bio2bel/mirbase

A Bio2BEL package for miRBase (http://www.mirbase.org)

Bio2BEL miRBase

Enumerate miRBase namespace, produce equivalency table, and predicted MTI relationships

Installation

bio2bel_mirbase can be installed from the latest code on GitHub with:

$ python3 -m pip install git+https://github.com/bio2bel/mirbase.git@master

References

• http://www.mirbase.org/
• http://identifiers.org/mirbase/ and http://identifiers.org/mirbase.mature/
• Ana Kozomara, Sam Griffiths-Jones; miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 2014; 42 (D1): D68-D73.

mirbase's Issues

Move parser script to /src/bio2bel_mirbase

Create command line interface with click to wrap downloader, parser, and output

Make a file called /src/bio2bel_mirbase/cli.py inside which you should use the click package to make a simple command line interface.

• use absolute imports (i.e. from bio2bel_mirbase.parser import ...) so this script can be run from inside the src directory
• name your click function def main(...):
• add an if __name__ == '__main__': main() so it can be run from inside an IDE

Automated build procedure for namespaces

• make a tox script that has build entries for creating namespaces and equivalence files
• leverage Travis CI to deploy to artifactory using https://github.com/Parallels/artifactory. Perhaps in the future, travis will directly support deploying there

Re-write download function

This was a great first attempt:

mirbase/src/bio2bel_mirbase/download.py

Lines 10 to 12 in 3b4e811

	def download():
	urlretrieve(DATA_URL, DATA_PATH)
	return DATA_PATH

Now, we should implement this function to be smarter and not re-download the file each time. Here's an example from Bio2BEL ChEBI:

import logging

# build the logger using this module's name at runtime
log = logging.getLogger(__name__)

def download_compounds(force_download=False):
    """Downloads the compounds information

    :param bool force_download: If true, overwrites a previously cached file
    :rtype: str
    """
    if os.path.exists(COMPOUNDS_DATA_PATH) and not force_download:
        log.info('using cached data at %s', COMPOUNDS_DATA_PATH)
    else:
        log.info('downloading %s to %s', COMPOUNDS_URL, COMPOUNDS_DATA_PATH)
        urlretrieve(COMPOUNDS_URL, COMPOUNDS_DATA_PATH)

    return COMPOUNDS_DATA_PATH

Basically, it adds a check if the data file already exists and doesn't download it again if it does (and gives some nice logging).

Namespace(s) Equivalence Script

Serialize information about equivalences between miRBase identifiers and colloquial names using the two namespaces produced in #1

Create downloader function

Let's pair program this today.

Namespace(s) creation script

miRBase has an identifier system that looks like MIRXXXXX and a colloquial name system that's similar to the biological literature

Find EMBL parser in python