drosSRA 0.4.5

drosSRA builds a url for visualization of tracks based on user specified parameters (i.e. sex, tissue, cell type)

drosSRA

drosSRA builds a url containing all relevant GEO tracks based on one or more user specified parameters (i.e. sex, tissue, cell type)

• Free software: MIT license

• Documentation: https://drosSRA.readthedocs.io.

Installation

To download and install the latest version of drosSRA:

pip install drosSRA

Usage

There are five possible flags that users can use to search for tracks of interest: PubMed ID (-p), sex (-s), developmental stage (-d), tissue (-t), and cell type (-c). For example, if you are interested in viewing all tracks with testis data:

>> drosSRA -t testis
https://www.ncbi.nlm.nih.gov/genome/gdv/browser/?context=genome&acc=GCF_000001215.4&context=GEO&acc=ERX2162339%2CERX2162340%2CERX2162341%2CSRX014984%2CSRX014985%2CSRX1026313%2CSRX1045309%2CSRX1045369%2CSRX105953%2CSRX109278%2CSRX109279%2CSRX135547%2CSRX135548%2CSRX142027%2CSRX142028%2CSRX142029%2CSRX142030%2CSRX142031%2CSRX142032%2CSRX1512980%2CSRX1542553%2CSRX1542554%2CSRX1542555%2CSRX1542556%2CSRX1542557%2CSRX1637725%2CSRX1637726%2CSRX1637727%2CSRX1637728%2CSRX1637729%2CSRX1637730%2CSRX1637731%2CSRX1637732%2CSRX1637733%2CSRX1637734%2CSRX1637735%2CSRX1637736%2CSRX1720957%2CSRX1720958%2CSRX1842650%2CSRX1842775%2CSRX2166012%2CSRX2166014%2CSRX2166016%2CSRX2166017%2CSRX2166019%2CSRX2166020%2CSRX2166021%2CSRX2325622%2CSRX2325623%2CSRX2325625%2CSRX2325626%2CSRX2325628%2CSRX2325629%2CSRX2325630%2CSRX2325631%2CSRX2416970%2CSRX2416971%2CSRX2416972%2CSRX2416973%2CSRX2416974%2CSRX2416975%2CSRX2416976%2CSRX2416977%2CSRX2497546%2CSRX2497547%2CSRX2497548%2CSRX2497549%2CSRX2497550%2CSRX2497551%2CSRX2504297%2CSRX2504298%2CSRX2504299%2CSRX2504300%2CSRX2549197%2CSRX2549198%2CSRX2549199%2CSRX2677260%2CSRX2677261%2CSRX2677262%2CSRX2677263%2CSRX2683539%2CSRX2683540%2CSRX2683541%2CSRX2683542%2CSRX2683543%2CSRX2683545%2CSRX2683546%2CSRX2683547%2CSRX2683548%2CSRX2683550%2CSRX2683551%2CSRX2829107%2CSRX2829108%2CSRX2829109%2CSRX2829110%2CSRX3015350%2CSRX3015366%2CSRX319676%2CSRX319687%2CSRX320021%2CSRX320263%2CSRX321521%2CSRX321778%2CSRX3488043%2CSRX3488044%2CSRX3488045%2CSRX3488046%2CSRX3488047

Or, if you are interested in the intersection of two or more parameters,

>> drosSRA -d 'larval stage' -t CNS
 https://www.ncbi.nlm.nih.gov/genome/gdv/browser/?context=genome&acc=GCF_000001215.4&context=GEO&acc=ERX2162997%2CERX2162999

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.4.1 (2018-10-24)

• patch to fix deployment with travis

0.4.0 (2018-10-23)

• Genome browser automatically opens to pita

0.3.0 (2018-10-22)

• Rework of drosSRA.py to handle multiple flags

0.2.0 (2018-10-16)

• First release on PyPI. (0.1.0 got messed up)