https://github.com/poeli/epicov_downloader
Download all EpiCoV sequcnes from GISAID
https://github.com/poeli/epicov_downloader
Last synced: 6 months ago
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Download all EpiCoV sequcnes from GISAID
- Host: GitHub
- URL: https://github.com/poeli/epicov_downloader
- Owner: poeli
- License: gpl-3.0
- Created: 2020-03-03T01:23:05.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2022-06-21T17:50:43.000Z (over 3 years ago)
- Last Synced: 2025-03-26T10:36:21.300Z (7 months ago)
- Language: Python
- Size: 153 KB
- Stars: 32
- Watchers: 2
- Forks: 8
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# GISAID EpiCoV Downloader
[](https://doi.org/10.5281/zenodo.4323561)
[](https://github.com/poeli/EpiCoV_downloader/actions?query=workflow%3Agisaid)
This is a GISAID downloader to retrieve all EpiCoV sequences and the table. The script utilizes Selenium to acess the GISAID website through a Firefox webdriver.
> **_WARNING:_** By using this software you agree GISAID's [Terms of Use](https://www.gisaid.org/DAA) and reaffirm your understanding of these terms.
## Installation
We provide a package file (environment.yml) to create a new environment (gisaid) using conda:
```bash
$ git clone https://github.com/poeli/EpiCoV_downloader.git
$ cd EpiCoV_downloader/
$ conda env create -f environment.yml
$ conda activate gisaid
```
## Example
The username (-u) and password (-p) are required arguments for the script.
If you do not specify a range of submission and/or collection dates, the nextfasta and nextmeta provided in GISAID/EpiCoV/Downloads will be downloaded.
Downloading nextfasta and nextmeta provided in GISAID/EpiCoV/Downloads:
`./gisaid_EpiCoV_downloader.py -u $UNAME -p $PASSWD`
Downloading sequences and acknowledgement table for high quality genomes collected between 2019-12-26 and 2019-12-30:
`./gisaid_EpiCoV_downloader.py -u $UNAME -p $PASSWD -cs 2019-12-26 -ce 2019-12-30 -hc -le -cg`
Downloading sequences and acknowledgement table for genomes collected between from the USA:
`./gisaid_EpiCoV_downloader.py -u $UNAME -p $PASSWD -ss 2019-12-26 -se 2019-12-30 -l USA`
## Usage
```bash
usage: gisaid_EpiCoV_downloader.py [-h] -u [STR] -p [STR] [-o [STR]]
[-l [STR]] [-ht [STR]] [-cs [YYYY-MM-DD]]
[-ce [YYYY-MM-DD]] [-ss [YYYY-MM-DD]]
[-se [YYYY-MM-DD]] [-cg] [-hc] [-le]
[-t [INT]] [-r [INT]] [-i [INT]] [-m]
[--normal]
Download EpiCoV sequences from GISAID
optional arguments:
-h, --help show this help message and exit
-u [STR], --username [STR]
GISAID username
-p [STR], --password [STR]
GISAID password
-o [STR], --outdir [STR]
Output directory
-l [STR], --location [STR]
sample location
-ht [STR], --host [STR]
Specify a host of the sample. Default is human.
-cs [YYYY-MM-DD], --colstart [YYYY-MM-DD]
collection starts date
-ce [YYYY-MM-DD], --colend [YYYY-MM-DD]
collection ends date
-ss [YYYY-MM-DD], --substart [YYYY-MM-DD]
submitssion starts date
-se [YYYY-MM-DD], --subend [YYYY-MM-DD]
submitssion ends date
-cg, --complete complete genome only
-hc, --highcoverage high coverage only
-le, --lowcoverageExcl
low coverage excluding
-t [INT], --timeout [INT]
set action timeout seconds. Default is 90 secs.
-r [INT], --retry [INT]
retry how many times when the action fails. Default is
5 times.
-i [INT], --interval [INT]
time interval between retries in second(s). Default is
3 seconds.
--normal run firefox in normal mode.
```