Chado Loaders

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Kim Rutherford edited this page Dec 13, 2018 · 4 revisions

PomBase Chado loader types

The wrapper script for the loaders is pombase-import.pl which has six main arguments:

config file in YAML format
loader type (run pombase-import.pl with no arguments for a list)
- there are loader specific flags which must come after the loader type in the command line
- see below for examples
host name
database name
database user
database password

Generic

Loader for TSV file containing annotation that is simple enough that it doesn't need its own loader.

The input file has these columns:

systematic_id
feature_name (optional)
term_id
evidence_code (optional)
publication_id (optional)
date (optional)

Where "optional" means the column can have blank entries.

Example command line:

cd pombase-chado
./script/pombase-import.pl load-pombase-chado.yaml generic-annotation \
   --organism-taxonid=4896 localhost test-database user pw < generic.tsv