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Revert "Use csvtk to create test data"
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This reverts commit 021b64e.
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huddlej committed Aug 4, 2022
1 parent 021b64e commit 17c75ff
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Showing 2 changed files with 4 additions and 2 deletions.
3 changes: 1 addition & 2 deletions tests/annotate_metadata_with_index.t
Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,8 @@ Annotate metadata with an index where strains have numeric names.
Annotate metadata with an index where metadata uses the "name" column for strain names.
This should produce the same result as above, except with a "name" column in the output.

$ csvtk --tabs rename -f strain -n name numeric_strains/metadata.tsv > "$TMP/metadata.tsv"
$ python3 ../scripts/annotate_metadata_with_index.py \
> --metadata "$TMP/metadata.tsv" \
> --metadata numeric_strains/metadata_by_name.tsv \
> --sequence-index numeric_strains/sequence_index.tsv \
> --output "$TMP/metadata_with_index.tsv"
$ wc -l "$TMP/metadata_with_index.tsv"
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3 changes: 3 additions & 0 deletions tests/numeric_strains/metadata_by_name.tsv
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@@ -0,0 +1,3 @@
name virus gisaid_epi_isl genbank_accession date region country division location region_exposure country_exposure division_exposure segment length host age sex originating_lab submitting_lab authors url title date_submitted
1 ncov ? MT450922 2020-03-05 Oceania Australia Victoria Oceania Australia Victoria genome 29812 Homo sapiens ? ? ? ? Seemann et al https://www.ncbi.nlm.nih.gov/nuccore/MT450922 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/AUS/VIC05/2020 ORF1ab polyprotein (ORF1ab), ORF1a polyprotein (ORF1ab), surface glycoprotein (S), ORF3a protein (ORF3a), envelope protein (E), membrane glycoprotein (M), ORF6 protein (ORF6), ORF7a protein (ORF7a), ORF7b (ORF7b), ORF8 protein (ORF8), nucleocapsid phosphoprotein (N), and ORF10 protein (ORF10) genes, complete cds 2020-05-11
2 ncov ? MT451684 2020-03-31 Oceania Australia Victoria Oceania Australia Victoria genome 29806 Homo sapiens ? ? ? ? Seemann et al https://www.ncbi.nlm.nih.gov/nuccore/MT451684 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/AUS/VIC1000/2020, complete genome 2020-05-11

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