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.