test on zika

nextstrain · Oct 3, 2019 · 23c1ce3 · 23c1ce3
1 parent 1025bac
commit 23c1ce3
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/augur/parse.py b/augur/parse.py
@@ -102,7 +102,7 @@ def run(args):
         tmp_meta = {k:v for k,v in zip(args.fields, fields)}
 
         for field in args.prettify_fields:
-            tmp_meta[field] = prettify_fields(tmp_meta[field], camelCase=field!='author',
+            tmp_meta[field] = prettify(tmp_meta[field], camelCase=field!='author',
                                               etal='lower' if field=='author' else None)
 
         meta_data[seq.id] = tmp_meta

diff --git a/tests/builds/zika/Snakefile b/tests/builds/zika/Snakefile
@@ -25,14 +25,16 @@ rule parse:
         sequences = "results/sequences.fasta",
         metadata = "results/metadata.tsv"
     params:
-        fasta_fields = "strain virus accession date region country division city db segment authors url title journal paper_url"
+        fasta_fields = "strain virus accession date region country division city db segment authors url title journal paper_url",
+        prettify_fields = "region country division city"
     shell:
         """
         augur parse \
             --sequences {input.sequences} \
             --output-sequences {output.sequences} \
             --output-metadata {output.metadata} \
-            --fields {params.fasta_fields}
+            --fields {params.fasta_fields} \
+            --prettify-fields {params.prettify_fields}
         """
 
 rule filter: