| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2020-04-19 | added 'np/op' control for specimen_source | Andrea Guarracino | |
| 2020-04-19 | Further updates to our NCBI dictonaries to translate this s*** to our model | lltommy | |
| 2020-04-19 | fixed missing variable and managed comma in dicts | Andrea Guarracino | |
| 2020-04-19 | Updating NCBI dictonaries, adding UI options, small yaml schema changes | lltommy | |
| 2020-04-19 | Merge 984f74f7d7219c83d280b6eee46cba4aed4298bb | Pjotr Prins | |
| 2020-04-19 | Merge branch 'master' into patch-6 | Pjotr Prins | |
| 2020-04-19 | Merge pull request #27 from AndreaGuarracino/patch-7 | Pjotr Prins | |
| updated term-mapping dictionaries | |||
| 2020-04-19 | Merge pull request #23 from AndreaGuarracino/patch-3 | Pjotr Prins | |
| accessions list CoV-2 from NCBI Virus 2020/04/15 | |||
| 2020-04-18 | dictionaries for mapping | Andrea Guarracino | |
| 2020-04-18 | ncbi_speciesman_source mapping | Andrea Guarracino | |
| 2020-04-18 | Delete dict_ontology_standardization | Andrea Guarracino | |
| 2020-04-18 | ncbi_speciesman_source mapping | Andrea Guarracino | |
| 2020-04-18 | new script release | Andrea Guarracino | |
| - 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. | |||
| 2020-04-15 | added type id check | Andrea Guarracino | |
| what is not genomic DNA is removed | |||
| 2020-04-15 | accessions list CoV-2 from NCBI Virus 2020/04/15 | Andrea Guarracino | |
| 2020-04-14 | accessions list CoV-2 from NCBI Virus 2020/04/14 | Andrea Guarracino | |
| 2020-04-14 | Rename script/from_genbank_to_fasta_and_yaml.py to ↵ | Andrea Guarracino | |
| scripts/from_genbank_to_fasta_and_yaml.py | |||
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index : bh20-seq-resource | |
| Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis |
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