apollo.remote package

Module contents

Contains possible interactions with the Apollo Organisms Module

class apollo.remote.RemoteClient(webapolloinstance, **requestArgs)

Bases: apollo.client.Client

CLIENT_BASE = '/organism/'
add_organism(common_name, organism_data, blatdb=None, genus=None, species=None, public=None, non_default_translation_table=None, metadata=None)

Add an organism using the remote organism API.

The recommended structure for the genome data tarball is as follows:

names/
names/root.json
searchDatabaseData/blat_db.2bit
seq/
seq/fba/
seq/fba/da8/
seq/fba/da8/f3/
seq/fba/da8/f3/Mijalis-0.txt
seq/fba/da8/f3/Mijalis-1.txt
seq/fba/da8/f3/Mijalis-2.txt
seq/fba/da8/f3/Mijalis-3.txt
seq/fba/da8/f3/Mijalis-4.txt
seq/refSeqs.json
tracks/
trackList.json
tracks.conf

The genome name / hashed directories below the seq folder will obviously be specific to your organism.

Parameters:
  • common_name (str) – Organism common name
  • organism_data (file) – .tar.gz or .zip archive containing the data directory.
  • blatdb (file) – Path to 2bit index of the genome for Blat (Blat 2bit data can also be in organism_data in directory ‘searchDatabaseData’)
  • genus (str) – Genus
  • species (str) – Species
  • public (bool) – should the organism be public
  • non_default_translation_table (int) – The translation table number for the organism (if different than that of the server’s default)
  • metadata (str) – JSON formatted arbitrary metadata
Return type:

dict
Returns:

a dictionary with information about the new organism
add_track(organism_id, track_data, track_config)

Adds a tarball containing track data to an existing organism.

The recommended structure for your track data tarball is as follows:

tracks/testing2/
tracks/testing2/Mijalis/
tracks/testing2/Mijalis/hist-2000-0.json
tracks/testing2/Mijalis/lf-1.json
tracks/testing2/Mijalis/lf-2.json
tracks/testing2/Mijalis/lf-3.json
tracks/testing2/Mijalis/names.txt
tracks/testing2/Mijalis/trackData.json

And an example of the track_config supplied at the same time:

{
    "key": "Some human-readable name",
    "label": "my-cool-track",
    "storeClass": "JBrowse/Store/SeqFeature/NCList",
    "type": "FeatureTrack",
    "urlTemplate": "tracks/testing2/{refseq}/trackData.json"
}

This is only the recommended structure, other directory structures / parameter combinations may work but were not tested by the python-apollo author who wrote this documentation.

Parameters:
  • organism_id (str) – Organism ID Number
  • track_data (file) – .tar.gz or .zip archive containing the <track> directory.
  • track_config (dict) – Track configuration
Return type:

dict
Returns:

a dictionary with information about all tracks on the organism
delete_organism(organism_id)

Remove an organism completely.

Parameters:organism_id (str) – Organism ID Number
Return type:dict
Returns:a dictionary with information about the deleted organism
delete_track(organism_id, track_label)

Remove a track from an organism

Parameters:
  • organism_id (str) – Organism ID Number
  • track_label (str) – Track label
Return type:

dict
Returns:

a dictionary with information about the deleted track
update_organism(organism_id, organism_data, blatdb=None, common_name=None, genus=None, species=None, public=None, metadata=None, no_reload_sequences=False)

Update an organism using the remote organism API.

The recommended structure for the genome data tarball is as follows:

names/
names/root.json
searchDatabaseData/blat_db.2bit
seq/
seq/fba/
seq/fba/da8/
seq/fba/da8/f3/
seq/fba/da8/f3/Mijalis-0.txt
seq/fba/da8/f3/Mijalis-1.txt
seq/fba/da8/f3/Mijalis-2.txt
seq/fba/da8/f3/Mijalis-3.txt
seq/fba/da8/f3/Mijalis-4.txt
seq/refSeqs.json
tracks/
trackList.json
tracks.conf

The genome name / hashed directories below the seq folder will obviously be specific to your organism.

Parameters:
  • organism_id (str) – Organism ID Number
  • organism_data (file) – .tar.gz or .zip archive containing the data directory.
  • blatdb (file) – Path to 2bit index of the genome for Blat (Blat 2bit data can also be in organism_data in directory ‘searchDatabaseData’)
  • common_name (str) – Organism common name
  • genus (str) – Genus
  • species (str) – Species
  • public (bool) – User’s email
  • metadata (str) – JSON formatted arbitrary metadata
  • no_reload_sequences (bool) – Set this if you don’t want Apollo to reload genome sequences (no change in genome sequence)
Return type:

dict
Returns:

a dictionary with information about the updated organism
update_track(organism_id, track_config)

Update the configuration of a track that has already been added to the organism. Will not update data for the track.

And an example of the track_config supplied:

{
    "key": "Some human-readable name",
    "label": "my-cool-track",
    "storeClass": "JBrowse/Store/SeqFeature/NCList",
    "type": "FeatureTrack",
    "urlTemplate": "tracks/testing2/{refseq}/trackData.json"
}
Parameters:
  • organism_id (str) – Organism ID Number
  • track_config (dict) – Track configuration
Return type:

dict
Returns:

a dictionary with information about all tracks on the organism