPro_Analysis.ipynb b/.../Enterobacteriaceae_CinPro_Analysis.ipynb → .../Enterobacteriaceae_CinPro_Analysis.ipynb
diff --git a/...eriaceae_Cinful_oldVersion_Analysis.ipynb → ...eriaceae_Cinful_oldVersion_Analysis.ipynb b/...eriaceae_Cinful_oldVersion_Analysis.ipynb → ...eriaceae_Cinful_oldVersion_Analysis.ipynb
diff --git a/...DMDB/Comparison/cinful_micsearch_locs.csv → ...ysis/Comparison/cinful_micsearch_locs.csv b/...DMDB/Comparison/cinful_micsearch_locs.csv → ...ysis/Comparison/cinful_micsearch_locs.csv
diff --git a/...DB/Comparison/plots/cinful_old_search.svg → ...is/Comparison/plots/cinful_old_search.svg b/...DB/Comparison/plots/cinful_old_search.svg → ...is/Comparison/plots/cinful_old_search.svg
diff --git a/...Comparison/plots/cluster_size_barplot.svg → ...Comparison/plots/cluster_size_barplot.svg b/...Comparison/plots/cluster_size_barplot.svg → ...Comparison/plots/cluster_size_barplot.svg
diff --git a/...son/plots/comparison_micsearch_cinful.svg → ...son/plots/comparison_micsearch_cinful.svg b/...son/plots/comparison_micsearch_cinful.svg → ...son/plots/comparison_micsearch_cinful.svg
diff --git a/...rison/plots/fullmicrocinHMM_newsearch.svg → ...rison/plots/fullmicrocinHMM_newsearch.svg b/...rison/plots/fullmicrocinHMM_newsearch.svg → ...rison/plots/fullmicrocinHMM_newsearch.svg
diff --git a/...IBDMDB/Comparison/plots/merged_figure.svg → analysis/Comparison/plots/merged_figure.svg b/...IBDMDB/Comparison/plots/merged_figure.svg → analysis/Comparison/plots/merged_figure.svg
diff --git a/.../IBDMDB/Comparison/plots/venn_diagram.svg → analysis/Comparison/plots/venn_diagram.svg b/.../IBDMDB/Comparison/plots/venn_diagram.svg → analysis/Comparison/plots/venn_diagram.svg
diff --git a/...s/IBDMDB/Comparison/tmp/cf_ms_cluster.tsv → analysis/Comparison/tmp/cf_ms_cluster.tsv b/...s/IBDMDB/Comparison/tmp/cf_ms_cluster.tsv → analysis/Comparison/tmp/cf_ms_cluster.tsv
diff --git a/analysis/IBDMDB/Comparison/data/20230622_cinful10_best_hits.csv b/analysis/IBDMDB/Comparison/data/20230622_cinful10_best_hits.csv
diff --git a/analysis/IBDMDB/Comparison/data/20230622_cinful10_best_hits_35minute_timesave.csv b/analysis/IBDMDB/Comparison/data/20230622_cinful10_best_hits_35minute_timesave.csv
diff --git a/analysis/IBDMDB/Comparison/data/Enterobacteriaciae_accessions.csv b/analysis/IBDMDB/Comparison/data/Enterobacteriaciae_accessions.csv
diff --git a/analysis/IBDMDB/Comparison/data/Enterobacteriaciae_species.tree b/analysis/IBDMDB/Comparison/data/Enterobacteriaciae_species.tree
diff --git a/analysis/IBDMDB/Comparison/data/Enterobacteriaciae_species_merged_1000.csv b/analysis/IBDMDB/Comparison/data/Enterobacteriaciae_species_merged_1000.csv