fungidb_tools
Scripts for maintenance, data loading, and validation for FungiDB.
Prerequisites
- python3 compiled with _curses, _ssh
- biopython, lxml, gdata, decorator
Installation
python3 setup.py install
or
python3 setup.py develop
Modules
- Datasets
- datasets: Turn the Genomes spreadsheet into XML workflow config files.
- isf: Reformat and extract data from genome files.
- naming: Naming organisms with more consistent specifications than is enforced by EuPathDB.
- NCBI
- aspera: For downloading SRA datasets from NCBI.
- simple_eutils: Wrapper around NCBI eutils to combine/simplify functions.
- Other
- elementlib: Tools for working with XML files.
- json_gspread: Convert old-style Google Spreadsheet into JSON structure.
Scripts
- ISF (Insert Sequence Features)
- Reformatters, data extraction for gtf, gff3, fasta, and genbank filetypes.
- Datasets
- Interact with data pulled from the FungiDB Genomes spreadsheet.
Makefiles
- ISF
- Process genomic files for loading.
- Workflow
- Shortcuts to interact with the workflow and EuPath toolchain.