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propagate purpose of sequencing to genbank and gisaid #201

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Jan 26, 2021
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@dpark01 dpark01 commented Jan 26, 2021

This PR includes two changes:

  1. This propagates the NCBI BioSample's purpose_of_sequencing field (or, failing that, the purpose_of_sampling field) into the Genbank note field and the GISAID additional_host_info field, if either are available. If it is set to a PHA4GE-ontology-defined value for Variants of Concern screening, rewrite it to match a SPHERES-ontology-defined value for the same. The relevant python code is in the viral-phylo repo.
  2. Adds the align_to_ref_merged_reads_aligned and align_to_ref_merged_bases_aligned columns to the assembly_stats_tsv output from sarscov2_illumina_full and sarscov2_sra_to_genbank

@dpark01 dpark01 merged commit f16f57d into master Jan 26, 2021
@dpark01 dpark01 deleted the dp-sc2-full branch January 26, 2021 22:22
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