Add functional tests

- comma-delimited metadata
nextstrain · Apr 25, 2022 · 4404c25 · 4404c25
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diff --git a/tests/functional/filter.t b/tests/functional/filter.t
@@ -422,3 +422,14 @@ Filter out a sequence with invalid nucleotides.
   >  --output-metadata "$TMP/filtered_metadata.tsv" > /dev/null
   $ wc -l "$TMP/filtered_metadata.tsv"
   \s*11 .* (re)
+
+Try a comma-delimited file.
+
+  $ ${AUGUR} filter \
+  >  --metadata filter/metadata.csv \
+  >  --exclude-where "region=South America" "region=North America" "region=Southeast Asia" \
+  >  --include-where "country=Ecuador" \
+  >  --output-strains "$TMP/filtered_strains.txt" > /dev/null
+  $ wc -l "$TMP/filtered_strains.txt"
+  \s*2 .* (re)
+  $ rm -f "$TMP/filtered_strains.txt"
diff --git a/tests/functional/filter/metadata.csv b/tests/functional/filter/metadata.csv
@@ -0,0 +1,13 @@
+strain,virus,accession,date,region,country,division,city,db,segment,authors,url,title,journal,paper_url
+COL/FLR_00024/2015,zika,MF574569,,South America,Colombia,Colombia,Colombia,genbank,genome,Pickett et al,https://www.ncbi.nlm.nih.gov/nuccore/MF574569,Direct Submission,"Submitted (28-JUL-2017) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA",https://www.ncbi.nlm.nih.gov/pubmed/
+PRVABC59,zika,KU501215,2015-12-XX,North America,Puerto Rico,Puerto Rico,Puerto Rico,genbank,genome,Lanciotti et al,https://www.ncbi.nlm.nih.gov/nuccore/KU501215,"Phylogeny of Zika Virus in Western Hemisphere, 2015","Emerging Infect. Dis. 22 (5), 933-935 (2016)",https://www.ncbi.nlm.nih.gov/pubmed/27088323
+COL/FLR_00008/2015,zika,MF574562,2015-12,South America,Colombia,Colombia,Colombia,genbank,genome,Pickett et al,https://www.ncbi.nlm.nih.gov/nuccore/MF574562,Direct Submission,"Submitted (28-JUL-2017) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA",https://www.ncbi.nlm.nih.gov/pubmed/
+Colombia/2016/ZC204Se,zika,KY317939,2016-01-06,South America,Colombia,Colombia,Colombia,genbank,genome,Quick et al,https://www.ncbi.nlm.nih.gov/nuccore/KY317939,Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples,"Nat Protoc 12 (6), 1261-1276 (2017)",https://www.ncbi.nlm.nih.gov/pubmed/28538739
+ZKC2/2016,zika,KX253996,2016-02-16,Oceania,American Samoa,American Samoa,American Samoa,genbank,genome,Wu et al,https://www.ncbi.nlm.nih.gov/nuccore/KX253996,Direct Submission,"Submitted (18-MAY-2016) Center for Diseases Control and Prevention of Guangdong Province; National Institute of Viral Disease Control and Prevention, China",https://www.ncbi.nlm.nih.gov/pubmed/
+VEN/UF_1/2016,zika,KX702400,2016-03-25,South America,Venezuela,Venezuela,Venezuela,genbank,genome,Blohm et al,https://www.ncbi.nlm.nih.gov/nuccore/KX702400,Complete Genome Sequences of Identical Zika virus Isolates in a Nursing Mother and Her Infant,"Genome Announc 5 (17), e00231-17 (2017)",https://www.ncbi.nlm.nih.gov/pubmed/28450510
+DOM/2016/BB_0059,zika,KY785425,2016-04-04,North America,Dominican Republic,Dominican Republic,Dominican Republic,genbank,genome,Metsky et al,https://www.ncbi.nlm.nih.gov/nuccore/KY785425,Zika virus evolution and spread in the Americas,"Nature 546 (7658), 411-415 (2017)",https://www.ncbi.nlm.nih.gov/pubmed/28538734
+BRA/2016/FC_6706,zika,KY785433,2016-04-08,South America,Brazil,Brazil,Brazil,genbank,genome,Metsky et al,https://www.ncbi.nlm.nih.gov/nuccore/KY785433,Zika virus evolution and spread in the Americas,"Nature 546 (7658), 411-415 (2017)",https://www.ncbi.nlm.nih.gov/pubmed/28538734
+DOM/2016/BB_0183,zika,KY785420,2016-04-18,North America,Dominican Republic,Dominican Republic,Dominican Republic,genbank,genome,Metsky et al,https://www.ncbi.nlm.nih.gov/nuccore/KY785420,Zika virus evolution and spread in the Americas,"Nature 546 (7658), 411-415 (2017)",https://www.ncbi.nlm.nih.gov/pubmed/28538734
+EcEs062_16,zika,KX879603,2016-04-XX,South America,Ecuador,Ecuador,Ecuador,genbank,genome,Marquez et al,https://www.ncbi.nlm.nih.gov/nuccore/KX879603,First Complete Genome Sequences of Zika Virus Isolated from Febrile Patient Sera in Ecuador,"Genome Announc 5 (8), e01673-16 (2017)",https://www.ncbi.nlm.nih.gov/pubmed/28232448
+HND/2016/HU_ME59,zika,KY785418,2016-05-13,North America,Honduras,Honduras,Honduras,genbank,genome,Metsky et al,https://www.ncbi.nlm.nih.gov/nuccore/KY785418,Zika virus evolution and spread in the Americas,"Nature 546 (7658), 411-415 (2017)",https://www.ncbi.nlm.nih.gov/pubmed/28538734
+SG_018,zika,KY241688,2016,Southeast Asia,Singapore,Singapore,Singapore,genbank,genome,Ho et al,https://www.ncbi.nlm.nih.gov/nuccore/KY241688,"Outbreak of Zika virus infection in Singapore: an epidemiological, entomological, virological, and clinical analysis",Lancet Infect Dis (2017) In press,https://www.ncbi.nlm.nih.gov/pubmed/