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: * gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz * watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz * 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
Cite¶ ↑
This Ruby code is unpublished, but citing the SRAdb paper is probably good practice:
Biogems.info¶ ↑
This Biogem is published at biogems.info
Copyright¶ ↑
Copyright © 2012-2014 Ben J. Woodcroft. See LICENSE.txt for further details.