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¶