Fetch run information from the European Nucleotide Archive (ENA).
Project description
ffq
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 directory.
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