Metadata-Version: 2.1
Name: sra-downloader
Version: 1.0.6a0
Summary: A script for batch-downloading and automatic compression of data from NCBI Sequence Read Archive. Built on SRA-Toolkit.
Home-page: https://github.com/bioinf-mcb/sra-downloader
Author: Valentyn Bezshapkin & Witold Wydmański
Author-email: witold.wydmanski@uj.edu.pl
License: MIT
Description: # sra-downloader
        A script for batch-downloading and automatic compression of data from NCBI Sequence Read Archive. Built on SRA-Toolkit.
        
        Features:
         - Downloading SRAs using either accession IDs or NCBI generated files
         - Organizing sequences by projects that they come from
         - Detecting which runs have been already downloaded
        
        ## Requirements
        - python >= 3.6
        - sra-toolkit >= 2.9.6
        - pigz 
        
        ## Instalation
        ### 0. Docker
        1. Run `docker run wwydmanski/sra-downloader -h`
        
        ### 1. Conda (recommended, also downloads sra-toolkit)
        1. Run `conda install -c bioconda -c bioinf-mcb sra-downloader` 
        
        Note: if you don't specify the `bioconda` channel you will get a dependency error.
        
        ### 2. From PyPi
        1. Run `pip install sra-downloader`
        
        ### 3. From sources
        1. Download a repo into a folder
        2. Run `pip install .`
        
        ## Usage
        ```
        usage: sra-downloader [-h] [--fname FILENAME] [--save-dir SAVE_DIRECTORY] [--uncompressed [UNCOMPRESSED]] [--cores [CORES]] [sra_id [sra_id ...]]
        
        Download SRA data and organize them by projects
        
        positional arguments:
          sra_id                SRA IDs to download
        
        optional arguments:
          -h, --help            show this help message and exit
          --fname FILENAME      CSV file with list of SRAs to download. Header must include `Run` and `BioProject`.
          --save-dir SAVE_DIRECTORY
                                a directory that the files will be saved to. (default: ./downloaded)
          --uncompressed [UNCOMPRESSED]
                                if present, the files will not be compressed. (default: False)
          --cores [CORES]       Cores used for compression. (default is the number of online processors, or 8 if unknown)
        ```
        
        ### Examples
        ```
        sra-downloader ERR2177760 --uncompressed
        sra-downloader --fname SraRunTable.txt --save-dir ./SRAs --cores 4
        ```
        
        ## Sample output
        
        ```
        └─── save_folder
            ├── PRJEB14961
            │   ├── ERR1551967.sra_1.fastq.gz  # - raw read archived files from SRA
            │   ├── ERR1551967.sra_2.fastq.gz 
            │   └── SraRunTable.txt            # - original SraRunTable.txt with useful metadata about samples  
            └── PRJEB20463
                ├── ERR2177760.sra_1.fastq.gz
                ├── ERR2177760.sra_2.fastq.gz 
                ├── absent.txt                 # - entries that were unaccessible due to various reasons
                └── SraRunTable.txt
        ```
Platform: UNKNOWN
Description-Content-Type: text/markdown
