sra-quick-submit 1.8

Quick Python tool for making SRA submissions as part of the GenomeTrakr Next Generation Sequencing Network for Food Pathogen Traceability project.

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).

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:

$ sra_quick_submit PRJNA00000000 /path/to/a/miseq/output/folder/130730_M01836_0006_000000000-A3N78/ -o /another/path/