miSRA 0.0.3

A command-line interface to the miSRA API. It allow to remotely query over 90,000 miRNA-seq samples from the Sequence Read Archive

miSRA

a command line tool to remotely query over 90,000 miRNA-seq samples from the Sequence Read Archive.
For more info, please visit the GitHub repository.

Dependencies

miSRA requires Python >= 3.7 and the python package requests (automatically installed by pip)

How to install

(optional but recommended) Create a virtual environment and activate it

python3 -m venv env
source env/bin/activate

Install with pip (recommended)

pip3 install miSRA
# to test that it worked
miSRA --help

Run miSRA:

miSRA --config your_config.json

An example config.json could include the following parameters (for a detailed explanation of the different query modes, see miSRA modes ):

{
    "mode":"mirna",  # There are different modes to query miSRA (mirna, lib and spike). The mode mirna performs alignments to miRNA annotations using sRNAbench
    
    # mirna mode requires 2 miRNA annotation files, one for mature miRNAs and one for hairpins
    "mature":"mature_hsa.fa", # path to mature miRNA annotations in fasta format
    "hairpin":"hairpin_hsa.fa", # path to hairpin miRNA annotations in fasta format
    
    # you can specify which samples you want to profile either by specifying comma-separated SRA study or experiment accessions
    "studies":"SRP225193", # profile all samples from this study
    # "experiments":"SRX2349199,SRX2349197,SRX546025,SRX546026", # this would include these experiments
    
    "localOut":"RNAatlas", # local folder where the results will be downloaded to
    "mm": "1", # number of mismatches (optional)
    "alignType":"v" # bowtie alignment type (optional)
}

One could also download information about the database content. The following command will generate a file in the current working directory including the number of available samples and studies per species.

miSRA --db-stat

To obtain all samples and studies available for a specific species, you can do:

miSRA --taxonID TAXON_ID
## Where TAXON_ID is NCBI's taxonID. For instance, for human:
miSRA --taxonID 9606

miSRA modes:

There are 3 main modes to query samples in miSRA:

• miRNA: mature and hairpin miRNA sequences are used for profiling
• library: long reference sequences are used for profiling and mappings of reads to these sequences will be reported
• spike: short reference sequences are provided and only exact matches will be reported

For more info, please visit the GitHub repository or the tool manual.