bio-sra

bio-sra

A Sequence Read Archive (SRA) download script and Ruby interface to the SRAdb (SRA metadata) SQLite database.

Installation

$ gem install bio-sra

Download script usage

Download a single run file to the current directory:

$ sra_download ERR229501

Download a list of runs

$ cat srr_list.txt
ERR229501
ERR229498
$ sra_download -f srr_list.txt

Download all runs that are a part of the experiment ERP001779 "Microbial biogeography of public restroom surfaces". This requires an SRAdb database (i.e. a database of the SRA metadata), which can be downloaded from

$ sra_download -d '/path/to/SRAmetadb.sqlite' ERP001779

The SRAdb SQLite file can be downloaded from these mirrors:

• http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz
• http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz
• http://dl.dropbox.com/u/51653511/SRAmetadb.sqlite.gz

Ruby interface script

require 'bio-sra'

# Connect to the database
Bio::SRA::Connection.connect '/path/to/SRAmetadb.sqlite'

Once connected, the each row of the Bio::SRA::Tables::SRA table represents an SRA run:

Bio::SRA::Tables::SRA.first.run_accession
# => "DRR000001"

Bio::SRA::Tables::SRA.first.submission_accession
# => "DRA000001"

Bio::SRA::Tables::SRA.first.submission_date
# => "2009-06-20"

Bio::SRA::Tables::SRA.first.submission_comment
# => "Bacillus subtilis subsp. natto BEST195 draft sequence, the chromosome and plasmid pBEST195S"

There is a description of each available table on the wiki.

There are also methods for working with accession numbers, e.g.

 Bio::SRA::Accession.classify_accession_type('ERP001779') #=> :study_accession

The API doc is online. For more code examples see the test files in the source tree.

Project home page

Information on the source tree, documentation, examples, issues and how to contribute, see

http://github.com/wwood/bioruby-sra

Cite

This Ruby code is unpublished, but citing the SRAdb paper is probably good practice:

• SRAdb: query and use public next-generation sequencing data from within R

Biogems.info

This Biogem is published at biogems.info

Copyright

Copyright (c) 2012-2014 Ben J. Woodcroft. See LICENSE.txt for further details.