writedb_entry_set

Repo to hold the writedb_entry_set Python code, extracted from the Sanger general GitLab repo. The main script, writedb_entries.py, provides a wrapper for the Artemis writedb_entry script and is used to extract Chado database feature data to GFF or EMBL file formats.

Installation

Required dependencies

• Python3 version >= 3.6.0

Install from source

Download the latest release from this github repository or clone it.

python3 setup.py install

Usage

Chado database connection details can be provided to the program by adding them to a configuration file (see config.ini.default) and then passing the file path using the -d command line argument.

Usage: writedb_entries.py [options]

Options:
  -h, --help            show this help message and exit
  -o ORGANISM, --organism=ORGANISM
                        the organism common_name (can specify many of these)
  -n ANNOTATED_ONLY, --annotated_only=ANNOTATED_ONLY
                        for the organisms specified with this option, only
                        retrieve top-level features that are deemed to have
                        annotations
  -e, --embl            export in EMBL format (defaults to GFF)
  -p PREFIX, --prefix=PREFIX
                        a prefix to prepend to the export folder name
  -b BUNDLE, --bundle=BUNDLE
                        if you wish to autogenerate a bundle, provide path
                        here
  -w WRITEDB_ENTRY, --writedb_entry=WRITEDB_ENTRY
                        the path to the ARtemis writedb_entry script
  -m MAX_FEATURE_INCREMENT, --max_feature_increment=MAX_FEATURE_INCREMENT
                        the max number features to be batched by artemis in
                        one go
  -f MAX_FILES_PER_FOLDER, --max_files_per_folder=MAX_FILES_PER_FOLDER
                        the max number of files per folder
  --single_file         write sorted, postprocessed single GFF file per
                        organism (requires GenomeTools `gt' executable in
                        PATH)
  -v, --verbose         output additional information while running
  -d DATABASE_CONNECTION, --database_connection=DATABASE_CONNECTION
                        either a database uri or a path to a conf_file
  -x EXPORT_FOLDER, --export_folder=EXPORT_FOLDER
                        the path to the destination_folder
  -a, --suffix_date_in_path
                        suffixes the base path with the starting date and time
  -t, --test            add the -test option
  -l, --flattened       if embl, flatten
  -s START_AT_FEATURE_UNIQUENAME, --start_at_feature_uniquename=START_AT_FEATURE_UNIQUENAME
                        start at the feature_id (for resuming stalled exports)
  -z, --emblsubmission  if embl, use submission format
  -i, --ignoreobsolete  do not export obsolete features

License

writedb_entry_set is free software, licensed under GPLv3.