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
README.md @master — view markup · raw · history · blame
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.