Tree @master (Download .tar.gz)
- ..
- create_sra_metadata
- db_enrichment
- dict_ontology_standardization
- docker
- esr_samples
- submit_ebi
- update_virtuoso
- uthsc_samples
- cleanup.py
- delete_entries_on_arvados.py
- fetch_from_genbank.cwl
- foreach.sh
- import.cwl
- import_from_genbank.cwl
- import_to_arvados.py
- README.md
- split_into_arrays.cwl
- upload.cwl
- utils.py
Instructions for download and/or prepare the data and/or the metadata
Just go into the download_genbank_data or download_sra_data directory and execute the python3 script inside.
download_genbank_data/from_genbank_to_fasta_and_yaml.pydownloads the data and the matadata, preparing the FASTA and the YAML files;download_sra_data/download_sra_data.pycreates the metadata in the form of YAML files from the SraExperimentPackage.XXX.xml.gz file in the same directory.
History of
scripts
@master
git clone https://klaus.systemreboot.net/bh20-seq-resource/
- code cleaning, checking and writing missing term on file Andrea Guarracino (commit: GitHub) 6 years ago
- created dict for host health status Andrea Guarracino (commit: GitHub) 6 years ago
- added some rows in the speciesman dict Andrea Guarracino (commit: GitHub) 6 years ago
- added some rows in the ncbi_countries dict Andrea Guarracino (commit: GitHub) 6 years ago
- updated IDs list - 2020/04/22 Andrea Guarracino (commit: GitHub) 6 years ago
- Small changes all around, trying to make the importer/metadata better lltommy 6 years ago
- Tweak handling of "coverage" also fix typo Peter Amstutz 6 years ago
- Working on NCBI import Peter Amstutz 6 years ago
- Updated shex and manditory fields and stuff lltommy 6 years ago
- Merge pull request #29 from inutano/fix-mappings LLTommy (commit: GitHub) 6 years ago
- Merge pull request #28 from AndreaGuarracino/patch-8 LLTommy (commit: GitHub) 6 years ago
- fix MinION to ONT Tazro Inutano Ohta 6 years ago
- Fixing string -> URI in speciman, plus other things lltommy 6 years ago
- added 'np/op' control for specimen_source Andrea Guarracino (commit: GitHub) 6 years ago
- Further updates to our NCBI dictonaries to translate this s*** to our model lltommy 6 years ago
- fixed missing variable and managed comma in dicts Andrea Guarracino (commit: GitHub) 6 years ago
- Updating NCBI dictonaries, adding UI options, small yaml schema changes lltommy 6 years ago
- Merge 984f74f7d7219c83d280b6eee46cba4aed4298bb Pjotr Prins 6 years ago
- Merge branch 'master' into patch-6 Pjotr Prins (commit: GitHub) 6 years ago
- Merge pull request #27 from AndreaGuarracino/patch-7 Pjotr Prins (commit: GitHub) 6 years ago
- Merge pull request #23 from AndreaGuarracino/patch-3 Pjotr Prins (commit: GitHub) 6 years ago
- dictionaries for mapping Andrea Guarracino (commit: GitHub) 6 years ago
- ncbi_speciesman_source mapping Andrea Guarracino (commit: GitHub) 6 years ago
- Delete dict_ontology_standardization Andrea Guarracino (commit: GitHub) 6 years ago
- ncbi_speciesman_source mapping Andrea Guarracino (commit: GitHub) 6 years ago
- new script release Andrea Guarracino (commit: GitHub) 6 years ago
- added type id check Andrea Guarracino (commit: GitHub) 6 years ago
- accessions list CoV-2 from NCBI Virus 2020/04/15 Andrea Guarracino (commit: GitHub) 6 years ago
- accessions list CoV-2 from NCBI Virus 2020/04/14 Andrea Guarracino (commit: GitHub) 6 years ago
- Rename script/from_genbank_to_fasta_and_yaml.py to scripts/from_genbank_to_fasta_and_yaml.py Andrea Guarracino (commit: GitHub) 6 years ago