`bycon` Arguments and Parameters¶

The following is a list of arguments and parameters used in the bycon package as well as the byconaut tools.

Definitions¶

`user_name`¶

type: string
pattern: ^\w+$
cmdFlags: --userName
description: faking a user name

`test_mode`¶

type: boolean
cmdFlags: -t,--testMode
description: test setting, i.e. returning some random documents
default: False

`skip`¶

type: integer
cmdFlags: --skip
description: pages to be skipped
default: 0

`limit`¶

type: integer
cmdFlags: -l,--limit
description: limit number of documents; a value of 0 sets to unlimited
default: 200

`requested_granularity`¶

type: string
pattern: ^\w+$
description: The requested granularity of the beacon
cmdFlags: --requestedGranularity
default: record

`request_entity_path_id`¶

type: string
cmdFlags: --requestEntityPathId
description: data entry point, equal to the first REST path element in Beacon

`requested_schema`¶

type: string
cmdFlags: --requestedSchema
description: requested schema, e.g. biosample

`include_resultset_responses`¶

type: string
cmdFlags: --includeResultsetResponses
description:

include resultset responses, e.g. HIT, MISS
kind of a holdover from Beacon pre-v1

`dataset_ids`¶

type: array
items: string
cmdFlags: -d,--datasetIds
description: dataset ids

`filters`¶

type: array
items: string
cmdFlags: --filters
description: prefixed filter values, comma concatenated

`filter_precision`¶

type: string
cmdFlags: --filterPrecision
description: either start or exact (exact being internal default) for matching filter values
default: exact

`filter_logic`¶

type: string
cmdFlags: --filterLogic
description: either OR or AND (translated to the MongoDB $and etc.)
default: AND

`include_descendant_terms`¶

type: boolean
cmdFlags: --includeDescendantTerms
description: global treatment of descendant terms
default: True

`assembly_id`¶

type: string
pattern: ^\w+?[\w\-\.]*?\w*?$
db_key: assembly_id
cmdFlags: --assemblyId
description: assembly id

`reference_name`¶

type: string
db_key: location.sequence_id
pattern: ^\w+.*?\w?$
cmdFlags: --referenceName
description: chromosome

`mate_name`¶

type: string
db_key: location.sequence_id
pattern: ^\w+.*?\w?$
cmdFlags: --mateName
description: chromosome

`reference_bases`¶

type: string
db_key: reference_sequence
pattern: ^[ACGTN]+$
cmdFlags: --referenceBases
description: reference bases

`alternate_bases`¶

type: string
db_key: sequence
pattern: ^[ACGTN]+$
cmdFlags: --alternateBases
description: alternate bases

`variant_type`¶

type: string
db_key: variant_state.id
pattern: ^\w+[\w \-\:]\w+?$
cmdFlags: --variantType
description: variant type, e.g. DUP

`start`¶

type: array
db_key: location.start
items:
- type: integer
- pattern: ^\d+?$
cmdFlags: --start
description: genomic start position

`end`¶

type: array
db_key: location.end
items:
- type: integer
- pattern: ^\d+?$
cmdFlags: --end
description: genomic end position

`variant_min_length`¶

type: integer
db_key: info.var_length
pattern: ^\d+?$
cmdFlags: --variantMinLength
description: variantMinLength: The minimal variant length in bases for e.g. CNV queries.

`variant_max_length`¶

type: integer
db_key: info.var_length
pattern: ^\d+?$
cmdFlags: --variantMaxLength
description: variantMaxLength: The maximum variant length in bases for e.g. CNV queries.

`gene_id`¶

type: string
db_key: None
pattern: ^\w+?(\w+?(\-\w+?)?)?$
cmdFlags: --geneId
description: gene id

`aminoacid_change`¶

type: string
db_key: molecular_attributes.aminoacid_changes
pattern: ^\w+?$
examples: V600E,M734V,G244A
cmdFlags: --aminoacidChange
description: Aminoacid alteration in 1 letter format

`genomic_allele_short_form`¶

type: string
db_key: identifiers.genomicHGVS_id
pattern: ^\w+.*\w$
examples: NC_000017.11:g.7674232C>G
cmdFlags: --genomicAlleleShortForm
description: Genomic HGVSId descriptor

`variant_internal_id`¶

type: string
db_key: variant_internal_id
pattern: ^\w[\w\:\-\,]+?\w$
examples: 11:52900000-134452384:EFO_0030067
cmdFlags: --variantInternalId
description: An id value used for all variant instances of the same composition; a kind of digest

`accessid`¶

type: string
db_key: id
pattern: ^\w[\w\-]+?\w$
examples: b59857bc-0c4a-4ac8-804b-6596c6566494
cmdFlags: --accessid
description: An accessid for retrieving handovers etc.

`file_id`¶

type: string
pattern: ^\w[\w\-]+?\w$
examples: 90e19951-1443-4fa8-8e0b-6b5d8c5e45cc
cmdFlags: --fileId
description: A file id e.g. as generated by the uploader service

`id`¶

type: string
db_key: id
pattern: ^\w[\w\:\-\,]+?\w$
examples: pgxvar-5bab576a727983b2e00b8d32,pgxind-kftx25eh
cmdFlags: --id
description: An id; this parameter only makes sense for specific REST entry types

`ids`¶

type: array
items: string
cmdFlags: --ids
description: One or more ids; this parameter only makes sense for specific REST entry types

`biosample_ids`¶

type: array
items: string
byc_entity: biosample
cmdFlags: --biosampleIds
description: biosample ids

`analysis_ids`¶

type: array
items: string
byc_entity: analysis
cmdFlags: --analysisIds
description: callset / analysis ids

`individual_ids`¶

type: array
items: string
byc_entity: individual
cmdFlags: --individualIds
description: subject ids

`variant_ids`¶

type: array
items: string
byc_entity: genomicVariant
cmdFlags: --variantIds
description: variant ids

`debug_mode`¶

type: boolean
cmdFlags: --debugMode
description: debug setting

`show_help`¶

type: boolean
cmdFlags: --showHelp
description: specific help display

`test_mode_count`¶

type: integer
cmdFlags: --testModeCount
description: setting the number of documents reurned in test mode
default: 5

`output`¶

type: string
cmdFlags: --output
description: For defining a special output format, mostly for byconaut services use. Examples:

cnvstats, for analyses, to present some CNV statistics
pgxseg, using the .pgxseg variant file format
text, for some services to deliver a text table instead of JSON

`include_handovers`¶

type: boolean
default: True
cmdFlags: --includeHandovers
description: only used for web requests & testing

`only_handovers`¶

type: boolean
default: False
cmdFlags: --onlyHandovers
description: only used for web requests & testing

`method`¶

type: string
cmdFlags: --method
description: special method
default: None

`group_by`¶

type: string
cmdFlags: -g,--groupBy
description: group parameter e.g. for subset splitting
default: text

`parse`¶

type: string
cmdFlags: -p,--parse
description: input value to be parsed

`mode`¶

type: string
cmdFlags: -m,--mode
description: mode, e.g. file type

`key`¶

type: string
cmdFlags: -k,--key
description: some key or word

`update`¶

type: string
cmdFlags: -u,--update
description: update existing records
default: False

`inputfile`¶

type: string
cmdFlags: -i,--inputfile
description: a custom file to specify input data, usually tab-delimited with special header

`outputdir`¶

type: string
cmdFlags: --outputdir
description: output directory where supported (cmd line)

`outputfile`¶

type: string
cmdFlags: -o,--outputfile
description: output file where supported (cmd line)

`randno`¶

type: integer
cmdFlags: -r,--randno
description: random number to limit processing, where supported
default: 0

`min_number`¶

type: integer
cmdFlags: --minNumber
description: minimal number, e.g. for collations, where supported
default: 0

`source`¶

type: string
cmdFlags: -s,--source
description: some source label, e.g. analyses

`delivery_keys`¶

type: array
items: string
cmdFlags: --deliveryKeys
description: delivery keys

`collation_types`¶

type: array
items: string
cmdFlags: --collationTypes
description: selected collation types, e.g. "EFO"

`with_samples`¶

type: integer
cmdFlags: --withSamples
description: only for the collations; number of code_matches...

`selected_beacons`¶

type: array
items: string

`genome_binning`¶

type: string
default: 1Mb
cmdFlags: --genomeBinning
description: one of the predefined genome binning keys - default 1Mb

`cyto_bands`¶

type: string
db_key: None
pattern: ^(?:chro?)?([12]?[\dXY])([pq](?:(?:ter)|(?:cen)|(?:[1-4](?:\d(?:\.\d\d*?)?)?)?))?\-?([pq](?:(?:cen)|(?:ter)|(?:[1-4](?:\d(?:\.\d\d*?)?)?)?))?$
cmdFlags: --cytoBands
description: cytobands, e.g. 8q21q24.1

`chro_bases`¶

type: string
db_key: None
pattern: ^(chro?)?([12]?[\dXY])\:(\d+?)(\-(\d+?))?$
cmdFlags: --chroBases
description: only for the cytoband converter ... e.g. 8:0-120000000

`city`¶

type: string
cmdFlags: -c,--city
description: only for the geolocations...

`geo_latitude`¶

type: number
cmdFlags: --geoLatitude
description: only for the geolocations...

`geo_longitude`¶

type: number
cmdFlags: --geoLongitude
description: only for the geolocations...

`geo_distance`¶

type: integer
cmdFlags: --geoDistance
description: only for the geolocations...

`marker_type`¶

type: string
cmdFlags: --markerType
description: marker type, only for the geolocations...

`plot_pars`¶

type: string
cmdFlags: --plotPars
description: plot parameters in form par=value concatenated by ::

`plot_type`¶

type: string
cmdFlags: --plotType
description: plot type (histoplot, samplesplot, arrayplot - more?)

bycon Arguments and Parameters¶

Definitions¶

user_name¶

test_mode¶

skip¶

limit¶

requested_granularity¶

request_entity_path_id¶

requested_schema¶

include_resultset_responses¶

dataset_ids¶

filters¶

filter_precision¶

filter_logic¶

include_descendant_terms¶

assembly_id¶

reference_name¶

mate_name¶

reference_bases¶

alternate_bases¶

variant_type¶

start¶

end¶

variant_min_length¶

variant_max_length¶

gene_id¶

aminoacid_change¶

genomic_allele_short_form¶

variant_internal_id¶

accessid¶

file_id¶

id¶

ids¶

biosample_ids¶

analysis_ids¶

individual_ids¶

variant_ids¶

debug_mode¶

show_help¶

test_mode_count¶

output¶

include_handovers¶

only_handovers¶

method¶

group_by¶

parse¶

mode¶

key¶

update¶

inputfile¶

outputdir¶

outputfile¶

randno¶

min_number¶

source¶

delivery_keys¶

collation_types¶

with_samples¶

selected_beacons¶

genome_binning¶

cyto_bands¶

chro_bases¶

city¶

geo_latitude¶

geo_longitude¶

geo_distance¶

marker_type¶

plot_pars¶

plot_type¶