https://github.com/glarue/jgi-query
A simple command-line tool to download data from Joint Genome Institute databases
https://github.com/glarue/jgi-query
bioinformatics cli genomes genomics python
Last synced: 4 months ago
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A simple command-line tool to download data from Joint Genome Institute databases
- Host: GitHub
- URL: https://github.com/glarue/jgi-query
- Owner: glarue
- License: mpl-2.0
- Created: 2015-07-21T00:08:50.000Z (almost 11 years ago)
- Default Branch: main
- Last Pushed: 2023-01-19T19:18:36.000Z (over 3 years ago)
- Last Synced: 2023-10-26T08:51:33.466Z (over 2 years ago)
- Topics: bioinformatics, cli, genomes, genomics, python
- Language: Python
- Homepage:
- Size: 220 KB
- Stars: 43
- Watchers: 4
- Forks: 16
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
# jgi-query
A command-line tool for querying and downloading from databases hosted by the [Joint Genome Institute (JGI)](https://jgi.doe.gov/). Useful for accessing JGI data from command-line-only resources such as remote servers, or as a lightweight alternative to JGI's other [GUI-based download tools](https://genome.jgi.doe.gov/portal/help/download.jsf).
### Dependencies
- A [user account with JGI](https://contacts.jgi.doe.gov/registration/new) (free)
- [cURL](http://curl.haxx.se/), required by the JGI download API
- [Python](https://www.python.org/downloads/) 3.x (current development) or 2.7.x (deprecated but provided -- now *significantly outdated*)
### Installation
1. Download `jgi-query.py`
2. Ensure that you're running the correct version of Python with `python --version`. If this reports Python 2.x, run the script using `python3` instead of `python`
3. From the command line, run the script with the command `python jgi-query.py` to show usage information and further instructions
#### Usage information
```
usage: jgi-query.py [-h] [-x [XML]] [-c] [-s] [-f] [-u] [-n RETRY_N]
[-l logfile] [-r REGEX] [-a]
[organism_abbreviation]
This script will list and retrieve files from JGI using the curl API. It will
return a list of all files available for download for a given query organism.
positional arguments:
organism_abbreviation
organism name formatted per JGI's abbreviation. For
example, 'Nematostella vectensis' is abbreviated by
JGI as 'Nemve1'. The appropriate abbreviation may be
found by searching for the organism on JGI; the name
used in the URL of the 'Info' page for that organism
is the correct abbreviation. The full URL may also be
used for this argument (default: None)
optional arguments:
-h, --help show this help message and exit
-x [XML], --xml [XML]
specify a local xml file for the query instead of
retrieving a new copy from JGI (default: None)
-c, --configure initiate configuration dialog to overwrite existing
user/password configuration (default: False)
-s, --syntax_help
-f, --filter_files filter organism results by config categories instead
of reporting all files listed by JGI for the query
(work in progress) (default: False)
-u, --usage print verbose usage information and exit (default:
False)
-n RETRY_N, --retry_n RETRY_N
number of times to retry downloading files with errors
(0 to skip such files) (default: 4)
-l logfile, --load_failed logfile
retry downloading from URLs listed in log file
(default: None)
-r REGEX, --regex REGEX
Regex pattern to use to auto-select and download files
(no interactive prompt) (default: None)
-a, --all Auto-select and download all files for query (no
interactive prompt) (default: False)
```
### Author's note
This is a somewhat better-commented (emphasis on "somewhat") version of a script I wrote for grabbing various datasets using a headless Linux server. For a lot of my lab's bioinformatics work, we don't store/manipulate data on our local computers, and I was not able to find a good tool that allowed for convenient queries of the JGI database without additional software.
JGI also no longer allows simple downloading of many of their datasets (via `wget`, for example), which is another reason behind the creation of this script.
I highly encourage anyone with more advanced Python skills (read: almost everyone) to fork and submit pull requests.
### General overview
JGI uses a [cURL-based API](https://docs.google.com/document/d/1UXovE52y1ab8dZVa-LYNJtgUVgK55nHSQR3HQEJJ5-A/view) to provide information/download links to files in their database.
In brief, `jgi-query` begins by using cURL to grab an XML file for the query text. The XML file describes all of the available files and their parent categories. For example, the file for *Aureobasidium subglaciale* (JGI abbreviation "Aurpu_var_sub1") begins:
`jgi-query` will parse the XML file to find entries with a `filename` attribute and, depending on command-line arguments, a parent category from the list of categories in `jgi-query.config`. It then displays the available files with minimal metadata, and prompts the user to enter their selection.
### File selection
Main file categories in the report are numbered, as are files within each category. The selection syntax is `category_number`:`file_selection`, where `file_selection` is either a comma-separated list (e.g. `file1`, `file2`) or a contiguous range (e.g. `file1`-`file4`). For multiple parent categories and associated files, category/file list groupings are linked with semicolons (e.g. `category1`:`file1`,`file2`;`category2`:`file5`-`file8`).
### Bulk file downloading
Additionally, there is a regex-based file selection option (enter "r" at the file selection prompt) which may be useful for selecting a large number of related files (see the [Python regex documentation](https://docs.python.org/3/library/re.html#re-syntax) for syntax information). For example, to retrieve all files with "AllModels" in their names, the regex to enter at the regex prompt would be `.*AllModels.*`.
### Use in a larger pipeline
For programmatic use, `jgi-query` also has command-line arguments, `-a` and `-r`, that allow retrieval of either complete or regex-filtered datasets, respectively, while bypassing interactive prompts. For example, to retrieve all gzipped GFF3 files with "FilteredModels1" for _Schizophyllum commune_:
`python3 jgi-query.py Schco3 -r 'FilteredModels1.*\.gff3\.gz$'`
### Sample output for _Nematostella vectensis_ ('Nemve1')
```
➜ python3 jgi-query.py Nemve1
Retrieving information from JGI for query 'Nemve1' using command 'curl 'https://genome.jgi.doe.gov/ext-api/downloads/get-directory?organism=Nemve1' -L -b cookies > Nemve1_jgi_index.xml'
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 379 100 379 0 0 1857 0 --:--:-- --:--:-- --:--:-- 1857
100 4350 0 4350 0 0 3958 0 --:--:-- 0:00:01 --:--:-- 4248k
QUERY RESULTS FOR 'Nemve1'
======================= 1: All models, Filtered and Not ========================
Genes:
1:[1] Nemve1.AllModels.gff.gz-----------------------------------[20 MB|03/2012]
Proteins:
1:[2] proteins.Nemve1AllModels.fasta.gz-------------------------[29 MB|03/2012]
Transcripts:
1:[3] transcripts.Nemve1AllModels.fasta.gz----------------------[55 MB|03/2012]
=================================== 2: Files ===================================
Additional Files:
2:[1] N.vectensis_ABAV.modified.scflds.p2g.gz------------------[261 KB|03/2012]
2:[2] Nemve1.FilteredModels1.txt.gz------------------------------[2 MB|03/2012]
2:[3] Nemve1.fasta.gz-------------------------------------------[81 MB|10/2005]
2:[4] Nemve_JGIest.fasta.gz-------------------------------------[30 MB|03/2012]
2:[5] Nemve_JGIestCL.fasta.gz------------------------------------[8 MB|03/2012]
2:[6] NvTRjug.fasta.gz-------------------------------------------[4 KB|03/2012]
========================= 3: Filtered Models ("best") ==========================
Genes:
3:[1] Nemve1.FilteredModels1.gff.gz------------------------------[3 MB|03/2012]
3:[2] Nvectensis_19_PAC2_0.GFF3.gz-------------------------------[2 MB|03/2012]
Proteins:
3:[3] proteins.Nemve1FilteredModels1.fasta.gz--------------------[5 MB|03/2012]
Transcripts:
3:[4] transcripts.Nemve1FilteredModels1.fasta.gz-----------------[8 MB|03/2012]
Enter file selection ('q' to quit, 'usage' to review syntax, 'a' for all, 'r' for regex-based filename matching):
> 2:3;3:1
Total download size for 2 files: 84.02 MB
Continue? (y/n/[p]review files): y
Downloading 'Nemve1.FilteredModels1.gff.gz' using command:
curl -m 120 'https://genome.jgi.doe.gov/portal/Nemve1/download/Nemve1.FilteredModels1.gff.gz' -b cookies > Nemve1.FilteredModels1.gff.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 3078k 100 3078k 0 0 4918k 0 --:--:-- --:--:-- --:--:-- 4918k
Downloading 'Nemve1.fasta.gz' using command:
curl -m 120 'https://genome.jgi.doe.gov/portal/Nemve1/download/Nemve1.fasta.gz' -b cookies > Nemve1.fasta.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 81.0M 100 81.0M 0 0 5320k 0 0:00:15 0:00:15 --:--:-- 2881k
Finished downloading 2 files.
Decompress all downloaded files? (y/n/k=decompress and keep original): y
Finished decompressing all files.
Keep temporary files ('Nemve1_jgi_index.xml' and 'cookies')? (y/n): n
Removing temp files and exiting
~ took 1m 17s
➜
```