Metadata-Version: 1.2
Name: sra-quick-submit
Version: 1.8
Summary: Pip package for SRA Quick-Submit, a goofy SRA submission tool from 2013.
Home-page: https://github.com/crashfrog/sra_quick_submit
Author: Justin Payne
Author-email: justin.payne@fda.hhs.gov
License: UNKNOWN
Description: 
        sra-quick-submit
        ================
        
        Quick Python tool for making SRA submissions as part of the GenomeTrakr Next Generation Sequencing Network for Food Pathogen Traceability project.
        
        .. code-block::
        
           usage: sra_quick_submit [-h] [-o PATH] [-d YYYY-MM-DD] [-l CHARACTER]
                                   [-n NAME] [-e email@email.email]
                                   <PRJNAxxxxxxx> <PATH | FILE>
        
               SRA Quick Submit
           Aug 16, Justin Payne 
           ORISE FDA-CFSAN-ORS-DM-MMSB
           justin.payne@fda.hhs.gov
           v1.6b
        
           positional arguments:
             <PRJNAxxxxxxx>
             <PATH | FILE>
        
           optional arguments:
             -h, --help            show this help message and exit
             -o PATH, --output PATH
                                   Output directory. Will be created if it doesn't
                                   already exist. [default:$PWD]
             -d YYYY-MM-DD, --hold-date YYYY-MM-DD
                                   Hold this submission until specified date. SRA allows
                                   up to a one-year hold.
             -l CHARACTER, --delimiter CHARACTER
                                   Character used as delimiter in table. [default: \t]
             -n NAME, --name NAME  Submitter name.
             -e email@email.email, --email email@email.email
                                   Submitter email.
             -m INT, --library-length INT
                                   Nominal library insert length [default: 500]
             -r INT, --read-length INT
                                   Total read length (number of primary flows) [default:
                                   250]
             -g <sample name | 'all'>, --merge <sample name | 'all'>
                                   Merge identical sample names into single experiment.
                                   This should be done if the same library was re-used
                                   for multiple runs. Specify the sample names to merge
                                   or "all" to merge all multiply-present samples
                                   [default: do not merge]
             --make-table          Instead of producing a submission, produce a table
                                   template which this script can accept as input.
        
        
        
        Import a table file of metadata or a MiSeq output directory and generate 
        submittable XML tarballs that can be uploaded to NCBI SRA. Accepts any line
        ending (Mac, PC, Linux).
        
        .. code-block::
        
           Change history:
           Aug 29 v1.1b: protection from sample name collision. 
           Sep 6  v1.2b: -p flag for specifying BioProject ID.
           Sep 16 v1.5b:  release version for GenomeTrakr community.
           Sep 16 v1.5b: release version for GenomeTrakr community.
           Sep 27 v1.6b: -g flag to merge runs with existing experiments, if possible 
        
        
        
        Usage example:
        
        .. code-block::
        
           $ sra_quick_submit PRJNA00000000 /path/to/a/miseq/output/folder/130730_M01836_0006_000000000-A3N78/ -o /another/path/
        
        
        =======
        History
        =======
        
        1.8 (2021-02-02)
        ------------------
        
        * First release on PyPI.
        
        1.6b (2013-09-27)
        -----------------
        
        * -g flag to merge runs with existing experiments, if possible.
        
        1.5b (2013-08-16)
        -----------------
        
        * release version for GenomeTrakr community.
        
        1.2b (2013-09-06)
        -----------------
        
        * -p flag for specifying BioProject ID.
        
        1.1b (2013-08-29)
        -----------------
        
        * protection from sample name collision. 
Keywords: sra_quick_submit_package
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.5
