getENA
Sometimes we need to download a sequencing project from ENA; fortunately ENA offers in its platform a link to the file that we need. However, we can spend a lot of time downloading files manually if the amount of files is large.
I have developed a small project in Python to be able to do this work in an automated and parallel way to increase the performance.
Installation
From GitHub (last version)
pip install git+https://github.com/EnzoAndree/getENA
Alternatively, from pip
pip install getENA
Usage
Let's say I'm interested in Clostridium perfringens sequencing projects (WGS in Illumina platform, not RNA-seq nor Metagenomics); we have to search ENA for public sequencing projects at https://www.ebi.ac.uk/ena/browser/text-search?query=clostridium%20perfringens. Here, we choose the codes that we need, for example:
PRJNA350702 PRJNA285473 PRJNA508810
We have 2 options to download the FASTQ files, (1) add the project codes to the command line separated by spaces as an argument, or (2) make a file containing a list of all the project codes that need.
For the first option (recommended for few projects, e.g. >= 5) we run the following
getENA.py -acc PRJNA350702 PRJNA285473 PRJNA508810
For the second option (recommended for many projects, e.g. >= 5) we run the following
getENA.py -accfile ena.list.txt
Where ena.list.txt is the file containing a list of all the project codes.
Instead, if you only want to download a few selected genomes from the project, simply add the run_accession as a parameter
getENA.py -acc SRR096826 SRR8867692 SRR7601184
If you want, you can increase the performance by increasing the number of reads that are downloaded in parallel (-t option). However, be careful, because ENA aborts the connection if it detects that you have many connections at the same time with its FTP. Empirically I have observed that 12 parallel connections work properly without ENA cancelling the download.
As a crazy example of many parallel connections of the above commands would be the following:
getENA.py -t 64 -acc PRJNA350702 PRJNA285473 PRJNA508810
One of the main features of getENA.py is that it automatically confirms the integrity of the FASTQ file when you download it. If the connection is lost, if ENA cancels the connection or if the getENA.py is stopped, you can run the program again and restart the download without losing the files that were already downloaded.
By default the output directory of getENA.py is a folder called ENA_out in the current directory. It can be modified with the -o argument. For example:
getENA.py -o Cperfringens -t 64 -acc PRJNA350702 PRJNA285473 PRJNA508810
Output files
The scheme of the files and folders created follows the next format:
|ENA_out
|-- metadata.tsv
|-- ERR0001_1.fastq.gz
|-- ERR0001_2.fastq.gz
|-- ...
|-- ERR0009_1.fastq.gz
|-- ERR0009_2.fastq.gz
|-- tmp
|---- PRJNA350702.tsv
|---- PRJNA285473.tsv
|---- PRJNA508810.tsv
Where PRJNA350702.tsv, PRJNA285473.tsv and PRJNA508810.tsv are the metadata of selected projects and metadata.tsv is a merge of this three files. The folder ENA_out, contain all FASTQ file of each project
If you only want to get all C. perfringens reads reported in ENA, you can get all the FASTA files for a given taxon ID. In this case the taxon id of C. perfringens is 1502. So the command line to download all reads of this species is:
getENA.py -o Cperfringens -tax 1502
This command line will generate a Cperfringens directory contains all reads reported to date. Using this option two tsv documents will be generated in the tmp directory inside Cperfringens: metadata_1502_*.tsv and metadata_filtred_1502_*.tsv where the first one contains all the public data of the species and the second one has the data of the codes that are WGS.
Licence
Citations
You should also cite this software (currently unpublished) as:
Guerrero-Araya E, getENA Github https://github.com/EnzoAndree/getENA
Author
- Enzo Guerrero-Araya
- Twitter: @eguerreroaraya
