Pip package for SRA Quick-Submit, a goofy SRA submission tool from 2013.
Project description
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/
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.
Project details
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