get_fastq_urls: Get urls for downloading fastq files

In joseah/srametadata: Getting and cleaning metadata from Sequence Read Archive (SRA)

Description

Gets all urls, file names and md5 values associated with run accessions.

Usage

get_fastq_urls(runacc, db_conn)

Arguments

runacc

A vector with run accessions

Value

urls A nested list with run accessions separated depending on whether they are associated with one, two or three files. If all run accessions provided are only associated with one category, a data frame is returned for that category.

Examples

library('srametadata')

# Get path to sqlite database
sqlfile <- file.path('.', 'SRAmetadb.sqlite')

# Create connection
conn <- dbConnect(SQLite(),sqlfile)

# one file
get_fastq_urls(runacc = c("DRR001482"), db_con = conn)

# two files
get_fastq_urls(runacc = c("DRR001627"),  db_con = conn)

# three files
get_fastq_urls(runacc = c("ERR204978"),  db_con = conn)

# one file and two files
get_fastq_urls(runacc = c("DRR001482", "DRR001627"),  db_con = conn)

# one file and three files
get_fastq_urls(runacc = c("DRR001482", "ERR204978"),  db_con = conn)

# one file and three files
get_fastq_urls(runacc = c("DRR001627", "ERR204978"),  db_con = conn)

# one file, two files and three files
get_fastq_urls(runacc = c("DRR001482", "DRR001627", "ERR204978"),
               db_con = conn)

joseah/srametadata documentation built on May 19, 2019, 8:45 p.m.