sra-quick-submit 1.8
Pip package for SRA Quick-Submit, a goofy SRA submission tool from 2013.
Requires Python: >=3.5
Keywords: sra_quick_submit_package

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.