Metadata-Version: 2.1
Name: ffq
Version: 0.0.2
Summary: Fetch run information from the European Nucleotide Archive (ENA).
Home-page: https://github.com/pachterlab/ffq
Author: Kyung Hoi (Joseph) Min, Sina Booeshaghi
Author-email: phoenixter96@gmail.com, alisina@caltech.edu
Maintainer: Pachter Lab
Maintainer-email: lpachter@caltech.edu
License: MIT
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Utilities
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: beautifulsoup4 (>=4.8.2)
Requires-Dist: lxml (>=4.5.0)
Requires-Dist: requests (>=2.23.0)

# ffq
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Fetch run information from the European Nucleotide Archive (ENA).

## Installation

```
pip install ffq
```

## Usage

### Fetch information of an SRA run and display it in the terminal
```
ffq [SRR]
```
where `[SRR]` is the run accession.

### Fetch information of multiple SRA runs and display it in the terminal
```
ffq [SRR1] [SRR2] ...
```
where `[SRR1]` and `[SRR2]` are run accessions.

### Write SRA run information to a single JSON file
```
ffq -o [JSON_PATH] [SRRS]
```
where `[JSON_PATH]` is the path to the JSON file that will contain run
information and `[SRRS]` is a space-delimited list of one or more
run accessions.

### Write SRA run information to multiple JSON files, one file per run
```
ffq -o [OUT_DIR] --split [SRRS]
```
where `[OUT_PATH]` is the path to directory to which to write the JSON files.
Information about each run will be written to its own separate JSON file named
`[ACCESSION].json`. `[SRRS]` is a space-delimited list of one or more
run accessions.

### Fetch information of one or more SRA study (and all of their runs)
```
ffq -t SRP [SRPS]
```
where `[SRPS]` is a space-delimited list of one or more SRA study accessions. The output is a JSON-formatted string (or a JSON file if `-o` is provided) with study accessions as keys. When `--split` is also provided, each study is written to its own separate JSON.

### Fetch information of one or more GEO study (and all of their runs)
```
ffq -t GSE [GSES]
```
where `[GSES]` is a space-delimited list of one or more GEO study accessions. The output is a JSON-formatted string (or a JSON file if `-o` is provided) with study accessions as keys. When `--split` is also provided, each study is written to its own separate JSON.

### Fetch information of all studies (and all of their runs) in one or more papers
```
ffq -t DOI [DOIS]
```
where `[DOIS]` is a space-delimited list of one or more DOIs. The output is a JSON-formatted string (or a JSON file if `-o` is provided) with SRA study accessions as keys. When `--split` is also provided, each study is written to its own separate JSON.

## Examples
Examples are available in the [examples](examples) directory.


