semvec/pypi-packages huggingface dataset:
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
Requires Python: >=3.7.0

# 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](https://github.com/bioinfoUGR/miSRA).

## 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*](https://github.com/bioinfoUGR/miSRA/tree/master/src/example_configs/miSRA_example_config.json) could include the following parameters (for a detailed explanation of the different query modes, [see **miSRA modes** ](##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](https://github.com/bioinfoUGR/miSRA) or the tool [manual](https://github.com/bioinfoUGR/miSRA/blob/main/manual.pdf).