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Python package wrapping some of the encode project APIs.

Project description

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Python package wrapping some of the encode project APIs.

How do I install this package?

As usual, just download it using pip:

pip install encodeproject

Tests Coverage

Since some software handling coverages sometimes get slightly different results, here’s three of them:

Coveralls Coverage SonarCloud Coverage Code Climate Coverate

Usage Examples

The package contains both methods to run queries on the Encode Project APIs and methods to filter the responses. Every available method has a comprehensive docstring attached to it, so I welcome you to read the source code.

Queries

The library currently offers to query methods that already integrate some filtering properties: one for the experiments and one for the biosamples.

For querying the experiments you can run the following:

from encodeproject import experiment

my_experiment_query_response = experiment(
    assembly="hg19", # The assembly label, for instance "hg19".
    status="released", # The release status, can be either "released", "archived" or "revoked".
    cell_line="HepG2", # The label for the chosen cell line for instance "HepG2".
    target="ARID3A", # The target name, for instance "ARID3A".
    parameters = {} # Additional query parameters
)

All parameters are optional, they just act as additional filters.

For querying the biosamples you can run the following:

from encodeproject import biosample

my_biosample_query_response = biosample(
    accession="ENCSR000EDP", # The accession code for the desired biosample
)

For running multiple queries for biosamples at once you can run the following:

from encodeproject import biosamples

responses = biosamples(
    accessions=["ENCSR000EDP", "ENCSR030EDP", "ENCSR067EDP"], # The accessions code for the desired biosamples
)

Filters

Since the response files can get quite big and hard to read, I’ve prepared also a couple filter functions.

For filtering the accessions codes from an experiment response you can use:

from encodeproject import accessions

codes = accessions(my_experiment_query_response)

For filtering the download URLs from a biosample response you can use:

from encodeproject import download_urls

codes = download_urls(my_biosample_query_response)

Utilities

Download utility

I’ve added also a method to download from a given URL, showing a loading bar, based on this answer from StackOverflow.

from encodeproject import download

download("https://encode-public.s3.amazonaws.com/2012/07/01/074e1b37-2be1-4f6a-aa42-6c512fd1834b/ENCFF000XOW.bigWig")

Sample to DataFrame instruction

Utility to convert a sample to a relatively simple pandas DataFrame.

from encodeproject import biosample_to_dataframe

df = biosample_to_dataframe(my_biosample_query_response)

Issues and Feature Requests

This library started out of necessity to script some queries on the encodeproject. If you need some specific feature that isn’t currently already offered by the library, please do proceed with a pull request (quickest way: add the feature yourself and push it on the library) or alternatively you can open an issue and when I’ll get the time I’ll see to it.

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