The National Centre for Biotechnology Information (NCBI) maintains the Sequence Read Archive (SRA), a repository for next generation sequencing (NGS) data. Runs of NGS data are each assigned an accession number that is prefixed with SRR. These runs are in turn associated with other information such as the Series (GSE).
This repository contains a simple Perl script that maps SRR accession number to other pieces of information. All of this is contained in a flat file at ftp://ftp.ncbi.nlm.nih.gov/sra/reports/Metadata/SRA_Accessions.tab that is periodically updated. As of November 2018, the size of this file is 4.4 GB. Thus, this script merely makes multiple passes over this file.
As an aside, there are alternatives to this script, including using NCBI's esearch and efetch utilities, as described here. This Perl script is merely an alternative.
Download the file of SRA accessions and store it in the current directory.
| Software | Version | Required? | Ubuntu package | Anaconda package |
|---|---|---|---|---|
| Perl | 5.26.1 | Yes | perl | perl |
| AppConfig (Perl module) | 1.71-2 | Yes | libappconfig-perl | perl-appconfig |
Experiments with this software have been successfully run on Ubuntu 18.04.
The versions represent the tools used during software development or when running the script. The software requirements are quite modest and lower versions should work without problems.
After cloning this repository from GitHub, the following directory structure is obtained:
├── Examples Examples to test SRR-Lookup against.
│ ├── * Files related to a very simple test case.
├── LICENSE Software license (GNU GPL v3).
├── srr-lookup.pl The Perl main script.
└── README.md This README file.
In the Examples/ directory is a small test case that includes a set of SRR accession numbers and a tiny subset of the SRA_Accessions file. The script can be run on this example by typing the following:
cat Examples/test.txt | perl ./srr-lookup.pl --sra Examples/SRA_Accessions-small.tab
Output is sent to standard out in tab-separated format and should look like this:
Run Experiment GSM Submission Sample Study Biosample Bioproject Replacement
SRR6795732 SRX3754750 GSM3024344 SRA663352 SRS3010770 SRP133768 SAMN08628238 PRJNA436570 -
SRR6795733 SRX3754751 GSM3024345 SRA663352 SRS3010769 SRP133768 SAMN08628237 PRJNA436570 -
SRR6795734 SRX3754752 GSM3024346 SRA663352 SRS3010771 SRP133768 SAMN08628236 PRJNA436570 -
SRR6795735 SRX3754753 GSM3024347 SRA663352 SRS3010773 SRP133768 SAMN08628235 PRJNA436570 -
SRR6795736 SRX3754754 GSM3024348 SRA663352 SRS3010772 SRP133768 SAMN08628234 PRJNA436570 -
SRR6795737 SRX3754755 GSM3024349 SRA663352 SRS3010774 SRP133768 SAMN08628233 PRJNA436570 -
SRR6795738 SRX3754756 GSM3024350 SRA663352 SRS3010775 SRP133768 SAMN08628232 PRJNA436570 -
SRR6795739 SRX3754757 GSM3024351 SRA663352 SRS3010776 SRP133768 SAMN08628231 PRJNA436570 -
This software was written for during the preparation for the following manuscript:
E. van der Wal, P. Herrero-Hernandez, R. Wan, M. Broeders, S. L. M. in 't Groen, T. J. M. van Gestel, W. F. J. van IJcken, T. H. Cheung, A. T. van der Ploeg, G. J. Schaaf, W. W. M. P. Pijnappel. Large-Scale Expansion of Human iPSC-Derived Skeletal Muscle Cells for Disease Modeling and Cell-Based Therapeutic Strategies. Stem Cell Report, 10(6): 1975-1990, 2018.
It was implemented by Raymond Wan as part of my employment at the Hong Kong University of Science and Technology. My contact details:
E-mails: rwan.work@gmail.com
OR
raymondwan@ust.hk
My homepage is here.
The latest version of SRR-Lookup can be downloaded from GitHub.
If you have any information about bugs, suggestions for the documentation or just have some general comments, feel free to write to one of the above addresses.
SRR-Lookup (SRR Lookup)
Copyright (C) 2018 by Raymond Wan
SRR-Lookup is distributed under the terms of the GNU General Public License (GPL, version 3 or later) -- see the file LICENSE for details.
Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts and no Back-Cover Texts. A copy of the license is included with the archive as LICENSE.
Thursday, November 1, 2018