Ingest and query genomic intervals from multiple BED files

Overview

Region search with tileDB

Ingest and query genomic intervals from multiple BED files.

Ingest

>>> import glob
>>> import tiles
# Get paths to local BED files.
>>> files = sorted(glob.glob('/path/to/beds/*.bed.gz'))
>>> files[:5]
[
    'ENCFF001SOF.bed.gz',
    'ENCFF001SOH.bed.gz',
    'ENCFF001SOM.bed.gz',
    'ENCFF001SON.bed.gz',
    'ENCFF001SOO.bed.gz',
]
# Create chromosome by genomic position database.
>>> tiles.create_region_array('regions')
# Load first five BEDs into tileDB.
>>> tiles.load_local('regions', files[:5])
...
generating positions
writing data
done
...
# Save accession to file index maps.
>>> tiles.save_maps('regions')
# Consolidate and vacuum database.
>>> tiles.clean('regions')

Query

>>> import tiles
# Load accession to file index maps.
>> tiles.load_maps('regions')
# Get first five intervals around POMC gene on chromosome two.
>>> tiles.query_region('regions', 2, 25132492, 25192278, limit=5)
[
    ('ENCFF001SOF.bed.gz', 25139665, 25139815),
    ('ENCFF001SOF.bed.gz', 25141485, 25141635),
    ('ENCFF001SOF.bed.gz', 25141625, 25141775),
    ('ENCFF001SOF.bed.gz', 25142065, 25142215),
    ('ENCFF001SOF.bed.gz', 25142665, 25142815),
]
# Get total number of intervals in that region.
>>> len(tiles.query_region('regions', 2, 25132492, 25192278, limit=1000))
52
# Get files with intervals in that region.
>>> tiles.query_file('regions', 2, 25132492, 25192278)
[
    'ENCFF001SOF.bed.gz',
    'ENCFF001SOH.bed.gz',
    'ENCFF001SOM.bed.gz',
]
๐ŸŒ Local tile server for viewing geospatial raster files with ipyleaflet

๐ŸŒ Local Tile Server for Geospatial Rasters Need to visualize a rather large raster (gigabytes) you have locally? This is for you. A Flask application

Bane Sullivan 192 Jan 04, 2023
A set of utility functions for working with GeoJSON annotations in Kaibu

kaibu-utils A set of utility functions for working with Kaibu. Create a new repository Create a new repository and select imjoy-team/imjoy-python-temp

ImJoy Team 0 Dec 12, 2021
PySAL: Python Spatial Analysis Library Meta-Package

Python Spatial Analysis Library PySAL, the Python spatial analysis library, is an open source cross-platform library for geospatial data science with

Python Spatial Analysis Library 1.1k Dec 18, 2022
GeoNode is an open source platform that facilitates the creation, sharing, and collaborative use of geospatial data.

Table of Contents What is GeoNode? Try out GeoNode Install Learn GeoNode Development Contributing Roadmap Showcase Most useful links Licensing What is

GeoNode Development Team 1.2k Dec 26, 2022
Centroids as a Service

Centroids! This application reads a valid geojson FeatureCollection and returns a valid geojson FeatureColleciton of centroids. In the output: All pro

Lyzi Diamond 20 Aug 29, 2021
A trivia questions about Europe

EUROPE TRIVIA QUIZ IN PYTHON Project Outline Ask user if he / she knows more about Europe. If yes show the Trivia main screen, else show the end Trivi

David Danso 1 Nov 17, 2021
Spatial Interpolation Toolbox is a Python-based GUI that is able to interpolate spatial data in vector format.

Spatial Interpolation Toolbox This is the home to Spatial Interpolation Toolbox, a graphical user interface (GUI) for interpolating geographic vector

Michael Ward 2 Nov 01, 2021
peartree: A library for converting transit data into a directed graph for sketch network analysis.

peartree ๐Ÿ ๐ŸŒณ peartree is a library for converting GTFS feed schedules into a representative directed network graph. The tool uses Partridge to conve

Kuan Butts 183 Dec 29, 2022
WhiteboxTools Python Frontend

whitebox-python Important Note This repository is related to the WhiteboxTools Python Frontend only. You can report issues to this repo if you have pr

Qiusheng Wu 304 Dec 15, 2022
Script that allows to download data with satellite's orbit height and create CSV with their change in time.

Satellite orbit height โ—พ Requirements Python = 3.8 Packages listen in reuirements.txt (run pip install -r requirements.txt) Account on Space Track โ—พ

Alicja Musiaล‚ 2 Jan 17, 2022
Search and download Copernicus Sentinel satellite images

sentinelsat Sentinelsat makes searching, downloading and retrieving the metadata of Sentinel satellite images from the Copernicus Open Access Hub easy

837 Dec 28, 2022
A Python package for delineating nested surface depressions from digital elevation data.

Welcome to the lidar package lidar is Python package for delineating the nested hierarchy of surface depressions in digital elevation models (DEMs). I

Qiusheng Wu 166 Jan 03, 2023
gpdvega is a bridge between GeoPandas and Altair that allows to seamlessly chart geospatial data

gpdvega gpdvega is a bridge between GeoPandas a geospatial extension of Pandas and the declarative statistical visualization library Altair, which all

Ilia Timofeev 49 Jul 25, 2022
This repository contains the scripts to derivate the ENU and ECEF coordinates from the longitude, latitude, and altitude values encoded in the NAD83 coordinates.

This repository contains the scripts to derivate the ENU and ECEF coordinates from the longitude, latitude, and altitude values encoded in the NAD83 coordinates.

Luigi Cruz 1 Feb 07, 2022
WIP: extracting Geometry utilities from datacube-core

odc.geo This is still work in progress. This repository contains geometry related code extracted from Open Datacube. For details and motivation see OD

Open Data Cube 34 Jan 09, 2023
Documentation and samples for ArcGIS API for Python

ArcGIS API for Python ArcGIS API for Python is a Python library for working with maps and geospatial data, powered by web GIS. It provides simple and

Esri 1.4k Dec 30, 2022
Geospatial web application developed uisng earthengine, geemap, and streamlit.

geospatial-streamlit Geospatial web applications developed uisng earthengine, geemap, and streamlit. App 1 - Land Surface Temperature A simple, code-f

13 Nov 27, 2022
Bacon - Band-limited Coordinate Networks for Multiscale Scene Representation

BACON: Band-limited Coordinate Networks for Multiscale Scene Representation Project Page | Video | Paper Official PyTorch implementation of BACON. BAC

Stanford Computational Imaging Lab 144 Dec 29, 2022
Hapi is a Python library for building Conceptual Distributed Model using HBV96 lumped model & Muskingum routing method

Current build status All platforms: Current release info Name Downloads Version Platforms Hapi - Hydrological library for Python Hapi is an open-sourc

Mostafa Farrag 15 Dec 26, 2022
Zora is a python program that searches for GeoLocation info for given CIDR networks , with options to search with API or without API

Zora Zora is a python program that searches for GeoLocation info for given CIDR networks , with options to search with API or without API Installing a

z3r0day 1 Oct 26, 2021