support for vConTACT v0.11.3

lazzarigioele · Oct 23, 2023 · 8824dbd · 8824dbd
1 parent 86ac1b7
commit 8824dbd
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Showing 17 changed files with 486 additions and 362 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,30 @@
+**/.DS_Store
+**/.ipynb_checkpoints
+**/__pycache__
+vc2test/.ipynb_checkpoints/1Oct2023_vConTACT2_gene_to_genome-checkpoint.csv
+vc2test/combined_g.faa
+vc2test/1Oct2023_vConTACT2_proteins.faa
+vc2test/outdir/modules.ntwk
+vc2test/outdir/vConTACT_proteins.csv
+vc2test/outdir/combined_g.dmnd
+vc2test/outdir/combined_g.self-diamond.tab
+vc2test/outdir/combined_g.self-diamond.tab.abc
+vc2test/outdir/c1.ntw
+vc2test/outdir/combined_g.self-diamond.tab.mci
+vc2test/combined_g2g.csv
+vc2test/1Oct2023_vConTACT2_gene_to_genome.csv
+testinput_tmp/testinput-big/.ipynb_checkpoints/c1-checkpoint.ntw
+testinput_tmp/testinput-big/c1.ntw
+testinput_tmp/testinput-small/c1.ntw
+testinput_tmp/testinput-new/c1.ntw
+#assets
+busco/busco
 testoutput*/
 testinput/*
 !testinput/*.tar.gz
 **/.DS_Store
-locals/
+locals/
+
+vc2test/*
+testinput_tmp/*
+tmp.ipynb
diff --git a/.gitignore_dim b/.gitignore_dim
@@ -0,0 +1,16 @@
+52M	./vc2test/.ipynb_checkpoints/1Oct2023_vConTACT2_gene_to_genome-checkpoint.csv
+444M	./vc2test/combined_g.faa
+444M	./vc2test/1Oct2023_vConTACT2_proteins.faa
+554M	./vc2test/outdir/modules.ntwk
+69M	./vc2test/outdir/vConTACT_proteins.csv
+467M	./vc2test/outdir/combined_g.dmnd
+2.5G	./vc2test/outdir/combined_g.self-diamond.tab
+1.4G	./vc2test/outdir/combined_g.self-diamond.tab.abc
+65M	./vc2test/outdir/c1.ntw
+873M	./vc2test/outdir/combined_g.self-diamond.tab.mci
+52M	./vc2test/combined_g2g.csv
+52M	./vc2test/1Oct2023_vConTACT2_gene_to_genome.csv
+64M	./testinput_tmp/testinput-big/.ipynb_checkpoints/c1-checkpoint.ntw
+64M	./testinput_tmp/testinput-big/c1.ntw
+47M	./testinput_tmp/testinput-small/c1.ntw
+65M	./testinput_tmp/testinput-new/c1.ntw
diff --git a/README.md b/README.md
diff --git a/assets/screenshot-v1.5.1.png b/assets/screenshot-v1.5.1.png
diff --git a/assets/vOTU_26_hovered_v1.5.1.png b/assets/vOTU_26_hovered_v1.5.1.png
diff --git a/assets/vOTU_26_v1.5.1.png b/assets/vOTU_26_v1.5.1.png
diff --git a/assets/vOTU_56_hovered_v1.5.1.png b/assets/vOTU_56_hovered_v1.5.1.png
diff --git a/assets/vOTU_56_v1.5.1.png b/assets/vOTU_56_v1.5.1.png
diff --git a/env/env_linux.yml b/env/env_linux.yml
diff --git a/env/env_macosx.yml b/env/env_macosx.yml