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| author | Andrea Guarracino | 2020-04-18 22:15:01 +0200 |
|---|---|---|
| committer | GitHub | 2020-04-18 22:15:01 +0200 |
| commit | 3bee6777fb4a61febbf1c22e62d71d933cfba4b0 (patch) | |
| tree | edd1ae1b9c1080c2e9e28ec49df5fb8d38fe2144 /scripts/foreach.sh | |
| parent | bbca5ac9b2538e410efe3e09651f87e5573145de (diff) | |
| download | bh20-seq-resource-3bee6777fb4a61febbf1c22e62d71d933cfba4b0.tar.gz bh20-seq-resource-3bee6777fb4a61febbf1c22e62d71d933cfba4b0.tar.lz bh20-seq-resource-3bee6777fb4a61febbf1c22e62d71d933cfba4b0.zip | |
new script release
- now the script is more gentle with the server, requesting metadata in batches, reducing the ovrall execution time;
- in the YAML files are created field for sample_sequencing_technology, sample_sequencing_technology2, sample_sequencing_technology3, specimen_source, and specimen_source2;
- in sequencing_coverage stuff like 'x', 'X', etc... is stripped, and the ',' replaced by '.';
- the script exploits the dictionaries in the /scripts/dict_ontology_standardization. Now I have used ncbi_specesman_source.csv, ncbi_sequencing_technology.csv, and ncbi_countries.csv.
- in ncbi_sequencing_technology.csv I've added 'Oxford Nanopore' and 'MinION Oxford Nanopore'
- for specimen_source, when there is one of 'NP/OP swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', or 'np/np swab', I put both of them.
Diffstat (limited to 'scripts/foreach.sh')
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