en_search: Search for data

In sckott/egnar: European Nucleotide Archive Client

Description

Search for data

Usage

en_search(query = NULL, result = NULL, limit = NULL, offset = NULL,
  max = NULL, ...)

Arguments

query	(character) Query terms
result	(character) result option, one of: sequence_release, assembly, coding_release, coding_update, read_run (are there others?)
limit	(integer) Number of results to return
offset	(integer) Result number to start at
max	(integer) Max results
...	Curl options passed to GET

Value

A list of lists, where each nested list is a record. in the future we hope to parse to a single data.frame

References

http://www.ebi.ac.uk/ena/browse/search-rest

Examples

## Not run: 
# sequence_release
res <- en_search(query = '"geo_circ(-0.587,-90.5713,170)"', result='sequence_release')
lapply(res, "[[", "seq")
## another eg.
en_search(query = '"geo_circ(-0.587,-90.5713,170)"', result='sequence_release', limit = 1)

# assembly
res <- en_search(query = '"tax_eq(10090)"', result = 'assembly')
dplyr::bind_rows(lapply(res, "[[", "chromosomes"), .id = "id")

# coding_release
res <- en_search(query = '"tax_tree(7147) AND dataclass="STD""', result = 'coding_release', limit = 5)
vapply(res, "[[", "", "desc")

# coding_update
res <- en_search(query = '"tax_tree(7147) AND dataclass="STD""', result = 'coding_update', limit = 5)
res$AAA08526$refs
res$AAA08526$features

## failing
# en_search(query = '"tax_tree(7147) AND dataclass="STD"')

## End(Not run)

sckott/egnar documentation built on May 29, 2019, 3:59 p.m.