Welcome to Python-Apollo’s documentation!¶

Apollo API Library¶

https://travis-ci.org/galaxy-genome-annotation/python-apollo.svg?branch=master

Apollo is a Python library for interacting with Apollo. Arrow is its companion CLI tool.

for the record … arrow makes working with Apollo SOOO much easier — Nathan Dunn, Apollo Developer

Installation¶

pip install apollo

Examples¶

Example code to create a new organism and add yourself in the permission list:

from apollo import ApolloInstance
wa = ApolloInstance('https://fqdn/apollo', 'jane.doe@fqdn.edu', 'password')

orgs = wa.organisms.add_organism(
    "Yeast",
    "/path/to/jbrowse/data",
    genus='Saccharomyces',
    species='cerevisiae',
    public=False
)

# Give Apollo a second to process the uploaded organism.
time.sleep(1)

# Then add yourself to permission list
data = wa.users.update_organism_permissions(
    "jane.doe@fqdn.edu",
    "Yeast",
    write=True,
    export=True,
    read=True,
)

If you have already created an Arrow config file (with command arrow init), you can also get an ApolloInstance without writing credentials explicitely:

from arrow.apollo import get_apollo_instance
wa = get_apollo_instance()

Or with the Arrow client:

$ arrow groups create_group university
{
    "publicGroup": false,
    "class": "org.bbop.apollo.UserGroup",
    "name": "university",
    "users": null,
    "id": 558319
}
# THEN
$ arrow users get_users | \
    jq '.[] | select(.username | contains("@tamu.edu")) | .username' | \
    xargs -n1 arrow users add_to_group university
# OR
$ arrow users get_users | \
    jq '.[] | select(.username | contains("@tamu.edu")) | .username' | \
    paste -s -d',' | \
    xargs arrow group update_membership 558319 --users

History¶

4.2.13
- Relax biopython requirements
4.2.12
- Do not filter out username from api responses
4.2.11
- Updated wrong version number
4.2.10
- Bugfix handling Shine-Dalgarno sequences (https://github.com/galaxy-genome-annotation/python-apollo/issues/48)
4.2.9
- Bugfix to update_organism when using suppress_output
4.2.8
- Added –suppress_output to update_organism
4.2.7
- Renamed –return_all option to –suppress_output
4.2.6
- Added –return_all option to add_organism and delete_organism methods
4.2.5
- Prevent from displaying login/password in the logs
4.2.4
- Remove unused dependency
4.2.3
- Fixed load_gff3 to more accurately load transcripts including the CDS as well as handle non-coding types more accurately.
4.2.2
- Drastically speed up load_gff3
- load_gff3 now uses the Apollo add_transcript method if it is a gene or mRNA type
- Added support for all of the current Apollo coding and non-coding types
- Drop support for Python 2.7
4.2.1
- Fix getting groups by name
- Add tests for group api
4.2
- Improve user update method
- Add tests for user api
4.1
- Fix loading attributes from gff3
- Better handling of genome sequence update, with or without the no_reload_sequences option
4.0.1
- Fix missing file in pypi package, no code change
4.0
- Added support for remote creation/update/deletion of organisms/tracks
- Added support for adding GFF3 in the annotation track
- Added tests
3.1
- Added user activate/inactivate
- Added get_creator for user, group and organisms
- Added omitEmptyOrganisms to get_users
- Added support for group admins
- Added support for bulk group creation/deletion
- Repaired GFF3/Fasta downloading
3.0.4
- Fixed bug in deleteFeatures (Thanks @NeillGibson)
3.0.3
- findAllOrganisms works correctly, client side filtering no longer necessary.
3.0.2
- Patch a bug discovered in io.write, thanks Morgan!
3.0
- “Arrow” CLI utility
- More pythonic API and many workarounds for Apollo bugs or oddities
- Complete package restructure
- Nearly all functions renamed
2.0
- Galaxy Functions
- TTL Cache to work around Galaxy’s behaviour
- Status and Canned* Clients from @abretaud
1.0
- Initial release

Development¶

The content of docs and arrow directories is automatically generated from the code in the apollo directory. To regenerate it, install the latest version of the code, then run:

make rebuild

License¶

Available under the MIT License

Support¶

This material is based upon work supported by the National Science Foundation under Grant Number (Award 1565146)

Commands¶

Arrow is a set of wrappers for Apollo’s API. It builds a set of small, useful utilities for talking to Apollo servers. Each utility is implemented as a subcommand of arrow. This section of the documentation describes these commands.

annotations¶

This section is auto-generated from the help text for the arrow command annotations.

`add_attribute` command¶

Usage:

arrow annotations add_attribute [OPTIONS] FEATURE_ID ATTRIBUTE_KEY

Help

Add an attribute to a feature

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`add_comment` command¶

Usage:

arrow annotations add_comment [OPTIONS] FEATURE_ID

Help

Set a feature’s description

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--comments TEXT  Feature comments
--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`add_dbxref` command¶

Usage:

arrow annotations add_dbxref [OPTIONS] FEATURE_ID DB ACCESSION

Help

Add a dbxref to a feature

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`add_feature` command¶

Usage:

arrow annotations add_feature [OPTIONS]

Help

Add a single feature

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--feature TEXT   Feature information
--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`add_features` command¶

Usage:

arrow annotations add_features [OPTIONS]

Help

Add a list of feature

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--features TEXT  Feature information
--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`add_transcript` command¶

Usage:

arrow annotations add_transcript [OPTIONS]

Help

Add a single transcript annotation

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--transcript TEXT   Transcript data
--suppress_history  Suppress the history of this operation
--suppress_events   Suppress instant update of the user interface
--organism TEXT     Organism Common Name
--sequence TEXT     Sequence Name
-h, --help          Show this message and exit.

`add_transcripts` command¶

Usage:

arrow annotations add_transcripts [OPTIONS]

Help

Add a list of transcript annotations

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--transcripts TEXT  Transcript data
--suppress_history  Suppress the history of this operation
--suppress_events   Suppress instant update of the user interface
--organism TEXT     Organism Common Name
--sequence TEXT     Sequence Name
-h, --help          Show this message and exit.

`delete_attribute` command¶

Usage:

arrow annotations delete_attribute [OPTIONS] FEATURE_ID ATTRIBUTE_KEY

Help

Delete an attribute from a feature

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`delete_dbxref` command¶

Usage:

arrow annotations delete_dbxref [OPTIONS] FEATURE_ID DB ACCESSION

Help

Delete a dbxref from a feature

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`delete_feature` command¶

Usage:

arrow annotations delete_feature [OPTIONS] FEATURE_ID

Help

Delete a feature

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`delete_sequence_alteration` command¶

Usage:

arrow annotations delete_sequence_alteration [OPTIONS] FEATURE_ID

Help

[UNTESTED] Delete a specific feature alteration

Output

A list of sequence alterations(?)

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`duplicate_transcript` command¶

Usage:

arrow annotations duplicate_transcript [OPTIONS] TRANSCRIPT_ID

Help

Duplicate a transcripte

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`flip_strand` command¶

Usage:

arrow annotations flip_strand [OPTIONS] FEATURE_ID

Help

Flip the strand of a feature

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`get_comments` command¶

Usage:

arrow annotations get_comments [OPTIONS] FEATURE_ID

Help

Get a feature’s comments

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`get_feature_sequence` command¶

Usage:

arrow annotations get_feature_sequence [OPTIONS] FEATURE_ID

Help

[CURRENTLY BROKEN] Get the sequence of a feature

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`get_features` command¶

Usage:

arrow annotations get_features [OPTIONS]

Help

Get the features for an organism / sequence

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`get_gff3` command¶

Usage:

arrow annotations get_gff3 [OPTIONS] FEATURE_ID

Help

Get the GFF3 associated with a feature

Output

GFF3 text content

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`get_search_tools` command¶

Usage:

arrow annotations get_search_tools [OPTIONS]

Help

Get the search tools available

Output

dictionary containing the search tools and their metadata.

For example:

{
    "sequence_search_tools": {
        "blat_prot": {
            "name": "Blat protein",
            "search_class": "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide",
            "params": "",
            "search_exe": "/usr/local/bin/blat"
        },
        "blat_nuc": {
            "name": "Blat nucleotide",
            "search_class": "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide",
            "params": "",
            "search_exe": "/usr/local/bin/blat"
        }
    }
}

Options:

-h, --help  Show this message and exit.

`get_sequence_alterations` command¶

Usage:

arrow annotations get_sequence_alterations [OPTIONS]

Help

[UNTESTED] Get all of the sequence’s alterations

Output

A list of sequence alterations(?)

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`load_gff3` command¶

Usage:

arrow annotations load_gff3 [OPTIONS] ORGANISM GFF3

Help

Load a full GFF3 into annotation track

Output

Loading report

Options:

--source TEXT                URL where the input dataset can be found.
--batch_size INTEGER         Size of batches before writing  [default: 1]
--test                       Run in dry run mode
--use_name                   Use the given name instead of generating one.
--disable_cds_recalculation  Disable CDS recalculation and instead use the one
                             provided

--timing                     Output loading performance metrics
-h, --help                   Show this message and exit.

`load_legacy_gff3` command¶

Usage:

arrow annotations load_legacy_gff3 [OPTIONS] ORGANISM GFF3

Help

Load a full GFF3 into annotation track (legacy version, kept for compatibility only)

Output

Loading report

Options:

--source TEXT  URL where the input dataset can be found.
-h, --help     Show this message and exit.

`merge_exons` command¶

Usage:

arrow annotations merge_exons [OPTIONS] EXON_A EXON_B

Help

Merge two exons

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`set_boundaries` command¶

Usage:

arrow annotations set_boundaries [OPTIONS] FEATURE_ID START END

Help

Set the boundaries of a genomic feature

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`set_description` command¶

Usage:

arrow annotations set_description [OPTIONS] FEATURE_ID DESCRIPTION

Help

Set a feature’s description

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`set_longest_orf` command¶

Usage:

arrow annotations set_longest_orf [OPTIONS] FEATURE_ID

Help

Automatically pick the longest ORF in a feature

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`set_name` command¶

Usage:

arrow annotations set_name [OPTIONS] FEATURE_ID NAME

Help

Set a feature’s name

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`set_readthrough_stop_codon` command¶

Usage:

arrow annotations set_readthrough_stop_codon [OPTIONS] FEATURE_ID

Help

Set the feature to read through the first encountered stop codon

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`set_sequence` command¶

Usage:

arrow annotations set_sequence [OPTIONS] ORGANISM SEQUENCE

Help

Set the sequence for subsequent requests. Mostly used in client scripts to avoid passing the sequence and organism on every function call.

Output

None

Options:

-h, --help  Show this message and exit.

`set_status` command¶

Usage:

arrow annotations set_status [OPTIONS] FEATURE_ID STATUS

Help

Set a feature’s description

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`set_symbol` command¶

Usage:

arrow annotations set_symbol [OPTIONS] FEATURE_ID SYMBOL

Help

Set a feature’s description

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`set_translation_end` command¶

Usage:

arrow annotations set_translation_end [OPTIONS] FEATURE_ID END

Help

Set a feature’s end

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`set_translation_start` command¶

Usage:

arrow annotations set_translation_start [OPTIONS] FEATURE_ID START

Help

Set the translation start of a feature

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`update_attribute` command¶

Usage:

arrow annotations update_attribute [OPTIONS] FEATURE_ID ATTRIBUTE_KEY

Help

Delete an attribute from a feature

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

`update_dbxref` command¶

Usage:

arrow annotations update_dbxref [OPTIONS] FEATURE_ID OLD_DB OLD_ACCESSION

Help

Delete a dbxref from a feature

Output

A standard apollo feature dictionary ({“features”: [{…}]})

Options:

--organism TEXT  Organism Common Name
--sequence TEXT  Sequence Name
-h, --help       Show this message and exit.

cannedcomments¶

This section is auto-generated from the help text for the arrow command cannedcomments.

`add_comment` command¶

Usage:

arrow cannedcomments add_comment [OPTIONS] COMMENT

Help

Add a canned comment

Output

A dictionnary containing canned comment description

Options:

--metadata TEXT  Optional metadata
-h, --help       Show this message and exit.

`delete_comment` command¶

Usage:

arrow cannedcomments delete_comment [OPTIONS] ID_NUMBER

Help

Update a canned comment

Output

an empty dictionary

Options:

-h, --help  Show this message and exit.

`get_comments` command¶

Usage:

arrow cannedcomments get_comments [OPTIONS]

Help

Get all canned comments available in this Apollo instance

Output

list of canned comment info dictionaries

Options:

-h, --help  Show this message and exit.

`show_comment` command¶

Usage:

arrow cannedcomments show_comment [OPTIONS] VALUE

Help

Get a specific canned comment

Output

A dictionnary containing canned comment description

Options:

-h, --help  Show this message and exit.

`update_comment` command¶

Usage:

arrow cannedcomments update_comment [OPTIONS] ID_NUMBER NEW_VALUE

Help

Update a canned comment

Output

an empty dictionary

Options:

--metadata TEXT  Optional metadata
-h, --help       Show this message and exit.

cannedkeys¶

This section is auto-generated from the help text for the arrow command cannedkeys.

`add_key` command¶

Usage:

arrow cannedkeys add_key [OPTIONS] KEY

Help

Add a canned key

Output

A dictionnary containing canned key description

Options:

--metadata TEXT  Optional metadata
-h, --help       Show this message and exit.

`delete_key` command¶

Usage:

arrow cannedkeys delete_key [OPTIONS] ID_NUMBER

Help

Update a canned key

Output

an empty dictionary

Options:

-h, --help  Show this message and exit.

`get_keys` command¶

Usage:

arrow cannedkeys get_keys [OPTIONS]

Help

Get all canned keys available in this Apollo instance

Output

list of canned key info dictionaries

Options:

-h, --help  Show this message and exit.

`show_key` command¶

Usage:

arrow cannedkeys show_key [OPTIONS] VALUE

Help

Get a specific canned key

Output

A dictionnary containing canned key description

Options:

-h, --help  Show this message and exit.

`update_key` command¶

Usage:

arrow cannedkeys update_key [OPTIONS] ID_NUMBER NEW_KEY

Help

Update a canned key

Output

an empty dictionary

Options:

--metadata TEXT  Optional metadata
-h, --help       Show this message and exit.

cannedvalues¶

This section is auto-generated from the help text for the arrow command cannedvalues.

`add_value` command¶

Usage:

arrow cannedvalues add_value [OPTIONS] VALUE

Help

Add a canned value

Output

A dictionnary containing canned value description

Options:

--metadata TEXT  Optional metadata
-h, --help       Show this message and exit.

`delete_value` command¶

Usage:

arrow cannedvalues delete_value [OPTIONS] ID_NUMBER

Help

Update a canned value

Output

an empty dictionary

Options:

-h, --help  Show this message and exit.

`get_values` command¶

Usage:

arrow cannedvalues get_values [OPTIONS]

Help

Get all canned values available in this Apollo instance

Output

list of canned value info dictionaries

Options:

-h, --help  Show this message and exit.

`show_value` command¶

Usage:

arrow cannedvalues show_value [OPTIONS] VALUE

Help

Get a specific canned value

Output

A dictionnary containing canned value description

Options:

-h, --help  Show this message and exit.

`update_value` command¶

Usage:

arrow cannedvalues update_value [OPTIONS] ID_NUMBER NEW_VALUE

Help

Update a canned value

Output

an empty dictionary

Options:

--metadata TEXT  Optional metadata
-h, --help       Show this message and exit.

groups¶

This section is auto-generated from the help text for the arrow command groups.

`create_group` command¶

Usage:

arrow groups create_group [OPTIONS] NAME

Help

Create a new group

Output

Group information dictionary

Options:

-h, --help  Show this message and exit.

`delete_group` command¶

Usage:

arrow groups delete_group [OPTIONS] GROUP

Help

Delete a group

Output

an empty dictionary

Options:

-h, --help  Show this message and exit.

`get_group_admin` command¶

Usage:

arrow groups get_group_admin [OPTIONS] GROUP

Help

Get the group’s admins

Output

a list containing group admins

Options:

-h, --help  Show this message and exit.

`get_group_creator` command¶

Usage:

arrow groups get_group_creator [OPTIONS] GROUP

Help

Get the group’s creator

Output

creator userId

Options:

-h, --help  Show this message and exit.

`get_groups` command¶

Usage:

arrow groups get_groups [OPTIONS]

Help

Get all the groups

Output

list of a dictionaries containing group information

Options:

--name TEXT  Only return group(s) with given name
-h, --help   Show this message and exit.

`get_organism_permissions` command¶

Usage:

arrow groups get_organism_permissions [OPTIONS] GROUP

Help

Get the group’s organism permissions

Output

a list containing organism permissions (if any)

Options:

-h, --help  Show this message and exit.

`show_group` command¶

Usage:

arrow groups show_group [OPTIONS] GROUP_ID

Help

Get information about a group

Output

a dictionary containing group information

Options:

-h, --help  Show this message and exit.

`update_group` command¶

Usage:

arrow groups update_group [OPTIONS] GROUP_ID NEW_NAME

Help

Update the name of a group

Output

a dictionary containing group information

Options:

-h, --help  Show this message and exit.

`update_group_admin` command¶

Usage:

arrow groups update_group_admin [OPTIONS] GROUP_ID

Help

Update the group’s admins

Output

dictionary of group information

Options:

--users TEXT  List of emails
-h, --help    Show this message and exit.

`update_membership` command¶

Usage:

arrow groups update_membership [OPTIONS]

Help

Update the group’s membership

Output

dictionary of group information

Options:

--group_id INTEGER  Group ID Number
--users TEXT        List of emails
--memberships TEXT  Bulk memberships to update of the form: [ {groupId:
                    <groupId>,users: ["user1", "user2", "user3"]},
                    {groupId:<another-groupId>, users: ["user2", "user8"]}
                    (users and groupId will be ignored)

-h, --help          Show this message and exit.

`update_organism_permissions` command¶

Usage:

arrow groups update_organism_permissions [OPTIONS] GROUP ORGANISM_NAME

Help

Update the group’s permissions on an organism

Output

list of group organism permissions

Options:

--administrate  Should the group have administrate privileges
--write         Should the group have write privileges
--read          Should the group have read privileges
--export        Should the group have export privileges
-h, --help      Show this message and exit.

io¶

This section is auto-generated from the help text for the arrow command io.

`download` command¶

Usage:

arrow io download [OPTIONS] UUID

Help

Download pre-prepared data by UUID

Output

The downloaded content

Options:

--output_format TEXT  Output format of the data, either "gzip" or "text"
                      [default: gzip]

-h, --help            Show this message and exit.

`write_downloadable` command¶

Usage:

arrow io write_downloadable [OPTIONS] ORGANISM

Help

Prepare a download for an organism

Output

a dictionary containing download information

Options:

--export_type TEXT    Export type. Choices: FASTA, GFF3, VCF  [default: FASTA]
--seq_type TEXT       Export selection. Choices: peptide, cds, cdna, genomic
                      [default: peptide]

--export_format TEXT  Export format, either gzip or text  [default: text]
--export_gff3_fasta   Export reference sequence when exporting GFF3
                      annotations.

--sequences TEXT      Names of references sequences to add (default is all)
--region TEXT         Region to export in form sequence:min..max e.g.,
                      chr3:1001..1034

-h, --help            Show this message and exit.

`write_text` command¶

Usage:

arrow io write_text [OPTIONS] ORGANISM

Help

[DEPRECATED, use write_downloadable] Download or prepare a download for an organism

Output

the exported data

Options:

--export_type TEXT    Export type. Choices: FASTA, GFF3, VCF  [default: FASTA]
--seq_type TEXT       Export selection. Choices: peptide, cds, cdna, genomic
                      [default: peptide]

--export_format TEXT  Export format, either gzip or text  [default: text]
--export_gff3_fasta   Export reference sequence when exporting GFF3
                      annotations.

--sequences TEXT      Names of references sequences to add (default is all)
--region TEXT         Region to export in form sequence:min..max e.g.,
                      chr3:1001..1034

-h, --help            Show this message and exit.

metrics¶

This section is auto-generated from the help text for the arrow command metrics.

`get_metrics` command¶

Usage:

arrow metrics get_metrics [OPTIONS]

Help

Get all server metrics

Output

A dictionary with all of the server timing / metrics

Options:

-h, --help  Show this message and exit.

organisms¶

This section is auto-generated from the help text for the arrow command organisms.

`add_organism` command¶

Usage:

arrow organisms add_organism [OPTIONS] COMMON_NAME DIRECTORY

Help

Add an organism

Output

a dictionary with information about the new organism

Options:

--blatdb TEXT      Server-side path to 2bit index of the genome for Blat
--genus TEXT       Genus
--species TEXT     Species
--public           Should the organism be public or not
--metadata TEXT    JSON formatted arbitrary metadata
--suppress_output  Suppress output of all organisms (true / false) (default
                   false)

-h, --help         Show this message and exit.

`delete_features` command¶

Usage:

arrow organisms delete_features [OPTIONS] ORGANISM_ID

Help

Remove features of an organism

Output

an empty dictionary

Options:

-h, --help  Show this message and exit.

`delete_organism` command¶

Usage:

arrow organisms delete_organism [OPTIONS] ORGANISM_ID

Help

Delete an organism

Output

A list of all remaining organisms

Options:

--suppress_output  Suppress return of all organisms (true / false) (default
                   false)

-h, --help         Show this message and exit.

`get_organism_creator` command¶

Usage:

arrow organisms get_organism_creator [OPTIONS] ORGANISM_ID

Help

Get the creator of an organism

Output

a dictionary containing user information

Options:

-h, --help  Show this message and exit.

`get_organisms` command¶

Usage:

arrow organisms get_organisms [OPTIONS]

Help

Get all organisms

Output

Organism information

Options:

--common_name TEXT  Optionally filter on common name
-h, --help          Show this message and exit.

`get_sequences` command¶

Usage:

arrow organisms get_sequences [OPTIONS] ORGANISM_ID

Help

Get the sequences for an organism

Output

The set of sequences associated with an organism

Options:

-h, --help  Show this message and exit.

`show_organism` command¶

Usage:

arrow organisms show_organism [OPTIONS] COMMON_NAME

Help

Get information about a specific organism.

Output

a dictionary containing the organism’s information

Options:

-h, --help  Show this message and exit.

`update_metadata` command¶

Usage:

arrow organisms update_metadata [OPTIONS] ORGANISM_ID METADATA

Help

Update the metadata for an existing organism.

Output

An empty, useless dictionary

Options:

-h, --help  Show this message and exit.

`update_organism` command¶

Usage:

arrow organisms update_organism [OPTIONS] ORGANISM_ID COMMON_NAME

Help

Update an organism

Output

a dictionary with information about the updated organism

Options:

--blatdb TEXT          Server-side Blat directory for the organism
--species TEXT         Species
--genus TEXT           Genus
--public               User's email
--no_reload_sequences  Set this if you don't want Apollo to reload genome
                       sequences (no change in genome sequence)

--suppress_output      Suppress output of all organisms (true / false)
                       (default false)

-h, --help             Show this message and exit.

remote¶

This section is auto-generated from the help text for the arrow command remote.

`add_organism` command¶

Usage:

arrow remote add_organism [OPTIONS] COMMON_NAME ORGANISM_DATA

Help

Add an organism using the remote organism API.

Output

a dictionary with information about the new organism

Options:

--blatdb FILENAME               Path to 2bit index of the genome for Blat
                                (Blat 2bit data can also be in organism_data
                                in directory 'searchDatabaseData')

--genus TEXT                    Genus
--species TEXT                  Species
--public                        should the organism be public
--non_default_translation_table INTEGER
                                The translation table number for the organism
                                (if different than that of the server's
                                default)

--metadata TEXT                 JSON formatted arbitrary metadata
-h, --help                      Show this message and exit.

`add_track` command¶

Usage:

arrow remote add_track [OPTIONS] ORGANISM_ID TRACK_DATA TRACK_CONFIG

Help

Adds a tarball containing track data to an existing organism.

Output

a dictionary with information about all tracks on the organism

Options:

-h, --help  Show this message and exit.

`delete_organism` command¶

Usage:

arrow remote delete_organism [OPTIONS] ORGANISM_ID

Help

Remove an organism completely.

Output

a dictionary with information about the deleted organism

Options:

-h, --help  Show this message and exit.

`delete_track` command¶

Usage:

arrow remote delete_track [OPTIONS] ORGANISM_ID TRACK_LABEL

Help

Remove a track from an organism

Output

a dictionary with information about the deleted track

Options:

-h, --help  Show this message and exit.

`update_organism` command¶

Usage:

arrow remote update_organism [OPTIONS] ORGANISM_ID ORGANISM_DATA

Help

Update an organism using the remote organism API.

Output

a dictionary with information about the updated organism

Options:

--blatdb FILENAME      Path to 2bit index of the genome for Blat (Blat 2bit
                       data can also be in organism_data in directory
                       'searchDatabaseData')

--common_name TEXT     Organism common name
--genus TEXT           Genus
--species TEXT         Species
--public               User's email
--metadata TEXT        JSON formatted arbitrary metadata
--no_reload_sequences  Set this if you don't want Apollo to reload genome
                       sequences (no change in genome sequence)

-h, --help             Show this message and exit.

`update_track` command¶

Usage:

arrow remote update_track [OPTIONS] ORGANISM_ID TRACK_CONFIG

Help

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

Output

a dictionary with information about all tracks on the organism

Options:

-h, --help  Show this message and exit.

status¶

This section is auto-generated from the help text for the arrow command status.

`add_status` command¶

Usage:

arrow status add_status [OPTIONS] STATUS

Help

Add a status value

Output

A dictionnary containing status description

Options:

-h, --help  Show this message and exit.

`delete_status` command¶

Usage:

arrow status delete_status [OPTIONS] ID_NUMBER

Help

Delete a status

Output

an empty dictionary

Options:

-h, --help  Show this message and exit.

`get_statuses` command¶

Usage:

arrow status get_statuses [OPTIONS]

Help

Get all statuses available in this Apollo instance

Output

list of status info dictionaries

Options:

-h, --help  Show this message and exit.

`show_status` command¶

Usage:

arrow status show_status [OPTIONS] STATUS

Help

Get a specific status

Output

A dictionnary containing status description

Options:

-h, --help  Show this message and exit.

`update_status` command¶

Usage:

arrow status update_status [OPTIONS] ID_NUMBER NEW_VALUE

Help

Update a status name

Output

an empty dictionary

Options:

-h, --help  Show this message and exit.

users¶

This section is auto-generated from the help text for the arrow command users.

`activate_user` command¶

Usage:

arrow users activate_user [OPTIONS] USER

Help

Activate a user

Output

an empty dictionary

Options:

-h, --help  Show this message and exit.

`add_to_group` command¶

Usage:

arrow users add_to_group [OPTIONS] GROUP USER

Help

Add a user to a group

Output

an empty dictionary

Options:

-h, --help  Show this message and exit.

`create_user` command¶

Usage:

arrow users create_user [OPTIONS] EMAIL FIRST_NAME LAST_NAME PASSWORD

Help

Create a new user

Output

an empty dictionary

Options:

--role TEXT      User's default role, one of "admin" or "user"  [default:
                 user]

--metadata TEXT  User metadata
-h, --help       Show this message and exit.

`delete_user` command¶

Usage:

arrow users delete_user [OPTIONS] USER

Help

Delete a user

Output

an empty dictionary

Options:

-h, --help  Show this message and exit.

`get_organism_permissions` command¶

Usage:

arrow users get_organism_permissions [OPTIONS] USER

Help

Display a user’s organism permissions

Output

a dictionary containing user’s organism permissions

Options:

-h, --help  Show this message and exit.

`get_user_creator` command¶

Usage:

arrow users get_user_creator [OPTIONS] USER

Help

Get the creator of a user

Output

a dictionary containing user information

Options:

-h, --help  Show this message and exit.

`get_users` command¶

Usage:

arrow users get_users [OPTIONS]

Help

Get all users known to this Apollo instance

Output

list of user info dictionaries

Options:

--omit_empty_organisms  Will omit users having no access to any organism
-h, --help              Show this message and exit.

`inactivate_user` command¶

Usage:

arrow users inactivate_user [OPTIONS] USER

Help

Activate a user

Output

an empty dictionary

Options:

-h, --help  Show this message and exit.

`remove_from_group` command¶

Usage:

arrow users remove_from_group [OPTIONS] GROUP USER

Help

Remove a user from a group

Output

an empty dictionary

Options:

-h, --help  Show this message and exit.

`show_user` command¶

Usage:

arrow users show_user [OPTIONS] USER

Help

Get a specific user

Output

a dictionary containing user information

Options:

-h, --help  Show this message and exit.

`update_organism_permissions` command¶

Usage:

arrow users update_organism_permissions [OPTIONS] USER ORGANISM

Help

Update the permissions of a user on a specified organism

Output

a dictionary containing user’s organism permissions

Options:

--administrate  Grants administrative privileges
--write         Grants write privileges
--export        Grants export privileges
--read          Grants read privileges
-h, --help      Show this message and exit.

`update_user` command¶

Usage:

arrow users update_user [OPTIONS] EMAIL FIRST_NAME LAST_NAME

Help

Update an existing user

Output

a dictionary containing user information

Options:

--password TEXT   User's password (omit to keep untouched)
--metadata TEXT   User metadata
--new_email TEXT  User's new email (if you want to change it)
-h, --help        Show this message and exit.

apollo package¶

Subpackages¶

apollo.annotations package¶

Module contents¶

Contains possible interactions with the Apollo’s Annotations

class apollo.annotations.AnnotationsClient(webapolloinstance, **requestArgs)¶

Bases: apollo.client.Client

CLIENT_BASE = '/annotationEditor/'¶

add_attribute(feature_id, attribute_key, attribute_value, organism=None, sequence=None)¶

Add an attribute to a feature

Parameters:	feature_id (str) – Feature UUID attribute_key (str) – Attribute Key attribute_value (str) – Attribute Value organism (str) – Organism Common Name sequence (str) – Sequence Name

This seems to show two attributes being added, but it behaves like those two are one.

Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

add_comment(feature_id, comments=[], organism=None, sequence=None)¶

Set a feature’s description

Parameters:	feature_id (str) – Feature UUID comments (list) – Feature comments organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

add_dbxref(feature_id, db, accession, organism=None, sequence=None)¶

Add a dbxref to a feature

Parameters:	feature_id (str) – Feature UUID db (str) – DB Name (e.g. PMID) accession (str) – Accession Value organism (str) – Organism Common Name sequence (str) – Sequence Name

This seems to show two attributes being added, but it behaves like those two are one.

Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

add_feature(feature={}, organism=None, sequence=None)¶

Add a single feature

Parameters:	feature (dict) – Feature information organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

add_features(features=[], organism=None, sequence=None)¶

Add a list of feature

Parameters:	features (list) – Feature information organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

add_transcript(transcript={}, suppress_history=False, suppress_events=False, organism=None, sequence=None)¶

Add a single transcript annotation

Parameters:	transcript (dict) – Transcript data suppress_history (bool) – Suppress the history of this operation suppress_events (bool) – Suppress instant update of the user interface organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

add_transcripts(transcripts=[], suppress_history=False, suppress_events=False, organism=None, sequence=None)¶

Add a list of transcript annotations

Parameters:	transcripts (list) – Transcript data suppress_history (bool) – Suppress the history of this operation suppress_events (bool) – Suppress instant update of the user interface organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

delete_attribute(feature_id, attribute_key, attribute_value, organism=None, sequence=None)¶

Delete an attribute from a feature

Parameters:	feature_id (str) – Feature UUID attribute_key (str) – Attribute Key attribute_value (str) – Attribute Value organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

delete_dbxref(feature_id, db, accession, organism=None, sequence=None)¶

Delete a dbxref from a feature

Parameters:	feature_id (str) – Feature UUID db (str) – DB Name (e.g. PMID) accession (str) – Accession Value organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

delete_feature(feature_id, organism=None, sequence=None)¶

Delete a feature

Parameters:	feature_id (str) – Feature UUID organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

delete_sequence_alteration(feature_id, organism=None, sequence=None)¶

[UNTESTED] Delete a specific feature alteration

Parameters:	feature_id (str) – Feature UUID organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	list
Returns:	A list of sequence alterations(?)

duplicate_transcript(transcript_id, organism=None, sequence=None)¶

Duplicate a transcripte

Parameters:	transcript_id (str) – Transcript UUID organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

flip_strand(feature_id, organism=None, sequence=None)¶

Flip the strand of a feature

Parameters:	feature_id (str) – Feature UUID organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

get_comments(feature_id, organism=None, sequence=None)¶

Get a feature’s comments

Parameters:	feature_id (str) – Feature UUID organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

get_feature_sequence(feature_id, organism=None, sequence=None)¶

[CURRENTLY BROKEN] Get the sequence of a feature

Parameters:	feature_id (str) – Feature UUID organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

get_features(organism=None, sequence=None)¶

Get the features for an organism / sequence

Parameters:	organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

get_gff3(feature_id, organism=None, sequence=None)¶

Get the GFF3 associated with a feature

Parameters:	feature_id (str) – Feature UUID organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	str
Returns:	GFF3 text content

get_search_tools()¶

Get the search tools available

Return type: dict

Returns:

dictionary containing the search tools and their metadata. For example:

{
    "sequence_search_tools": {
        "blat_prot": {
            "name": "Blat protein",
            "search_class": "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide",
            "params": "",
            "search_exe": "/usr/local/bin/blat"
        },
        "blat_nuc": {
            "name": "Blat nucleotide",
            "search_class": "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide",
            "params": "",
            "search_exe": "/usr/local/bin/blat"
        }
    }
}

get_sequence_alterations(organism=None, sequence=None)¶

[UNTESTED] Get all of the sequence’s alterations

Parameters:	organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	list
Returns:	A list of sequence alterations(?)

load_gff3(organism, gff3, source=None, batch_size=1, test=False, use_name=False, disable_cds_recalculation=False, timing=False)¶

Load a full GFF3 into annotation track

Parameters:	organism (str) – Organism Common Name gff3 (str) – GFF3 to load source (str) – URL where the input dataset can be found. batch_size (int) – Size of batches before writing test (bool) – Run in dry run mode use_name (bool) – Use the given name instead of generating one. disable_cds_recalculation (bool) – Disable CDS recalculation and instead use the one provided timing (bool) – Output loading performance metrics
Return type:	str
Returns:	Loading report

load_legacy_gff3(organism, gff3, source=None)¶

Load a full GFF3 into annotation track (legacy version, kept for compatibility only)

Parameters:	organism (str) – Organism Common Name gff3 (str) – GFF3 to load source (str) – URL where the input dataset can be found.
Return type:	str
Returns:	Loading report

merge_exons(exon_a, exon_b, organism=None, sequence=None)¶

Merge two exons

Parameters:	exon_a (str) – Feature UUID exon_b (str) – Feature UUID organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

set_boundaries(feature_id, start, end, organism=None, sequence=None)¶

Set the boundaries of a genomic feature

Parameters:	feature_id (str) – Feature UUID start (int) – Feature start end (int) – Feature end organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

set_description(feature_id, description, organism=None, sequence=None)¶

Set a feature’s description

Parameters:	feature_id (str) – Feature UUID description (str) – Feature description organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

set_longest_orf(feature_id, organism=None, sequence=None)¶

Automatically pick the longest ORF in a feature

Parameters:	feature_id (str) – Feature UUID organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

set_name(feature_id, name, organism=None, sequence=None)¶

Set a feature’s name

Parameters:	feature_id (str) – Feature UUID name (str) – Feature name organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

set_readthrough_stop_codon(feature_id, organism=None, sequence=None)¶

Set the feature to read through the first encountered stop codon

Parameters:	feature_id (str) – Feature UUID organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

set_sequence(organism, sequence)¶

Set the sequence for subsequent requests. Mostly used in client scripts to avoid passing the sequence and organism on every function call.

Parameters:	organism (str) – Organism Name sequence (str) – Sequence Name
Return type:	None
Returns:	None

set_status(feature_id, status, organism=None, sequence=None)¶

Set a feature’s description

Parameters:	feature_id (str) – Feature UUID status (str) – Feature status organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

set_symbol(feature_id, symbol, organism=None, sequence=None)¶

Set a feature’s description

Parameters:	feature_id (str) – Feature UUID symbol (str) – Feature symbol organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

set_translation_end(feature_id, end, organism=None, sequence=None)¶

Set a feature’s end

Parameters:	feature_id (str) – Feature UUID end (int) – Feature end organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

set_translation_start(feature_id, start, organism=None, sequence=None)¶

Set the translation start of a feature

Parameters:	feature_id (str) – Feature UUID start (int) – Feature start organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

update_attribute(feature_id, attribute_key, old_value, new_value, organism=None, sequence=None)¶

Delete an attribute from a feature

Parameters:	feature_id (str) – Feature UUID attribute_key (str) – Attribute Key old_value (str) – Old attribute value new_value (str) – New attribute value organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

update_dbxref(feature_id, old_db, old_accession, new_db, new_accession, organism=None, sequence=None)¶

Delete a dbxref from a feature

Parameters:	feature_id (str) – Feature UUID old_db (str) – Old DB Name (e.g. PMID) old_accession (str) – Old accession Value new_db (str) – New DB Name (e.g. PMID) new_accession (str) – New accession Value organism (str) – Organism Common Name sequence (str) – Sequence Name
Return type:	dict
Returns:	A standard apollo feature dictionary ({“features”: [{…}]})

class apollo.annotations.FeatureType¶

Bases: enum.Enum

An enumeration.

FEATURE = 1¶

TRANSCRIPT = 2¶

apollo.cannedcomments package¶

Module contents¶

Contains possible interactions with the Apollo Canned Comments Module

class apollo.cannedcomments.CannedCommentsClient(webapolloinstance, **requestArgs)¶

Bases: apollo.client.Client

CLIENT_BASE = '/cannedComment/'¶

add_comment(comment, metadata='')¶

Add a canned comment

Parameters:	comment (str) – New canned comment metadata (str) – Optional metadata
Return type:	dict
Returns:	A dictionnary containing canned comment description

delete_comment(id_number)¶

Update a canned comment

Parameters:	id_number (int) – canned comment ID number
Return type:	dict
Returns:	an empty dictionary

get_comments()¶

Get all canned comments available in this Apollo instance

Return type:	list of dicts
Returns:	list of canned comment info dictionaries

show_comment(value)¶

Get a specific canned comment

Parameters:	value (str) – Canned comment to show
Return type:	dict
Returns:	A dictionnary containing canned comment description

update_comment(id_number, new_value, metadata=None)¶

Update a canned comment

Parameters:	id_number (int) – canned comment ID number new_value (str) – New canned comment value metadata (str) – Optional metadata
Return type:	dict
Returns:	an empty dictionary

apollo.cannedkeys package¶

Module contents¶

Contains possible interactions with the Apollo Canned Keys Module

class apollo.cannedkeys.CannedKeysClient(webapolloinstance, **requestArgs)¶

Bases: apollo.client.Client

CLIENT_BASE = '/cannedKey/'¶

add_key(key, metadata='')¶

Add a canned key

Parameters:	key (str) – New canned key metadata (str) – Optional metadata
Return type:	dict
Returns:	A dictionnary containing canned key description

delete_key(id_number)¶

Update a canned key

Parameters:	id_number (int) – canned key ID number
Return type:	dict
Returns:	an empty dictionary

get_keys()¶

Get all canned keys available in this Apollo instance

Return type:	list of dicts
Returns:	list of canned key info dictionaries

show_key(value)¶

Get a specific canned key

Parameters:	value (str) – Canned key to show
Return type:	dict
Returns:	A dictionnary containing canned key description

update_key(id_number, new_key, metadata=None)¶

Update a canned key

Parameters:	id_number (int) – canned key ID number new_key (str) – New canned key value metadata (str) – Optional metadata
Return type:	dict
Returns:	an empty dictionary

apollo.cannedvalues package¶

Module contents¶

Contains possible interactions with the Apollo Canned Values Module

class apollo.cannedvalues.CannedValuesClient(webapolloinstance, **requestArgs)¶

Bases: apollo.client.Client

CLIENT_BASE = '/cannedValue/'¶

add_value(value, metadata='')¶

Add a canned value

Parameters:	value (str) – New canned value metadata (str) – Optional metadata
Return type:	dict
Returns:	A dictionnary containing canned value description

delete_value(id_number)¶

Update a canned value

Parameters:	id_number (int) – canned value ID number
Return type:	dict
Returns:	an empty dictionary

get_values()¶

Get all canned values available in this Apollo instance

Return type:	list of dicts
Returns:	list of canned value info dictionaries

show_value(value)¶

Get a specific canned value

Parameters:	value (str) – Canned value to show
Return type:	dict
Returns:	A dictionnary containing canned value description

update_value(id_number, new_value, metadata=None)¶

Update a canned value

Parameters:	id_number (int) – canned value ID number new_value (str) – New canned value value metadata (str) – Optional metadata
Return type:	dict
Returns:	an empty dictionary

apollo.groups package¶

Module contents¶

Contains possible interactions with the Apollo Groups

class apollo.groups.GroupsClient(webapolloinstance, **requestArgs)¶

Bases: apollo.client.Client

CLIENT_BASE = '/group/'¶

create_group(name)¶

Create a new group

Parameters:	name (str) – Group name (or a list of groups to create)
Return type:	dict
Returns:	Group information dictionary

delete_group(group)¶

Delete a group

Parameters:	group (str) – Group name (or a list of groups to delete)
Return type:	dict
Returns:	an empty dictionary

get_group_admin(group)¶

Get the group’s admins

Parameters:	group (str) – group name
Return type:	list
Returns:	a list containing group admins

get_group_creator(group)¶

Get the group’s creator

Parameters:	group (str) – group name
Return type:	list
Returns:	creator userId

get_groups(name=None)¶

Get all the groups

Parameters:	name (str) – Only return group(s) with given name
Return type:	list of dicts
Returns:	list of a dictionaries containing group information

get_organism_permissions(group)¶

Get the group’s organism permissions

Parameters:	group (str) – group name
Return type:	list
Returns:	a list containing organism permissions (if any)

show_group(group_id)¶

Get information about a group

Parameters:	group_id (int) – Group ID Number
Return type:	dict
Returns:	a dictionary containing group information

update_group(group_id, new_name)¶

Update the name of a group

Parameters:	group_id (int) – group ID number new_name (str) – New name for the group
Return type:	dict
Returns:	a dictionary containing group information

update_group_admin(group_id, users=[])¶

Update the group’s admins

Parameters:	group_id (int) – Group ID Number users (list of str) – List of emails
Return type:	dict
Returns:	dictionary of group information

update_membership(group_id=None, users=[], memberships=[])¶

Update the group’s membership

Parameters:	group_id (int) – Group ID Number users (list of str) – List of emails memberships (list) – Bulk memberships to update of the form: [ {groupId: <groupId>,users: [“user1”, “user2”, “user3”]}, {groupId:<another-groupId>, users: [“user2”, “user8”]} (users and groupId will be ignored)
Return type:	dict
Returns:	dictionary of group information

update_organism_permissions(group, organism_name, administrate=False, write=False, read=False, export=False)¶

Update the group’s permissions on an organism

Parameters:	group (str) – group name organism_name (str) – Organism name administrate (bool) – Should the group have administrate privileges read (bool) – Should the group have read privileges write (bool) – Should the group have write privileges export (bool) – Should the group have export privileges
Return type:	list
Returns:	list of group organism permissions

apollo.io package¶

Module contents¶

Contains possible interactions with the Apollo IO Module

class apollo.io.IOClient(webapolloinstance, **requestArgs)¶

Bases: apollo.client.Client

CLIENT_BASE = '/IOService/'¶

download(uuid, output_format='gzip')¶

Download pre-prepared data by UUID

Parameters:	uuid (str) – Data UUID output_format (str) – Output format of the data, either “gzip” or “text”
Return type:	str
Returns:	The downloaded content

write_downloadable(organism, export_type='FASTA', seq_type='peptide', export_format='text', export_gff3_fasta=False, sequences=[], region=None)¶

Prepare a download for an organism

Parameters:	organism (str) – organism common name sequences (str) – Names of references sequences to add (default is all) export_type (str) – Export type. Choices: FASTA, GFF3, VCF seq_type (str) – Export selection. Choices: peptide, cds, cdna, genomic export_format (str) – Export format, either gzip or text export_gff3_fasta (bool) – Export reference sequence when exporting GFF3 annotations. region (str) – Region to export in form sequence:min..max e.g., chr3:1001..1034
Return type:	dict
Returns:	a dictionary containing download information

write_text(organism, export_type='FASTA', seq_type='peptide', export_format='text', export_gff3_fasta=False, sequences=[], region=None)¶

[DEPRECATED, use write_downloadable] Download or prepare a download for an organism

Parameters:	organism (str) – organism common name sequences (str) – Names of references sequences to add (default is all) export_type (str) – Export type. Choices: FASTA, GFF3, VCF seq_type (str) – Export selection. Choices: peptide, cds, cdna, genomic export_format (str) – Export format, either gzip or text export_gff3_fasta (bool) – Export reference sequence when exporting GFF3 annotations. region (str) – Region to export in form sequence:min..max e.g., chr3:1001..1034
Return type:	str
Returns:	the exported data

apollo.metrics package¶

Module contents¶

Contains possible interactions with the Apollo Metrics

class apollo.metrics.MetricsClient(webapolloinstance, **requestArgs)¶

Bases: apollo.client.Client

CLIENT_BASE = '/metrics/'¶

get_metrics()¶

Get all server metrics

Return type:	dict
Returns:	A dictionary with all of the server timing / metrics

apollo.organisms package¶

Module contents¶

Contains possible interactions with the Apollo Organisms Module

class apollo.organisms.OrganismsClient(webapolloinstance, **requestArgs)¶

Bases: apollo.client.Client

CLIENT_BASE = '/organism/'¶

add_organism(common_name, directory, blatdb=None, genus=None, species=None, public=False, metadata=None, suppress_output=False)¶

Add an organism

Parameters:	common_name (str) – Organism common name directory (str) – Server-side directory blatdb (str) – Server-side path to 2bit index of the genome for Blat genus (str) – Genus species (str) – Species public (bool) – Should the organism be public or not metadata (str) – JSON formatted arbitrary metadata suppress_output (bool) – Suppress output of all organisms (true / false) (default false)
Return type:	dict
Returns:	a dictionary with information about the new organism

delete_features(organism_id)¶

Remove features of an organism

Parameters:	organism_id (str) – Organism ID Number
Return type:	dict
Returns:	an empty dictionary

delete_organism(organism_id, suppress_output=False)¶

Delete an organism

Parameters:	organism_id (str) – Organism ID Number suppress_output (bool) – Suppress return of all organisms (true / false) (default false)
Return type:	list
Returns:	A list of all remaining organisms

get_organism_creator(organism_id)¶

Get the creator of an organism

Parameters:	organism_id (str) – Organism ID Number
Return type:	dict
Returns:	a dictionary containing user information

get_organisms(common_name=None)¶

Get all organisms

Parameters:	common_name (str) – Optionally filter on common name
Return type:	list
Returns:	Organism information

get_sequences(organism_id)¶

Get the sequences for an organism

Parameters:	organism_id (str) – Organism ID Number
Return type:	list of dict
Returns:	The set of sequences associated with an organism

show_organism(common_name)¶

Get information about a specific organism.

Parameters:	common_name (str) – Organism Common Name
Return type:	dict
Returns:	a dictionary containing the organism’s information

update_metadata(organism_id, metadata)¶

Update the metadata for an existing organism.

Parameters:	organism_id (str) – Organism ID Number metadata (str) – Organism metadata. (Recommendation: use a structured format like JSON)
Return type:	dict
Returns:	An empty, useless dictionary

update_organism(organism_id, common_name, directory, blatdb=None, species=None, genus=None, public=False, no_reload_sequences=False, suppress_output=False)¶

Update an organism

Parameters:	organism_id (str) – Organism ID Number common_name (str) – Organism common name directory (str) – Server-side directory blatdb (str) – Server-side Blat directory for the organism genus (str) – Genus species (str) – Species public (bool) – User’s email no_reload_sequences (bool) – Set this if you don’t want Apollo to reload genome sequences (no change in genome sequence) suppress_output (bool) – Suppress output of all organisms (true / false) (default false)
Return type:	dict
Returns:	a dictionary with information about the updated organism

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

apollo.status package¶

Module contents¶

Contains possible interactions with the Apollo Status Module

class apollo.status.StatusClient(webapolloinstance, **requestArgs)¶

Bases: apollo.client.Client

CLIENT_BASE = '/availableStatus/'¶

add_status(status)¶

Add a status value

Parameters:	status (str) – New status
Return type:	dict
Returns:	A dictionnary containing status description

delete_status(id_number)¶

Delete a status

Parameters:	id_number (int) – status ID number
Return type:	dict
Returns:	an empty dictionary

get_statuses()¶

Get all statuses available in this Apollo instance

Return type:	list of dicts
Returns:	list of status info dictionaries

show_status(status)¶

Get a specific status

Parameters:	status (str) – Status to show
Return type:	dict
Returns:	A dictionnary containing status description

update_status(id_number, new_value)¶

Update a status name

Parameters:	id_number (int) – status ID number new_value (str) – The new status name
Return type:	dict
Returns:	an empty dictionary

apollo.users package¶

Module contents¶

Contains possible interactions with the Apollo Users Module

class apollo.users.UsersClient(webapolloinstance, **requestArgs)¶

Bases: apollo.client.Client

CLIENT_BASE = '/user/'¶

activate_user(user)¶

Activate a user

Parameters:	user (str) – User’s email
Return type:	dict
Returns:	an empty dictionary

add_to_group(group, user)¶

Add a user to a group

Parameters:	user (str) – User’s email group (str) – Group name
Return type:	dict
Returns:	an empty dictionary

create_user(email, first_name, last_name, password, role='user', metadata={})¶

Create a new user

Parameters:	email (str) – User’s email first_name (str) – User’s first name last_name (str) – User’s last name password (str) – User’s password role (str) – User’s default role, one of “admin” or “user” metadata (dict) – User metadata
Return type:	dict
Returns:	an empty dictionary

delete_user(user)¶

Delete a user

Parameters:	user (str) – User’s email
Return type:	dict
Returns:	an empty dictionary

get_organism_permissions(user)¶

Display a user’s organism permissions

Parameters:	user (str) – User’s email
Return type:	dict
Returns:	a dictionary containing user’s organism permissions

get_user_creator(user)¶

Get the creator of a user

Parameters:	user (str) – User Email
Return type:	dict
Returns:	a dictionary containing user information

get_users(omit_empty_organisms=False)¶

Get all users known to this Apollo instance

Parameters:	omit_empty_organisms (bool) – Will omit users having no access to any organism
Return type:	list of dicts
Returns:	list of user info dictionaries

inactivate_user(user)¶

Activate a user

Parameters:	user (str) – User’s email
Return type:	dict
Returns:	an empty dictionary

remove_from_group(group, user)¶

Remove a user from a group

Parameters:	user (str) – User’s email group (str) – Group name
Return type:	dict
Returns:	an empty dictionary

show_user(user)¶

Get a specific user

Parameters:	user (str) – User Email
Return type:	dict
Returns:	a dictionary containing user information

update_organism_permissions(user, organism, administrate=False, write=False, export=False, read=False)¶

Update the permissions of a user on a specified organism

Parameters:	user (str) – User’s email organism (str) – organism common name administrate (bool) – Grants administrative privileges write (bool) – Grants write privileges read (bool) – Grants read privileges export (bool) – Grants export privileges
Return type:	dict
Returns:	a dictionary containing user’s organism permissions

update_user(email, first_name, last_name, password=None, metadata={}, new_email=None)¶

Update an existing user

Parameters:	email (str) – User’s email first_name (str) – User’s first name last_name (str) – User’s last name password (str) – User’s password (omit to keep untouched) metadata (dict) – User metadata new_email (str) – User’s new email (if you want to change it)
Return type:	dict
Returns:	a dictionary containing user information

Submodules¶

apollo.client module¶

Base apollo client

class apollo.client.Client(webapolloinstance, **requestArgs)¶

Bases: object

Base client class implementing methods to make requests to the server

CLIENT_BASE = '/'¶

get(client_method, get_params, is_json=True)¶: Make a GET request

post(client_method, data, post_params=None, is_json=True, files=None, autoconvert_to_json=True)¶: Make a POST request

apollo.decorators module¶

apollo.exceptions module¶

exception apollo.exceptions.APIErrorResponseException¶: Bases: Exception

exception apollo.exceptions.UnknownUserException¶: Bases: Exception

apollo.util module¶

apollo.util.AssertAdmin(user)¶

apollo.util.AssertUser(user_list)¶

apollo.util.CnOrGuess(parser)¶

apollo.util.GuessCn(args, wa)¶

apollo.util.GuessOrg(args, wa)¶

apollo.util.OrgOrGuess(parser)¶

apollo.util.WAAuth(parser)¶

apollo.util.add_property_to_feature(feature, property_key, property_value)¶

Parameters:	feature – property_key (str) – property_value (str) –
Returns:

apollo.util.features_to_apollo_schema(features, use_name=False, disable_cds_recalculation=False)¶

Parameters:	disable_cds_recalculation – use_name – features –
Returns:

apollo.util.features_to_feature_schema(features, use_name=False, disable_cds_recalculation=False)¶

Parameters:	disable_cds_recalculation – use_name – features –
Returns:

apollo.util.retry(closure, sleep=1, limit=5)¶

Apollo has the bad habit of returning 500 errors if you call APIs too quickly, largely because of the unholy things that happen in grails.

To deal with the fact that we cannot send an addComments call too quickly after a createFeature call, we have this function that will keep calling a closure until it works.

apollo.util.yieldApolloData(feature, use_name=False, disable_cds_recalculation=False)¶

Module contents¶

class apollo.ApolloInstance(url, username, password)¶: Bases: object

apollo.accessible_organisms(user, orgs, permission=None)¶: Get the list of organisms accessible to a user, filtered by orgs

class apollo.fakeTrans(username)¶

Bases: object

get_user()¶

apollo.galaxy_list_groups(trans, *args, **kwargs)¶

apollo.galaxy_list_orgs(trans, *args, **kwargs)¶

class apollo.obj¶: Bases: object

apollo.require_user(wa, email)¶: Require that the user has an account

apollo.set_logging_level(level)¶

Welcome to Python-Apollo’s documentation!¶

Apollo API Library¶

Installation¶

Examples¶

History¶

Development¶

License¶

Support¶

Commands¶

annotations¶

add_attribute command¶

add_comment command¶

add_dbxref command¶

add_feature command¶

add_features command¶

add_transcript command¶

add_transcripts command¶

delete_attribute command¶

delete_dbxref command¶

delete_feature command¶

delete_sequence_alteration command¶

duplicate_transcript command¶

flip_strand command¶

get_comments command¶

get_feature_sequence command¶

get_features command¶

get_gff3 command¶

get_search_tools command¶

get_sequence_alterations command¶

load_gff3 command¶

load_legacy_gff3 command¶

merge_exons command¶

set_boundaries command¶

set_description command¶

set_longest_orf command¶

set_name command¶

set_readthrough_stop_codon command¶

set_sequence command¶

set_status command¶

set_symbol command¶

set_translation_end command¶

set_translation_start command¶

update_attribute command¶

update_dbxref command¶

cannedcomments¶

add_comment command¶

delete_comment command¶

get_comments command¶

show_comment command¶

update_comment command¶

cannedkeys¶

add_key command¶

delete_key command¶

get_keys command¶

show_key command¶

update_key command¶

cannedvalues¶

add_value command¶

delete_value command¶

get_values command¶

show_value command¶

update_value command¶

groups¶

create_group command¶

delete_group command¶

get_group_admin command¶

get_group_creator command¶

get_groups command¶

get_organism_permissions command¶

show_group command¶

update_group command¶

update_group_admin command¶

update_membership command¶

update_organism_permissions command¶

io¶

download command¶

write_downloadable command¶

write_text command¶

metrics¶

get_metrics command¶

`add_attribute` command¶

`add_comment` command¶

`add_dbxref` command¶

`add_feature` command¶

`add_features` command¶

`add_transcript` command¶

`add_transcripts` command¶

`delete_attribute` command¶

`delete_dbxref` command¶

`delete_feature` command¶

`delete_sequence_alteration` command¶

`duplicate_transcript` command¶

`flip_strand` command¶

`get_comments` command¶

`get_feature_sequence` command¶

`get_features` command¶

`get_gff3` command¶

`get_search_tools` command¶

`get_sequence_alterations` command¶

`load_gff3` command¶

`load_legacy_gff3` command¶

`merge_exons` command¶

`set_boundaries` command¶

`set_description` command¶

`set_longest_orf` command¶

`set_name` command¶

`set_readthrough_stop_codon` command¶

`set_sequence` command¶

`set_status` command¶

`set_symbol` command¶

`set_translation_end` command¶

`set_translation_start` command¶

`update_attribute` command¶

`update_dbxref` command¶

`add_comment` command¶

`delete_comment` command¶

`get_comments` command¶

`show_comment` command¶

`update_comment` command¶

`add_key` command¶

`delete_key` command¶

`get_keys` command¶

`show_key` command¶

`update_key` command¶

`add_value` command¶

`delete_value` command¶

`get_values` command¶

`show_value` command¶

`update_value` command¶

`create_group` command¶

`delete_group` command¶

`get_group_admin` command¶

`get_group_creator` command¶

`get_groups` command¶

`get_organism_permissions` command¶

`show_group` command¶

`update_group` command¶

`update_group_admin` command¶

`update_membership` command¶

`update_organism_permissions` command¶

`download` command¶

`write_downloadable` command¶

`write_text` command¶

`get_metrics` command¶

`add_organism` command¶

`delete_features` command¶

`delete_organism` command¶

`get_organism_creator` command¶

`get_organisms` command¶

`get_sequences` command¶

`show_organism` command¶

`update_metadata` command¶

`update_organism` command¶

`add_organism` command¶

`add_track` command¶

`delete_organism` command¶

`delete_track` command¶

`update_organism` command¶

`update_track` command¶

`add_status` command¶