From 23c1ce3432790b18f0bbf7d742030f5cf0b89481 Mon Sep 17 00:00:00 2001 From: Richard Neher Date: Thu, 3 Oct 2019 18:45:06 +0200 Subject: [PATCH] test on zika --- augur/parse.py | 2 +- tests/builds/zika/Snakefile | 6 ++++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/augur/parse.py b/augur/parse.py index 77d08fbd5..5fad9a391 100644 --- 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 index 029239481..2c161d8dd 100644 --- 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: