Media export

The internal media database can be exported into files for inspection, reuse or for generating documentation tables.

Export all media

To export all media definitions as TSV files:

refinegems media export --media-names-or-config all --type tsv --dir media_export

The options can also be shortened to:

refinegems media export -m all -t tsv -d media_export

Export selected media

Multiple media names can be passed by repeating -m:

refinegems media export -m LB -m M9 --type csv --dir selected_media

Export from a media configuration file

The same command can use a media configuration file instead of explicit medium names:

refinegems media export -m media_config.yml --type tsv --dir configured_media

Export formats

The --type option controls the output format:

• tsv or csv for tabular files

• docs or rst for documentation-oriented tables

For tsv and csv exports, --flavour controls the table layout. The default substance_table export keeps the refineGEMs substance table format. The carveme_mimic export creates files closer to CarveMe-style media definitions.

Example output

For example, exporting M9 as substance_table starts with:

name        formula flux    source  db_id   db_type
Ammonia     H3N             NH4Cl   C00014  KEGG
Ammonia     H3N             NH4Cl   C01342  KEGG
Ammonia     H3N             NH4Cl   MNXM729302      MetaNetX
Ammonia     H3N             NH4Cl   nh3     BiGG

The same medium exported as carveme_mimic starts with:

medium      description     compound        name    flux
M9  M9 minimal medium       nh3     Ammonia 10.0
M9  M9 minimal medium       nh4     Ammonia 10.0
M9  M9 minimal medium       ca2     Calcium(II) cation [Ca(2+)]     10.0
M9  M9 minimal medium       cl      Chloride [Cl(-)]        10.0