bvbrc.ReturnFormat

class bvbrc.ReturnFormat(value)

Enumerator with return formats supported by the BV-BRC API.

This enumerator is intended to be used when submitting a request with one of the client objects to specify what the format of the reponse content should be.

Note

Many of the alternate return formats (besides the default JSON) do not work with the Client.get() method and can only be used with the Client.search() method.

Examples

Search for reference genomes and return the result in csv format:

>>> import bvbrc as bv
>>> genome = bv.GenomeClient()
>>> response = genome.search(
...     reference_genome="Reference",
...     select=["genome_id", "genome_name"],
...     limit=5,
...     return_format=bv.ReturnFormat.CSV,
... )
>>> print(response.text)
genome_id,genome_name
"11053.35","Dengue virus 1"
"1561705.5","Bovine polyomavirus 3 3S5"
"1303334.4","Human polyomavirus 12 hu1403"
"2051550.4","Cabbage cytorhabdovirus 1 FERA_050726"
"185639.16","Acheta domestica densovirus"

Get a protein sequence in FASTA format:

>>> gf = bv.GenomeFeatureClient()
>>> response = gf.search(
...     feature_id=""PATRIC.511145.12.NC_000913.CDS.650021.651079.rev"",
...     return_format=bv.ReturnFormat.PROTEIN_FASTA
... )
>>> print(response.text)
>fig|511145.12.peg.648|b0618|VBIEscCol129921_0648| [Citrate [pro-3S]-lyase] ligase (EC 6.2.1.22) [Escherichia coli str. K-12 substr. MG1655 | 511145.12]
MFGNDIFTRVKRSENKKMAEIAQFLHENDLSVDTTVEVFITVTRDEKLIACGGIAGNIIK
CVAISESVRGEGLALTLATELINLAYERHSTHLFIYTKTEYEALFRQCGFSTLTSVPGVM
VLMENSATRLKRYAESLKKFRHPGNKIGCIVMNANPFTNGHRYLIQQAAAQCDWLHLFLV
KEDSSRFPYEDRLDLVLKGTADIPRLTVHRGSEYIISRATFPCYFIKEQSVINHCYTEID
LKIFRQYLAPALGVTHRFVGTEPFCRVTAQYNQDMRYWLETPTISAPPIELVEIERLRYQ
EMPISASRVRQLLAKNDLTAIAPLVPAVTLHYLQNLLEHSRQDAAARQKTPA

JSON = 'application/json'

Standard JSON format (the default format)

SOLR_JSON = 'application/solr+json'

SOLR JSON format

CSV = 'text/csv'

A text response in CSV format

TSV = 'text/tsv'

A text response in TSV format

EXCEL = 'application/vnd.openxmlformats'

Return objects as an MS Excel document

DNA_FASTA = 'application/dna+fasta'

DNA sequences in FASTA format

PROTEIN_FASTA = 'application/protein+fasta'

Protein sequences in FASTA format

DNA_JSONH_FASTA = 'application/dna+jsonh+fasta'

DNA sequences in JSONH-FASTA format

PROTEIN_JSONH_FASTA = 'application/protein+jsonh+fasta'

Protein sequences in JSONH-FASTA format

GFF = 'application/gff'

GFF format for genomic features

static extract(string: str) → ReturnFormat

Extract a return format from a string using regex.

Parameters

stringstr

A string containing a return format specification within it to extract.

Returns

ReturnFormat

The extracted return format as an enumerator value.

Examples

>>> from bvbrc import ReturnFormat
>>> string = "this string has a return format in it (application/json)"
>>> ReturnFormat.extract(string)
<ReturnFormat.JSON: 'application/json'>