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Add test for annotating metadata with index with numeric strain names
Adds a functional test to cover a use case described in #948.
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Test script to annotate metadata with sequence index. | ||
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$ pushd "$TESTDIR" > /dev/null | ||
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Annotate metadata with an index where strains have numeric names. | ||
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$ python3 ../scripts/annotate_metadata_with_index.py \ | ||
> --metadata numeric_strains/metadata.tsv \ | ||
> --sequence-index numeric_strains/sequence_index.tsv \ | ||
> --output "$TMP/metadata_with_index.tsv" | ||
$ wc -l "$TMP/metadata_with_index.tsv" | ||
\s*3 .* (re) | ||
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$ rm -f "$TMP/metadata_with_index.tsv" | ||
$ popd > /dev/null |
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strain 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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strain length A C G T N other_IUPAC - ? invalid_nucleotides | ||
1 29812 8825 5433 5812 9498 242 2 0 0 0 | ||
2 29806 8876 5461 5849 9558 62 0 0 0 0 |