bio-sra 0.1.0 → 0.2.0
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- checksums.yaml +4 -4
- data/README.md +36 -15
- data/VERSION +1 -1
- data/bin/sra_download +18 -1
- metadata +1 -1
checksums.yaml
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metadata.gz:
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metadata.gz: 7ffa909e8f796caf46d17335cd68a8075cc5da00
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data.tar.gz: fdf1328d17f032197485359f73c313533649ca23
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metadata.gz: 5b457ed258b8fa212996f142b69049c9e1b86abd36b3f316522cecb8bfd009349a8920e112ee34e977c1300075a5a1240c93c6707d9f3d82c4e8f9eb4b1fd6b3
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data.tar.gz: 980aa9f9c2b0266b558ae16f7d0b643adf9f78837c67e21638a4be33b5fed224b1e49ca6aa39cef91bbdf17e102630ceb4c6d6eb2b6d38afb95d0f27011af2cb
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data/README.md
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# bio-sra
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[](http://travis-ci.org/wwood/bioruby-sra)
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A Sequence Read Archive (SRA) download script and Ruby interface to the [SRAdb](ncbi.nlm.nih.gov/pmc/articles/PMC3560148/) (SRA metadata) SQLite database.
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## Installation
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```sh
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gem install bio-sra
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$ gem install bio-sra
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```
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## Download script usage
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Download a single run file to the current directory:
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```sh
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sra_download
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$ sra_download ERR229501
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```
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Download a list of runs
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$ cat srr_list.txt
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ERR229501
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ERR229498
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$ sra_download
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$ sra_download -f srr_list.txt
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```
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Download all runs that are a part of the experiment ERP001779
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Download all runs that are a part of the experiment ERP001779 "Microbial biogeography of public restroom surfaces". This requires an [SRAdb](http://www.bioconductor.org/packages/release/bioc/html/SRAdb.html) database (i.e. a database of the SRA metadata), which can be downloaded from
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```sh
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$ sra_download ERP001779
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$ sra_download -d '/path/to/SRAmetadb.sqlite' ERP001779
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```
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The SRAdb SQLite file can be downloaded from these mirrors:
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* http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz
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* http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz
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* http://dl.dropbox.com/u/51653511/SRAmetadb.sqlite.gz
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## Ruby interface script
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```ruby
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require 'bio-sra'
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# Connect to the database
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Bio::SRA::Connection.connect '/path/to/SRAmetadb.sqlite'
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```
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Once connected, the each row of the Bio::SRA::Tables::SRA table represents an SRA run:
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```
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Bio::SRA::Tables::SRA.first.run_accession
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# => "DRR000001"
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Bio::SRA::Tables::SRA.first.submission_accession
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# => "DRA000001"
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Bio::SRA::Tables::SRA.first.submission_date
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# => "2009-06-20"
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Bio::SRA::Tables::SRA.first.submission_comment
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# => "Bacillus subtilis subsp. natto BEST195 draft sequence, the chromosome and plasmid pBEST195S"
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```
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There is a description of each available table on the [wiki](https://github.com/wwood/bioruby-sra/wiki).
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There are also methods for working with accession numbers, e.g.
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```ruby
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Bio::SRA::Accession.classify_accession_type('ERP001779') #=> :study_accession
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```
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The API doc is online. For more code examples see the test files in
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http://github.com/wwood/bioruby-sra
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The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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## Cite
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This Ruby code is unpublished, but
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This Ruby code is unpublished, but citing the SRAdb paper is probably good practice:
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* [
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* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
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* [SRAdb: query and use public next-generation sequencing data from within R](dx.doi.org/10.1186/1471-2105-14-19)
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## Biogems.info
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This Biogem is published at [
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This Biogem is published at [biogems.info](http://biogems.info/index.html)
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## Copyright
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Copyright (c) 2012 Ben J. Woodcroft. See LICENSE.txt for further details.
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Copyright (c) 2012-2014 Ben J. Woodcroft. See LICENSE.txt for further details.
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data/VERSION
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0.
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0.2.0
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data/bin/sra_download
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opts.on('-f', "--file FILENAME", "Provide a file of accession numbers, separated by whitespace or commas [default: not used, use the first argument <SRA_ACCESSION>]") do |f|
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options[:accessions_file] = f
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end
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opts.on('-d', '--db SRAmetaDB_PATH', "Path to the SRAmetadb downloaded from NCBI e.g. from the URL [required unless all accessions are runs (rather than e.g. studies or submissions)]") do |arg|
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options[:sradb] = arg
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end
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opts.on("--format FORMAT", "format for download [default: 'sra']") do |f|
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format_string_to_sym = {
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'sralite' => :sralite, # no longer supported by NCBI?
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# Connect to the database if required
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log.info "Connecting to database.."
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unless options[:treat_input_as_runs]
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if options[:sradb]
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Bio::SRA::Connection.connect options[:sradb]
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else
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Bio::SRA::Connection.connect
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end
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# Check for connection
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begin
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s = Bio::SRA::Tables::SRA.first
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rescue
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log.error "There was a problem connecting to the database at `#{options[:sradb] }', was it specified correctly?"
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exit 2
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end
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end
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log.info "Collecting a list of runs to download.."
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runs = []
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