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.