SRAdb (version 1.30.0)

getSRA: Fulltext search SRA meta data using SQLite fts3 module

Description

This function does Fulltext search on any SRA fields in any SRA data types with Fulltext capacity in the SQLite and returns SRA records

Usage

getSRA(search_terms, out_types=c('sra','submission','study','experiment','sample','run'), sra_con, acc_only=FALSE)

Arguments

search_terms

Free text search terms constructed according to SQLite query syntax defined here: http://www.sqlite.org/fts3.html#section_1_3

out_types

Character vector of the following SRA data types: 'sra','submission','study','sample','experiment','run'. Note: if 'sra' is within out_types, the out_types will be set to c('submission','study','sample','experiment').

sra_con

Connection to the SRAmetadb SQLite database

acc_only

logical, if TRUE, the function will return SRA accession for each out_types

Value

A data.frame containing all returned SRA records with fields defined by out_types.If acc_only=FALSE, a data.frame of matched accessions of out_types will be returned.

Details

Queries performed by this function could be Phrase queries, e.g. '"lin* app*"', or NEAR queries, e.g. '"ACID compliant" NEAR/2 sqlite', or with the Enhanced Query Syntax. Check Full Text Search section on the SQLite site for details. if 'acc_only=TRUE', a data.frame containing only SRA accessions will be returned, which can be used as input for sraGraph.

References

http://www.sqlite.org/

See Also

sraConvert

Examples

if(file.exists('SRAmetadb.sqlite')) {

	library(SRAdb)
	sra_dbname <- 'SRAmetadb.sqlite'	
	sra_con <- dbConnect(dbDriver("SQLite"), sra_dbname)
  
	## Fulltext search SRA meta data using SQLite fts3 module:
	# find all records with words of 'breast' and 'cancer' in a filed and there could be one to many words between 'breast' and 'cancer':   
	rs <- getSRA (search_terms ='breast cancer', out_types=c('run','study'), sra_con=sra_con)
 
	# find all records with exact phrase of 'breast cancer' in a filed:   
	rs <- getSRA (search_terms ='"breast cancer"', out_types=c('run','study'), sra_con=sra_con)
 
	# find records with words beginning with 'braes' and 'can', and the distance between them is equal or less than two words:
	rs <- getSRA (search_terms ='breas* NEAR/2 can*', out_types=c('run','study'), sra_con=sra_con)

	# the same as above except that only one space between the two words  
	rs <- getSRA (search_terms ='"breas* can*"', out_types=c('study'), sra_con=sra_con) 
 
	# find records with 'MCF7' or 'MCF-7' - adding double quote to avoid the SQLite to break down 'MCF-7' to 'MCF' and '7':
	rs <- getSRA (search_terms ='MCF7 OR "MCF-7"', out_types=c('sample'), sra_con=sra_con) 

	# the same as above, but only search the field of 'study_title':
	rs <- getSRA (search_terms ='study_title: brea* can*', out_types=c('run','study'), sra_con=sra_con)  

	# the same as above, but only search the field of 'study_title' and return only accessions:
	rs <- getSRA (search_terms ='study_title: brea* can*', out_types=c('run','study'), sra_con=sra_con, acc_only=TRUE) 

} else {
  	print("use getSRAdbFile() to get a copy of the SRAmetadb.sqlite file  and then rerun the example")
}