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.