correct y-axis to be per codon rather than per nt

blab · Aug 2, 2022 · 61f5e2f · 61f5e2f
1 parent 72c376a
commit 61f5e2f
Show file tree

Hide file tree

Showing 4,114 changed files with 542,599 additions and 336,813 deletions.
diff --git a/.gitignore b/.gitignore
diff --git a/229e/README.md b/229e/README.md
diff --git a/229e/Snakefile b/229e/Snakefile
@@ -21,27 +21,28 @@ rule files:
 
 files = rules.files.params
 
-rule download:
-    message: "Downloading sequences from fauna"
-    output:
-        sequences = "data/229e_{gene}.fasta"
-    params:
-        fasta_fields = "strain accession strain_name collection_date host country virus subtype type sequence_locus"
-    shell:
-        """
-        python3 ../fauna/vdb/download.py \
-            --database vdb \
-            --virus seasonal_corona \
-            --fasta_fields {params.fasta_fields} \
-            --select sequence_locus:{wildcards.gene} subtype: 229e \
-            --path $(dirname {output.sequences}) \
-            --fstem $(basename {output.sequences} .fasta)
-        """
+# rule download:
+#     message: "Downloading sequences from fauna"
+#     output:
+#         sequences = "data/229e_{gene}.fasta"
+#     params:
+#         fasta_fields = "strain accession strain_name collection_date host country virus subtype type sequence_locus"
+#     shell:
+#         """
+#         python3 ../fauna/vdb/download.py \
+#             --database vdb \
+#             --virus seasonal_corona \
+#             --fasta_fields {params.fasta_fields} \
+#             --select sequence_locus:{wildcards.gene} subtype: 229e \
+#             --path $(dirname {output.sequences}) \
+#             --fstem $(basename {output.sequences} .fasta)
+#         """
 
 rule parse:
     message: "Parsing fasta into sequences and metadata"
     input:
-        sequences = rules.download.output.sequences
+        sequences = 'data/229e_{gene}.fasta'
+        # sequences = rules.download.output.sequences
     output:
         sequences = "results/sequences_229e_{gene}.fasta",
         metadata = "results/metadata_229e_{gene}.tsv"
@@ -169,7 +170,7 @@ rule ancestral:
         augur ancestral \
             --tree {input.tree} \
             --alignment {input.alignment} \
-            --output {output.node_data} \
+            --output-node-data {output.node_data} \
             --inference {params.inference}
         """
 

diff --git a/229e/auspice/.DS_Store b/229e/auspice/.DS_Store
diff --git a/229e/auspice/seasonal_corona_229e_envelope.json b/229e/auspice/seasonal_corona_229e_envelope.json
diff --git a/229e/auspice/seasonal_corona_229e_envelope_root-sequence.json b/229e/auspice/seasonal_corona_229e_envelope_root-sequence.json
diff --git a/229e/auspice/seasonal_corona_229e_full.json b/229e/auspice/seasonal_corona_229e_full.json
diff --git a/229e/auspice/seasonal_corona_229e_full_root-sequence.json b/229e/auspice/seasonal_corona_229e_full_root-sequence.json
diff --git a/229e/auspice/seasonal_corona_229e_membrane.json b/229e/auspice/seasonal_corona_229e_membrane.json
diff --git a/229e/auspice/seasonal_corona_229e_membrane_root-sequence.json b/229e/auspice/seasonal_corona_229e_membrane_root-sequence.json
diff --git a/229e/auspice/seasonal_corona_229e_nucleocapsid.json b/229e/auspice/seasonal_corona_229e_nucleocapsid.json
diff --git a/229e/auspice/seasonal_corona_229e_nucleocapsid_root-sequence.json b/229e/auspice/seasonal_corona_229e_nucleocapsid_root-sequence.json
diff --git a/229e/auspice/seasonal_corona_229e_protein4a.json b/229e/auspice/seasonal_corona_229e_protein4a.json
diff --git a/229e/auspice/seasonal_corona_229e_protein4a_root-sequence.json b/229e/auspice/seasonal_corona_229e_protein4a_root-sequence.json
diff --git a/229e/auspice/seasonal_corona_229e_protein4b.json b/229e/auspice/seasonal_corona_229e_protein4b.json
diff --git a/229e/auspice/seasonal_corona_229e_protein4b_root-sequence.json b/229e/auspice/seasonal_corona_229e_protein4b_root-sequence.json
diff --git a/229e/auspice/seasonal_corona_229e_rdrp.json b/229e/auspice/seasonal_corona_229e_rdrp.json
diff --git a/229e/auspice/seasonal_corona_229e_rdrp_root-sequence.json b/229e/auspice/seasonal_corona_229e_rdrp_root-sequence.json
diff --git a/229e/auspice/seasonal_corona_229e_replicase1a.json b/229e/auspice/seasonal_corona_229e_replicase1a.json
diff --git a/229e/auspice/seasonal_corona_229e_replicase1a_root-sequence.json b/229e/auspice/seasonal_corona_229e_replicase1a_root-sequence.json
diff --git a/229e/auspice/seasonal_corona_229e_replicase1ab.json b/229e/auspice/seasonal_corona_229e_replicase1ab.json
diff --git a/229e/auspice/seasonal_corona_229e_replicase1ab_root-sequence.json b/229e/auspice/seasonal_corona_229e_replicase1ab_root-sequence.json
diff --git a/229e/auspice/seasonal_corona_229e_s1.json b/229e/auspice/seasonal_corona_229e_s1.json
diff --git a/229e/auspice/seasonal_corona_229e_s1_root-sequence.json b/229e/auspice/seasonal_corona_229e_s1_root-sequence.json
diff --git a/229e/auspice/seasonal_corona_229e_s2.json b/229e/auspice/seasonal_corona_229e_s2.json
diff --git a/229e/auspice/seasonal_corona_229e_s2_root-sequence.json b/229e/auspice/seasonal_corona_229e_s2_root-sequence.json